<86>Nov 24 03:43:27 userdel[76681]: delete user 'rooter'
<86>Nov 24 03:43:27 groupadd[76703]: group added to /etc/group: name=rooter, GID=561
<86>Nov 24 03:43:27 groupadd[76703]: group added to /etc/gshadow: name=rooter
<86>Nov 24 03:43:27 groupadd[76703]: new group: name=rooter, GID=561
<86>Nov 24 03:43:27 useradd[76714]: new user: name=rooter, UID=561, GID=561, home=/root, shell=/bin/bash
<86>Nov 24 03:43:27 userdel[76737]: delete user 'builder'
<86>Nov 24 03:43:27 userdel[76737]: removed group 'builder' owned by 'builder'
<86>Nov 24 03:43:27 userdel[76737]: removed shadow group 'builder' owned by 'builder'
<86>Nov 24 03:43:27 groupadd[76748]: group added to /etc/group: name=builder, GID=562
<86>Nov 24 03:43:27 groupadd[76748]: group added to /etc/gshadow: name=builder
<86>Nov 24 03:43:27 groupadd[76748]: new group: name=builder, GID=562
<86>Nov 24 03:43:27 useradd[76774]: new user: name=builder, UID=562, GID=562, home=/usr/src, shell=/bin/bash
warning: Macro %add_tcl_lib_path not found
<13>Nov 24 03:43:38 rpmi: libpng16-1.6.36-alt1 sisyphus+219478.100.1.1 1547633315 installed
<13>Nov 24 03:43:38 rpmi: xorg-proto-devel-2018.4-alt3 1527685079 installed
<13>Nov 24 03:43:38 rpmi: libjpeg-2:2.0.2-alt1 sisyphus+226996.100.1.1 1554902884 installed
<13>Nov 24 03:43:38 rpmi: libexpat-2.2.4-alt1 1503305341 installed
<13>Nov 24 03:43:38 rpmi: perl-Try-Tiny-0.30-alt1 1514318058 installed
<13>Nov 24 03:43:38 rpmi: perl-libnet-1:3.11-alt1 1511423541 installed
<13>Nov 24 03:43:38 rpmi: javapackages-tools-1:5.0.0-alt1_12jpp8 sisyphus+228348.2100.3.3 1556657006 installed
<13>Nov 24 03:43:38 rpmi: libglvnd-7:1.1.1-alt1 sisyphus+224993.100.4.1 1552634540 installed
<13>Nov 24 03:43:38 rpmi: perl-Module-Runtime-0.016-alt1 1509549848 installed
<13>Nov 24 03:43:38 rpmi: perl-HTTP-Date-6.02-alt1 1348645274 installed
<13>Nov 24 03:43:38 rpmi: perl-Term-ANSIColor-4.06-alt1 1479407083 installed
<13>Nov 24 03:43:38 rpmi: libICE-1.0.9-alt1 1409902719 installed
<13>Nov 24 03:43:38 rpmi: libgdbm-1.8.3-alt10 1454943313 installed
<13>Nov 24 03:43:38 rpmi: libSM-1.2.3-alt1 sisyphus+226734.100.2.1 1554586157 installed
<13>Nov 24 03:43:38 rpmi: tex-common-0.2-alt4 1244804096 installed
<13>Nov 24 03:43:38 rpmi: libopenblas-0.2.20-alt2 p9+229427.100.2.1 1558020504 installed
<13>Nov 24 03:43:38 rpmi: perl-Unicode-Normalize-1:5.28.1-alt1 sisyphus+219907.100.1.1 1548343070 installed
<13>Nov 24 03:43:38 rpmi: libpaper-1.1.26-alt1 sisyphus+221360.100.1.1 1549974198 installed
<13>Nov 24 03:43:39 rpmi: libicu64-1:6.4.2-alt1 sisyphus+227580.100.1.2 1555784315 installed
<13>Nov 24 03:43:39 rpmi: psutils-2:1.23-alt2 sisyphus+226711.100.1.1 1554520810 installed
<13>Nov 24 03:43:39 rpmi: perl-Dist-CheckConflicts-0.11-alt1 1397076608 installed
<13>Nov 24 03:43:39 rpmi: perl-Module-Implementation-0.09-alt1 1418836057 installed
<13>Nov 24 03:43:39 rpmi: libjasper-2.0.14-alt1 1530105213 installed
<13>Nov 24 03:43:39 rpmi: rpm-macros-info-install-6.5-alt2 sisyphus+220294.200.2.1 1548933637 installed
<13>Nov 24 03:43:39 rpmi: zlib-devel-1.2.11-alt1 sisyphus+221902.6000.4.1 1550600768 installed
<13>Nov 24 03:43:39 rpmi: liblksctp-1.0.17-alt2 1523113258 installed
<13>Nov 24 03:43:39 rpmi: libnspr-1:4.21-alt2 p9+235125.520.5.1 1565694807 installed
<13>Nov 24 03:43:39 rpmi: libidn2-2.2.0-alt1 p9+229971.100.2.1 1558696275 installed
<13>Nov 24 03:43:39 rpmi: libpixman-3:0.38.4-alt1 sisyphus+228006.100.1.1 1556013486 installed
<13>Nov 24 03:43:39 rpmi: libwayland-server-1.17.0-alt1 sisyphus+225894.100.1.1 1553872803 installed
<13>Nov 24 03:43:39 rpmi: libtcl-8.6.9-alt1 sisyphus+227145.100.1.2 1555606523 installed
<13>Nov 24 03:43:40 rpmi: tcl-8.6.9-alt1 sisyphus+227145.100.1.2 1555606523 installed
<13>Nov 24 03:43:40 rpmi: libsqlite3-3.29.0-alt1 p9+237498.100.1.1 1568303484 installed
<13>Nov 24 03:43:40 rpmi: python-module-sphinxcontrib-2.1.1-alt2.1.2 sisyphus+227529.1100.1.2 1555924423 installed
<13>Nov 24 03:43:40 rpmi: perl-Text-Unidecode-1.30-alt1 1480505027 installed
<13>Nov 24 03:43:40 rpmi: perl-IO-stringy-2.111-alt1 1432302202 installed
<13>Nov 24 03:43:40 rpmi: perl-MRO-Compat-0.13-alt1 1491292748 installed
<13>Nov 24 03:43:40 rpmi: perl-Devel-StackTrace-1:2.03-alt1 1511420922 installed
<13>Nov 24 03:43:40 rpmi: perl-Sub-Exporter-Progressive-0.001013-alt1 1479395404 installed
<13>Nov 24 03:43:40 rpmi: perl-File-Which-1.23-alt1 sisyphus.218871.100 1546337313 installed
<13>Nov 24 03:43:40 rpmi: perl-Tie-RefHash-1.39-alt1 1316492563 installed
<13>Nov 24 03:43:40 rpmi: perl-TimeDate-2.30-alt1 1374766201 installed
<13>Nov 24 03:43:40 rpmi: perl-IO-Socket-IP-0.39-alt1 1494508514 installed
<13>Nov 24 03:43:40 rpmi: perl-LWP-MediaTypes-6.04-alt1 sisyphus+225468.100.1.1 1553186684 installed
<13>Nov 24 03:43:40 rpmi: perl-Compress-Raw-Zlib-2.086-alt1 sisyphus+226395.100.1.2 1554269783 installed
<13>Nov 24 03:43:40 rpmi: perl-HTML-Tagset-3.20-alt2 1317725093 installed
<13>Nov 24 03:43:40 rpmi: libXau-1.0.9-alt1 sisyphus+223149.200.2.1 1551268156 installed
<13>Nov 24 03:43:40 rpmi: libwebp7-1.0.3-alt1 p9+234901.200.1.1 1563552213 installed
<13>Nov 24 03:43:40 rpmi: libjbig-2.1-alt1 1401380921 installed
<13>Nov 24 03:43:40 rpmi: libtiff5-4.0.10.0.57.f9fc01c3-alt1 sisyphus+226958.100.1.1 1554850937 installed
<13>Nov 24 03:43:40 rpmi: libopenjpeg2.0-2.3.1-alt1 sisyphus+226454.100.1.1 1554284336 installed
<13>Nov 24 03:43:40 rpmi: libquadmath0-8.3.1-alt5 p9+240194.100.1.1 1572928343 installed
<13>Nov 24 03:43:40 rpmi: libgfortran5-8.3.1-alt5 p9+240194.100.1.1 1572928343 installed
<13>Nov 24 03:43:40 rpmi: libgraphite2-1.3.13-alt2 sisyphus+226799.100.1.1 1554648233 installed
<13>Nov 24 03:43:40 rpmi: libharfbuzz-2.6.2-alt1 p9+238790.200.1.1 1570435797 installed
<13>Nov 24 03:43:40 rpmi: libfreetype-2.10.0-alt2 sisyphus+226881.100.2.1 1555676284 installed
<13>Nov 24 03:43:40 rpmi: fontconfig-2.13.1-alt1 sisyphus+226691.100.2.2 1554598717 installed
Updating fonts cache: <29>Nov 24 03:43:41 fontconfig: Updating fonts cache: succeeded
[ DONE ]
<13>Nov 24 03:43:41 rpmi: fonts-type1-urw-3:1.0.7pre44-alt3 sisyphus+224082.100.2.1 1552406640 installed
<13>Nov 24 03:43:41 rpmi: fonts-type1-xorg-7.0.0-alt4 1188553211 installed
<13>Nov 24 03:43:41 rpmi: libharfbuzz-icu-2.6.2-alt1 p9+238790.200.1.1 1570435797 installed
<13>Nov 24 03:43:41 rpmi: libgraphite2-devel-1.3.13-alt2 sisyphus+226799.100.1.1 1554648233 installed
<13>Nov 24 03:43:41 rpmi: libquadmath8-devel-8.3.1-alt5 p9+240194.100.1.1 1572928343 installed
<13>Nov 24 03:43:41 rpmi: libXau-devel-1.0.9-alt1 sisyphus+223149.200.2.1 1551268156 installed
<13>Nov 24 03:43:41 rpmi: perl-autodie-2.29-alt1 1445013559 installed
<13>Nov 24 03:43:41 rpmi: perl-File-HomeDir-1.004-alt1 1525450444 installed
<13>Nov 24 03:43:41 rpmi: perl-Devel-GlobalDestruction-1:0.14-alt1 1479389769 installed
<13>Nov 24 03:43:41 rpmi: perl-Role-Tiny-2.000006-alt1 1513709006 installed
<13>Nov 24 03:43:41 rpmi: perl-OLE-Storage_Lite-0.19-alt2 1291028388 installed
<13>Nov 24 03:43:42 rpmi: lksctp-tools-1.0.17-alt2 1523113258 installed
<13>Nov 24 03:43:42 rpmi: libpng-devel-1.6.36-alt1 sisyphus+219478.100.1.1 1547633315 installed
<13>Nov 24 03:43:42 rpmi: icu-utils-1:6.4.2-alt1 sisyphus+227580.100.1.2 1555784315 installed
<13>Nov 24 03:43:42 rpmi: libicu-devel-1:6.4.2-alt1 sisyphus+227580.100.1.2 1555784315 installed
<13>Nov 24 03:43:42 rpmi: perl-unicore-1:5.28.1-alt1 sisyphus+219907.100.1.1 1548343070 installed
<13>Nov 24 03:43:42 rpmi: perl-Net-IDN-Encode-2.500-alt1 sisyphus+221481.100.1.1 1550127189 installed
<13>Nov 24 03:43:42 rpmi: libopenblas-devel-0.2.20-alt2 p9+229427.100.2.1 1558020504 installed
<13>Nov 24 03:43:42 rpmi: libgdbm-devel-1.8.3-alt10 1454943313 installed
<13>Nov 24 03:43:42 rpmi: libICE-devel-1.0.9-alt1 1409902719 installed
<13>Nov 24 03:43:42 rpmi: libSM-devel-1.2.3-alt1 sisyphus+226734.100.2.1 1554586157 installed
<13>Nov 24 03:43:42 rpmi: perl-Data-Dump-1.23-alt1 1444601978 installed
<13>Nov 24 03:43:42 rpmi: perl-File-Listing-6.04-alt1 1329758996 installed
<13>Nov 24 03:43:42 rpmi: libOpenGL-7:1.1.1-alt1 sisyphus+224993.100.4.1 1552634540 installed
<13>Nov 24 03:43:42 rpmi: libGLES-7:1.1.1-alt1 sisyphus+224993.100.4.1 1552634540 installed
<13>Nov 24 03:43:42 rpmi: java-common-1.6.0-alt1 p9+234085.100.1.1 1562573623 installed
<13>Nov 24 03:43:42 rpmi: rpm-build-tcl-0.5.1-alt1 1519671307 installed
<13>Nov 24 03:43:42 rpmi: tcl-devel-8.6.9-alt1 sisyphus+227145.100.1.2 1555606523 installed
<13>Nov 24 03:43:42 rpmi: rpm-macros-java-1:5.0.0-alt1_12jpp8 sisyphus+228348.2100.3.3 1556657006 installed
<13>Nov 24 03:43:42 rpmi: perl-Algorithm-Diff-1.1903-alt1 1418755800 installed
<13>Nov 24 03:43:42 rpmi: perl-Unicode-EastAsianWidth-1.40-alt1 sisyphus.217785.100 1544703272 installed
<13>Nov 24 03:43:42 rpmi: libtre5-0.8.0-alt2.1 1334590818 installed
<13>Nov 24 03:43:42 rpmi: libpcre16-8.43-alt1 sisyphus+222771.100.1.1 1551029667 installed
<13>Nov 24 03:43:42 rpmi: pcretest-8.43-alt1 sisyphus+222771.100.1.1 1551029667 installed
<13>Nov 24 03:43:42 rpmi: libpcsclite-1.8.25-alt1 p9+236438.100.1.1 1566468036 installed
<13>Nov 24 03:43:42 rpmi: javazi-2019c-alt1 p9+238159.200.2.1 1569493946 installed
<13>Nov 24 03:43:42 rpmi: libgif-4.1.6-alt3 1299634266 installed
<13>Nov 24 03:43:42 rpmi: libalsa-1:1.1.9-alt2 sisyphus+229323.100.1.1 1557826762 installed
<13>Nov 24 03:43:42 rpmi: libgtk+2-locales-2.24.32-alt3 sisyphus+227306.100.1.3 1555646039 installed
<13>Nov 24 03:43:42 rpmi: libfribidi-1.0.7-alt1 p9+238309.200.1.1 1569787041 installed
<13>Nov 24 03:43:42 rpmi: libatk-locales-2.32.0-alt1 sisyphus+225059.600.3.2 1552845198 installed
<13>Nov 24 03:43:42 rpmi: libatk-2.32.0-alt1 sisyphus+225059.600.3.2 1552845198 installed
<13>Nov 24 03:43:42 rpmi: icon-theme-hicolor-0.17-alt1 1505715846 installed
<13>Nov 24 03:43:42 rpmi: shared-mime-info-1.13.1-alt1 p9+238204.100.1.1 1569496447 installed
<13>Nov 24 03:43:42 rpmi: libgdk-pixbuf-locales-2.38.2-alt1 p9+237353.1000.2.2 1568374008 installed
<13>Nov 24 03:43:43 rpmi: gsettings-desktop-schemas-data-3.32.0-alt1 sisyphus+225059.300.3.2 1552843929 installed
<13>Nov 24 03:43:43 rpmi: libgio-2.60.7-alt1 p9+237353.100.2.2 1568372980 installed
<13>Nov 24 03:43:43 rpmi: gsettings-desktop-schemas-3.32.0-alt1 sisyphus+225059.300.3.2 1552843929 installed
<13>Nov 24 03:43:43 rpmi: libgdk-pixbuf-2.38.2-alt1 p9+237353.1000.2.2 1568374008 installed
<13>Nov 24 03:43:43 rpmi: gtk-update-icon-cache-3.24.11-alt1 p9+237353.1200.2.2 1568374373 installed
<13>Nov 24 03:43:43 rpmi: libkpathsea6-2019-alt1_2 p9+238369.100.3.1 1569961493 installed
<13>Nov 24 03:43:43 rpmi: libptexenc1-2019-alt1_2 p9+238369.100.3.1 1569961493 installed
<13>Nov 24 03:43:43 rpmi: libsynctex2-2019-alt1_2 p9+238369.100.3.1 1569961493 installed
<13>Nov 24 03:43:43 rpmi: libtexlua5-2019-alt1_2 p9+238369.100.3.1 1569961493 installed
<13>Nov 24 03:43:43 rpmi: zziplib-0.13.69-alt3 p9+240930.100.1.1 1574080033 installed
<13>Nov 24 03:43:43 rpmi: liblcms2-2.9-alt1 1516411888 installed
<13>Nov 24 03:43:43 rpmi: publicsuffix-list-dafsa-20191108-alt1 p9+240483.100.2.1 1573432584 installed
<13>Nov 24 03:43:43 rpmi: libpsl-0.21.0-alt1 sisyphus+227314.100.1.2 1555618432 installed
<13>Nov 24 03:43:43 rpmi: libnghttp2-1.34.0-alt1 sisyphus+222625.100.1.1 1550947249 installed
<13>Nov 24 03:43:43 rpmi: libbrotlicommon-1.0.7-alt1 sisyphus+226738.100.2.1 1554554565 installed
<13>Nov 24 03:43:43 rpmi: libbrotlidec-1.0.7-alt1 sisyphus+226738.100.2.1 1554554565 installed
<13>Nov 24 03:43:43 rpmi: poppler-data-0.4.9-alt1 sisyphus.216033.100 1541141723 installed
<13>Nov 24 03:43:43 rpmi: libxshmfence-1.3-alt1 sisyphus+223149.1000.2.1 1551268594 installed
<13>Nov 24 03:43:43 rpmi: libwayland-client-1.17.0-alt1 sisyphus+225894.100.1.1 1553872803 installed
<13>Nov 24 03:43:43 rpmi: libpciaccess-1:0.14-alt1 1528969624 installed
<13>Nov 24 03:43:43 rpmi: libdrm-1:2.4.99-alt1 p9+236610.100.1.1 1566818101 installed
<13>Nov 24 03:43:43 rpmi: libgbm-4:19.1.8-alt1 p9+240059.100.2.1 1573599953 installed
<13>Nov 24 03:43:43 rpmi: t1utils-1.41-alt1 1502978415 installed
<13>Nov 24 03:43:43 rpmi: ttf2pt1-3.4.4-alt1.qa1 1366267504 installed
<13>Nov 24 03:43:43 rpmi: libqqwing-1.3.4-alt2 1436192940 installed
<13>Nov 24 03:43:43 rpmi: qqwing-1.3.4-alt2 1436192940 installed
<13>Nov 24 03:43:43 rpmi: python-module-imagesize-1.1.0-alt1 sisyphus+229015.100.2.1 1557233756 installed
<13>Nov 24 03:43:43 rpmi: python-sphinx-objects.inv-1:2.3.8.20190514-alt1 p9+229421.100.1.1 1557927689 installed
<13>Nov 24 03:43:43 rpmi: libxapian-1.4.5-alt3 sisyphus+222778.100.1.1 1551144769 installed
<13>Nov 24 03:43:43 rpmi: python-module-google-0.4.2-alt2.1 sisyphus+228356.1500.3.1 1556633038 installed
<13>Nov 24 03:43:43 rpmi: python-module-enum34-1.1.6-alt3 1527251693 installed
<13>Nov 24 03:43:43 rpmi: libnumpy-1:1.15.4-alt1 sisyphus+225625.25600.91.1 1555303051 installed
<13>Nov 24 03:43:43 rpmi: python-module-iniconfig-1.0.0-alt1 sisyphus+227494.1100.1.3 1555839106 installed
<13>Nov 24 03:43:43 rpmi: python-module-apipkg-1.5-alt1 1531926894 installed
<13>Nov 24 03:43:43 rpmi: libxblas-1.0.248-alt1.3 sisyphus+229150.100.1.1 1557388758 installed
<13>Nov 24 03:43:43 rpmi: liblapack-1:3.8.0-alt3 sisyphus+221521.100.1.1 1550134909 installed
<13>Nov 24 03:43:43 rpmi: python-modules-curses-2.7.16-alt1 sisyphus+226365.200.2.1 1554143277 installed
<13>Nov 24 03:43:43 rpmi: libverto-0.3.0-alt1_7 sisyphus+225932.100.1.1 1553994917 installed
<13>Nov 24 03:43:43 rpmi: libkeyutils-1.6-alt2 sisyphus+226520.100.2.1 1554512088 installed
<13>Nov 24 03:43:43 rpmi: libcom_err-1.44.6-alt1 sisyphus+224154.100.1.1 1552091653 installed
<13>Nov 24 03:43:43 rpmi: libdatrie-0.2.9-alt1_6 1511686677 installed
<13>Nov 24 03:43:43 rpmi: libthai-0.1.28-alt1_1 sisyphus+226107.100.1.1 1554123079 installed
<13>Nov 24 03:43:43 rpmi: libsombok-2.4.0-alt1_8 sisyphus+226104.100.1.1 1554121176 installed
<13>Nov 24 03:43:43 rpmi: perl-Unicode-Map-0.112-alt7.1 sisyphus+219907.5000.1.1 1548349925 installed
<13>Nov 24 03:43:43 rpmi: perl-Digest-Perl-MD5-1.9-alt1 1394057208 installed
<13>Nov 24 03:43:43 rpmi: perl-Crypt-RC4-2.02-alt1 1319549646 installed
<13>Nov 24 03:43:43 rpmi: perl-Math-Complex-1.59-alt1 1334229876 installed
<13>Nov 24 03:43:43 rpmi: perl-XML-RegExp-0.04-alt1 1348526543 installed
<13>Nov 24 03:43:43 rpmi: perl-DBI-1.642-alt1.1 sisyphus+219907.3200.1.1 1548345175 installed
<13>Nov 24 03:43:43 rpmi: perl-Package-Stash-XS-0.29-alt1.1 sisyphus+219907.3400.1.1 1548345296 installed
<13>Nov 24 03:43:43 rpmi: perl-Package-Stash-0.38-alt1 sisyphus.218845.100 1546250118 installed
<13>Nov 24 03:43:43 rpmi: perl-Sub-Identify-0.14-alt1.2 sisyphus+219907.3700.1.1 1548345423 installed
<13>Nov 24 03:43:43 rpmi: perl-Variable-Magic-0.62-alt1.2 sisyphus+219907.3600.1.1 1548345381 installed
<13>Nov 24 03:43:43 rpmi: perl-B-Hooks-EndOfScope-0.24-alt1 1524680298 installed
<13>Nov 24 03:43:43 rpmi: perl-namespace-clean-0.27-alt1 1464272543 installed
<13>Nov 24 03:43:43 rpmi: perl-namespace-autoclean-0.28-alt1 1444994071 installed
<13>Nov 24 03:43:43 rpmi: perl-Sub-Quote-2.006003-alt1 sisyphus+224895.100.1.1 1552434926 installed
<13>Nov 24 03:43:43 rpmi: perl-Class-Data-Inheritable-0.08-alt2 1316996762 installed
<13>Nov 24 03:43:43 rpmi: perl-Exception-Class-1.44-alt1 1513614520 installed
<13>Nov 24 03:43:43 rpmi: perl-PadWalker-2.3-alt1.2 sisyphus+219907.3500.1.1 1548345336 installed
<13>Nov 24 03:43:43 rpmi: perl-Devel-Caller-2.06-alt2.2 sisyphus+219907.4000.1.1 1548345464 installed
<13>Nov 24 03:43:43 rpmi: perl-Devel-LexAlias-0.05-alt3_17 sisyphus+219907.4100.1.1 1548345510 installed
<13>Nov 24 03:43:43 rpmi: perl-Eval-Closure-0.14-alt1 1465147597 installed
<13>Nov 24 03:43:43 rpmi: perl-Params-ValidationCompiler-0.30-alt1 1533170707 installed
<13>Nov 24 03:43:43 rpmi: perl-Mail-Sendmail-0.80-alt1 1504118031 installed
<13>Nov 24 03:43:43 rpmi: perl-Mail-Sender-1:0.903-alt1 1479576662 installed
<13>Nov 24 03:43:43 rpmi: perl-Email-Date-Format-1.005-alt1 1413796337 installed
<13>Nov 24 03:43:43 rpmi: ppp-common-0.5.1-alt1 1244040597 installed
<13>Nov 24 03:43:43 rpmi: sendmail-common-1.7-alt3 1353029717 installed
<13>Nov 24 03:43:43 rpmi: perl-Locale-Maketext-Simple-0.21-alt3 1321333616 installed
<13>Nov 24 03:43:43 rpmi: perl-IPC-System-Simple-1.25-alt2_1 1388863478 installed
<13>Nov 24 03:43:43 rpmi: perl-Term-Cap-1.17-alt1 1445018869 installed
<13>Nov 24 03:43:43 rpmi: perl-Pod-Escapes-1.07-alt1 1418767892 installed
<13>Nov 24 03:43:43 rpmi: perl-File-Copy-Recursive-0.44-alt1 1525447381 installed
<13>Nov 24 03:43:43 rpmi: perl-Digest-SHA1-2.13-alt5.2 sisyphus+219907.4500.1.1 1548349730 installed
<13>Nov 24 03:43:43 rpmi: less-530-alt1 sisyphus+226367.200.2.2 1554151813 installed
<13>Nov 24 03:43:43 rpmi: perl-Compress-Raw-Bzip2-2.086-alt1 sisyphus+226394.100.1.2 1554269409 installed
<13>Nov 24 03:43:43 rpmi: libdb4.7-devel-4.7.25-alt9 1490438456 installed
<13>Nov 24 03:43:44 rpmi: perl-devel-1:5.28.1-alt1 sisyphus+219907.100.1.1 1548343070 installed
<13>Nov 24 03:43:44 rpmi: perl-Test-Fatal-0.014-alt1 1418768336 installed
<13>Nov 24 03:43:44 rpmi: perl-Specio-0.43-alt1 sisyphus.215861.100 1540964587 installed
<13>Nov 24 03:43:44 rpmi: hd2u-1.0.3-alt2 1400842666 installed
<13>Nov 24 03:43:44 rpmi: perl-Filter-1.59-alt1.1 sisyphus+219907.400.1.1 1548343225 installed
<13>Nov 24 03:43:44 rpmi: perl-Encode-3.01-alt1 sisyphus+224923.100.1.1 1552474113 installed
<13>Nov 24 03:43:44 rpmi: perl-URI-1.76-alt1 sisyphus+220243.100.1.1 1548863244 installed
<13>Nov 24 03:43:44 rpmi: perl-HTML-Parser-3.72-alt1.2 sisyphus+219907.600.1.1 1548343407 installed
<13>Nov 24 03:43:44 rpmi: perl-IO-Compress-2.086-alt1 sisyphus+226399.100.2.1 1554270186 installed
<13>Nov 24 03:43:44 rpmi: perl-Net-HTTP-6.18-alt1 1526560501 installed
<13>Nov 24 03:43:44 rpmi: perl-Pod-Simple-3.35-alt1 1482098090 installed
<13>Nov 24 03:43:44 rpmi: perl-Pod-Usage-1.69-alt1 1464274721 installed
<13>Nov 24 03:43:44 rpmi: perl-podlators-4.11-alt1 1525935408 installed
<13>Nov 24 03:43:44 rpmi: perl-WWW-RobotRules-6.02-alt1 1329756211 installed
<13>Nov 24 03:43:44 rpmi: perl-Encode-Locale-1.05-alt1 1444608613 installed
<13>Nov 24 03:43:44 rpmi: perl-IO-HTML-1.001-alt1 1404821752 installed
<13>Nov 24 03:43:44 rpmi: perl-HTTP-Message-6.18-alt1 1528288416 installed
<13>Nov 24 03:43:44 rpmi: perl-HTTP-Cookies-6.04-alt1 1504116575 installed
<13>Nov 24 03:43:44 rpmi: perl-HTTP-Negotiate-6.01-alt1 1329760563 installed
<13>Nov 24 03:43:44 rpmi: perl-libwww-6.39-alt1 sisyphus+229237.100.1.1 1557650051 installed
<13>Nov 24 03:43:44 rpmi: perl-XML-Parser-2.44-alt2.2 sisyphus+219907.1300.1.1 1548343654 installed
<13>Nov 24 03:43:44 rpmi: perl-HTML-Tree-5.07-alt1 1506480309 installed
<13>Nov 24 03:43:44 rpmi: perl-HTML-Formatter-2.16-alt1 1482105372 installed
<13>Nov 24 03:43:44 rpmi: perl-XML-DOM-1.46-alt1 1474815568 installed
<13>Nov 24 03:43:44 rpmi: perl-XML-XPath-1.44-alt1 sisyphus.215541.100 1540451758 installed
<13>Nov 24 03:43:44 rpmi: perl-HTML-Form-6.04-alt1 sisyphus+225750.100.1.1 1553678430 installed
<13>Nov 24 03:43:44 rpmi: perl-WWW-Mechanize-1.91-alt1 sisyphus+219761.100.1.2 1548132822 installed
<13>Nov 24 03:43:44 rpmi: perl-XML-Writer-0.625-alt1 1402417374 installed
<13>Nov 24 03:43:44 rpmi: hwinfo-utils-21.23-alt1.1 sisyphus+223919.100.1.1 1551893088 installed
<13>Nov 24 03:43:44 rpmi: perl-MIME-Types-2.17-alt1 1517533413 installed
<13>Nov 24 03:43:44 rpmi: perl-Text-CSV_XS-1.39-alt1 sisyphus+225184.100.1.2 1552965519 installed
<13>Nov 24 03:43:44 rpmi: perl-Spreadsheet-ParseExcel-1:0.65-alt1 1395677487 installed
<13>Nov 24 03:43:44 rpmi: perl-MIME-Charset-1.012.2-alt1 1494353584 installed
<13>Nov 24 03:43:44 rpmi: perl-Unicode-LineBreak-2019.001-alt1.1 sisyphus+219907.4700.1.1 1548349872 installed
<13>Nov 24 03:43:44 rpmi: perl-YAML-Tiny-1.73-alt1 1520430664 installed
<13>Nov 24 03:43:44 rpmi: perl-libintl-1.31-alt1.1 sisyphus+219907.6300.1.1 1548352427 installed
<13>Nov 24 03:43:44 rpmi: libteckit-2.5.1-alt2.1 1319227424 installed
<13>Nov 24 03:43:44 rpmi: libteckit-utils-2.5.1-alt2.1 1319227424 installed
<13>Nov 24 03:43:44 rpmi: rgb-1.0.6-alt3 p9+229442.100.1.1 1557941137 installed
<13>Nov 24 03:43:44 rpmi: libnetpbm11-10.85.04-alt1 sisyphus+225727.140.8.1 1553672201 installed
<13>Nov 24 03:43:44 rpmi: mailx-8.1.2-alt7 1366314831 installed
<13>Nov 24 03:43:44 rpmi: sharutils-4.6.3-alt1.1.qa2.1 1449219807 installed
<13>Nov 24 03:43:44 rpmi: ncompress-4.2.4.4-alt1 1366160439 installed
<13>Nov 24 03:43:44 rpmi: libX11-locales-3:1.6.7-alt1 sisyphus+226735.100.2.2 1554615009 installed
<13>Nov 24 03:43:44 rpmi: libXdmcp-1.1.3-alt1 sisyphus+225206.600.1.2 1552949347 installed
<13>Nov 24 03:43:44 rpmi: libxcb-1.13.1-alt1 sisyphus+226527.100.2.2 1554593799 installed
<13>Nov 24 03:43:44 rpmi: libX11-3:1.6.7-alt1 sisyphus+226735.100.2.2 1554615009 installed
<13>Nov 24 03:43:44 rpmi: libXext-1.3.4-alt1 sisyphus+225206.700.1.2 1552949422 installed
<13>Nov 24 03:43:44 rpmi: libXrender-0.9.8-alt1 1371312110 installed
<13>Nov 24 03:43:44 rpmi: libXt-1.1.4-alt1 1369984716 installed
<13>Nov 24 03:43:44 rpmi: libXmu-1.1.3-alt1 sisyphus+225206.1200.1.2 1552949629 installed
<13>Nov 24 03:43:44 rpmi: libXft-2.3.3-alt1 sisyphus+225206.1000.3.2 1552987714 installed
<13>Nov 24 03:43:44 rpmi: libXfixes-5.0.3-alt1 sisyphus+226736.100.2.2 1554614842 installed
<13>Nov 24 03:43:44 rpmi: libXpm-3.5.12-alt1 sisyphus+223149.400.2.1 1551268300 installed
<13>Nov 24 03:43:44 rpmi: libXi-1.7.9-alt2 sisyphus+226377.100.1.2 1554260258 installed
<13>Nov 24 03:43:44 rpmi: libXdamage-1.1.5-alt1 sisyphus+225206.500.1.2 1552949282 installed
<13>Nov 24 03:43:44 rpmi: libXcomposite-0.4.5-alt1 sisyphus+225206.300.1.2 1552949136 installed
<13>Nov 24 03:43:46 rpmi: libxcb-devel-1.13.1-alt1 sisyphus+226527.100.2.2 1554593799 installed
<13>Nov 24 03:43:46 rpmi: libX11-devel-3:1.6.7-alt1 sisyphus+226735.100.2.2 1554615009 installed
<13>Nov 24 03:43:46 rpmi: libXrender-devel-0.9.8-alt1 1371312110 installed
<13>Nov 24 03:43:46 rpmi: libXext-devel-1.3.4-alt1 sisyphus+225206.700.1.2 1552949422 installed
<13>Nov 24 03:43:46 rpmi: libXt-devel-1.1.4-alt1 1369984716 installed
<13>Nov 24 03:43:46 rpmi: libXaw-1.0.12-alt1 1391072621 installed
<13>Nov 24 03:43:46 rpmi: libgd3-2.2.5-alt3 sisyphus+226800.200.2.1 1554649314 installed
<13>Nov 24 03:43:46 rpmi: libXcursor-1.2.0-alt1 sisyphus+225206.400.1.2 1552949214 installed
<13>Nov 24 03:43:46 rpmi: perl-Tk-804.034-alt1.2 sisyphus+219907.4300.1.1 1548345831 installed
<13>Nov 24 03:43:46 rpmi: libtk-8.6.9-alt1 sisyphus+227145.200.1.2 1555606663 installed
<13>Nov 24 03:43:46 rpmi: tk-8.6.9-alt1 sisyphus+227145.200.1.2 1555606663 installed
<13>Nov 24 03:43:46 rpmi: xset-1.2.4-alt1 sisyphus.213358.100 1537438593 installed
<13>Nov 24 03:43:46 rpmi: libXrandr-1.5.2-alt1 sisyphus+225206.1300.1.2 1552949698 installed
<13>Nov 24 03:43:46 rpmi: libXxf86vm-1.1.4-alt2 1527672159 installed
<13>Nov 24 03:43:46 rpmi: libGLX-mesa-4:19.1.8-alt1 p9+240059.100.2.1 1573599953 installed
<13>Nov 24 03:43:46 rpmi: libEGL-mesa-4:19.1.8-alt1 p9+240059.100.2.1 1573599953 installed
<13>Nov 24 03:43:46 rpmi: libEGL-7:1.1.1-alt1 sisyphus+224993.100.4.1 1552634540 installed
<13>Nov 24 03:43:46 rpmi: libGLX-7:1.1.1-alt1 sisyphus+224993.100.4.1 1552634540 installed
<13>Nov 24 03:43:46 rpmi: libGL-7:1.1.1-alt1 sisyphus+224993.100.4.1 1552634540 installed
<13>Nov 24 03:43:46 rpmi: libcairo-1:1.16.0-alt1 sisyphus+226534.100.2.3 1554515520 installed
<13>Nov 24 03:43:46 rpmi: libpango-1.44.6-alt1 p9+237353.700.2.2 1568373865 installed
<13>Nov 24 03:43:46 rpmi: libglvnd-devel-7:1.1.1-alt1 sisyphus+224993.100.4.1 1552634540 installed
<13>Nov 24 03:43:46 rpmi: libEGL-devel-4:19.1.8-alt1 p9+240059.100.2.1 1573599953 installed
<13>Nov 24 03:43:46 rpmi: libGL-devel-4:19.1.8-alt1 p9+240059.100.2.1 1573599953 installed
<13>Nov 24 03:43:46 rpmi: libXinerama-1.1.4-alt1 sisyphus+223149.300.2.1 1551268223 installed
<13>Nov 24 03:43:46 rpmi: libXtst-1.2.2-alt1 1369984880 installed
<13>Nov 24 03:43:46 rpmi: netpbm-10.85.04-alt1 sisyphus+225727.140.8.1 1553672201 installed
<13>Nov 24 03:43:46 rpmi: xprop-1.2.4-alt1 sisyphus+225764.100.1.1 1553680701 installed
<13>Nov 24 03:43:46 rpmi: xdg-utils-1.1.3-alt5 sisyphus.216143.100 1541504685 installed
<13>Nov 24 03:43:46 rpmi: liblz4-1:1.9.2-alt1 p9+238696.500.1.1 1570228072 installed
<13>Nov 24 03:43:46 rpmi: libgpg-error-1.36-alt1 sisyphus+225621.300.1.1 1553521088 installed
<13>Nov 24 03:43:46 rpmi: libgcrypt20-1.8.4-alt2 sisyphus+229280.100.1.1 1557741896 installed
<13>Nov 24 03:43:47 rpmi: libxslt-1.1.33-alt1 sisyphus+226936.100.1.1 1554820927 installed
<13>Nov 24 03:43:47 rpmi: libsystemd-1:242-alt12 p9+239240.100.1.1 1571079054 installed
<13>Nov 24 03:43:47 rpmi: libdbus-1.12.16-alt2 p9+240607.100.1.1 1573553670 installed
<13>Nov 24 03:43:47 rpmi: libavahi-0.6.32-alt1 1500485694 installed
<13>Nov 24 03:43:47 rpmi: libcups-2.2.11-alt1 sisyphus+225793.100.1.1 1553701171 installed
<13>Nov 24 03:43:47 rpmi: libgtk+2-2.24.32-alt3 sisyphus+227306.100.1.3 1555646039 installed
<13>Nov 24 03:43:47 rpmi: libgail-2.24.32-alt3 sisyphus+227306.100.1.3 1555646039 installed
<13>Nov 24 03:43:48 rpmi: libgs-9.27-alt1 p9+230401.100.1.1 1558957679 installed
<13>Nov 24 03:43:49 rpmi: ghostscript-common-9.27-alt1 p9+230401.100.1.1 1558957679 installed
<13>Nov 24 03:43:49 rpmi: ghostscript-classic-9.27-alt1 p9+230401.100.1.1 1558957679 installed
<13>Nov 24 03:43:49 rpmi: ghostscript-module-X-9.27-alt1 p9+230401.100.1.1 1558957679 installed
<13>Nov 24 03:43:49 rpmi: gcc-fortran-common-1.4.23-alt1 sisyphus+221902.2500.4.1 1550596716 installed
<13>Nov 24 03:43:49 rpmi: libgfortran8-devel-8.3.1-alt5 p9+240194.100.1.1 1572928343 installed
<13>Nov 24 03:43:50 rpmi: gcc8-fortran-8.3.1-alt5 p9+240194.100.1.1 1572928343 installed
<13>Nov 24 03:43:50 rpmi: gcc-c++-common-1.4.23-alt1 sisyphus+221902.2500.4.1 1550596716 installed
<13>Nov 24 03:43:51 rpmi: libstdc++8-devel-8.3.1-alt5 p9+240194.100.1.1 1572928343 installed
<13>Nov 24 03:43:51 rpmi: gcc8-c++-8.3.1-alt5 p9+240194.100.1.1 1572928343 installed
<13>Nov 24 03:43:51 rpmi: xml-utils-1:2.9.10-alt2 p9+240157.100.1.1 1572735290 installed
<13>Nov 24 03:43:52 rpmi: rpm-build-gir-0.7.3-alt2 p9+234356.40.2.1 1562933848 installed
<13>Nov 24 03:43:52 rpmi: ed-1:0.2-alt10 1449768441 installed
<13>Nov 24 03:43:52 rpmi: libdialog-1.3.20171209-alt1 1529583087 installed
<13>Nov 24 03:43:52 rpmi: dialog-1.3.20171209-alt1 1529583087 installed
<13>Nov 24 03:43:52 rpmi: libruby-2.5.5-alt3 p9+231429.100.1.1 1559580197 installed
<13>Nov 24 03:43:52 rpmi: libp11-kit-0.23.15-alt1 sisyphus+226408.100.2.1 1554288187 installed
<13>Nov 24 03:43:52 rpmi: libtasn1-4.14-alt1 p9+235792.100.2.1 1565425233 installed
<13>Nov 24 03:43:52 rpmi: libyaml2-0.2.2-alt1 sisyphus+229134.100.1.1 1557342720 installed
<13>Nov 24 03:43:52 rpmi: bc-1:1.07.1-alt1 sisyphus+221902.700.4.1 1550587848 installed
<13>Nov 24 03:43:52 rpmi: rpm-macros-alternatives-0.5.1-alt1 sisyphus+226946.100.1.1 1554830426 installed
<13>Nov 24 03:43:52 rpmi: alternatives-0.5.1-alt1 sisyphus+226946.100.1.1 1554830426 installed
<13>Nov 24 03:43:52 rpmi: libnss-3.45.0-alt1 p9+235125.540.6.1 1565821478 installed
<13>Nov 24 03:43:52 rpmi: ca-certificates-2019.10.28-alt1 p9+240634.100.1.1 1573575926 installed
<13>Nov 24 03:43:52 rpmi: ca-trust-0.1.2-alt1 p9+233349.100.1.1 1561655062 installed
<13>Nov 24 03:43:52 rpmi: p11-kit-trust-0.23.15-alt1 sisyphus+226408.100.2.1 1554288187 installed
<13>Nov 24 03:43:52 rpmi: libcrypto1.1-1.1.1d-alt1.1 p9+237853.200.3.1 1569251778 installed
<13>Nov 24 03:43:52 rpmi: libssl1.1-1.1.1d-alt1.1 p9+237853.200.3.1 1569251778 installed
<13>Nov 24 03:43:52 rpmi: libpython3-3.7.4-alt2 p9+239459.100.1.1 1571444591 installed
<13>Nov 24 03:43:52 rpmi: python3-3.7.4-alt2 p9+239459.100.1.1 1571444591 installed
<13>Nov 24 03:43:53 rpmi: python3-base-3.7.4-alt2 p9+239459.100.1.1 1571444591 installed
<13>Nov 24 03:43:53 rpmi: ruby-rubygems-update-3.0.3-alt1 sisyphus+226411.5400.6.1 1554381326 installed
<13>Nov 24 03:43:53 rpmi: gem-did-you-mean-1.3.0-alt1 sisyphus+219587.100.1.1 1547808061 installed
<13>Nov 24 03:43:53 rpmi: ruby-minitest-5.11.3-alt1 sisyphus+219345.3500.8.1 1547631954 installed
<13>Nov 24 03:43:53 rpmi: ruby-net-telnet-0.2.0-alt1 sisyphus+219345.2700.8.1 1547631566 installed
<13>Nov 24 03:43:53 rpmi: gem-power-assert-1.1.4-alt1 sisyphus+226411.3200.6.1 1554380195 installed
<13>Nov 24 03:43:53 rpmi: rake-12.3.2-alt2 sisyphus+218713.60.1.1 1547734935 installed
<13>Nov 24 03:43:53 rpmi: ruby-rake-12.3.2-alt2 sisyphus+218713.60.1.1 1547734935 installed
<13>Nov 24 03:43:53 rpmi: ruby-test-unit-1:3.3.1-alt1 sisyphus+226411.5300.6.1 1554381151 installed
<13>Nov 24 03:43:53 rpmi: ruby-xmlrpc-0.3.0-alt1 sisyphus+219345.3300.8.1 1547631818 installed
<13>Nov 24 03:43:53 rpmi: gem-2.5.5-alt3 p9+231429.100.1.1 1559580197 installed
<13>Nov 24 03:43:53 rpmi: ri-6.1.1-alt3 sisyphus+220149.7500.44.1 1552167568 installed
<13>Nov 24 03:43:53 rpmi: rdoc-6.1.1-alt3 sisyphus+220149.7500.44.1 1552167568 installed
<13>Nov 24 03:43:54 rpmi: ruby-rdoc-6.1.1-alt3 sisyphus+220149.7500.44.1 1552167568 installed
<13>Nov 24 03:43:54 rpmi: ruby-stdlibs-2.5.5-alt3 p9+231429.100.1.1 1559580197 installed
<13>Nov 24 03:43:54 rpmi: erb-2.5.5-alt3 p9+231429.100.1.1 1559580197 installed
<13>Nov 24 03:43:54 rpmi: irb-2.5.5-alt3 p9+231429.100.1.1 1559580197 installed
<13>Nov 24 03:43:54 rpmi: ruby-bundler-2.0.1-alt1 sisyphus+218713.700.2.1 1547736109 installed
<13>Nov 24 03:43:54 rpmi: bundle-2.0.1-alt1 sisyphus+218713.700.2.1 1547736109 installed
<13>Nov 24 03:43:54 rpmi: ruby-2.5.5-alt3 p9+231429.100.1.1 1559580197 installed
<86>Nov 24 03:43:54 groupadd[2931]: group added to /etc/group: name=_keytab, GID=499
<86>Nov 24 03:43:54 groupadd[2931]: group added to /etc/gshadow: name=_keytab
<86>Nov 24 03:43:54 groupadd[2931]: new group: name=_keytab, GID=499
<13>Nov 24 03:43:54 rpmi: libkrb5-1.16.3-alt1 sisyphus+223678.100.1.1 1551746443 installed
<13>Nov 24 03:43:54 rpmi: glib2-devel-2.60.7-alt1 p9+237353.100.2.2 1568372980 installed
<13>Nov 24 03:43:54 rpmi: libharfbuzz-devel-2.6.2-alt1 p9+238790.200.1.1 1570435797 installed
<13>Nov 24 03:43:54 rpmi: libfreetype-devel-2.10.0-alt2 sisyphus+226881.100.2.1 1555676284 installed
<13>Nov 24 03:43:55 rpmi: fontconfig-devel-2.13.1-alt1 sisyphus+226691.100.2.2 1554598717 installed
<13>Nov 24 03:43:55 rpmi: python3-module-six-1.12.0-alt1 sisyphus+219665.100.2.1 1548148570 installed
<13>Nov 24 03:43:55 rpmi: libXft-devel-2.3.3-alt1 sisyphus+225206.1000.3.2 1552987714 installed
<13>Nov 24 03:43:55 rpmi: libcairo-devel-1:1.16.0-alt1 sisyphus+226534.100.2.3 1554515520 installed
<13>Nov 24 03:43:55 rpmi: libtirpc-1.0.3-alt1 1532008015 installed
<13>Nov 24 03:43:55 rpmi: libnsl2-1.1.0-alt1_1 1511548748 installed
<13>Nov 24 03:43:55 rpmi: python-modules-encodings-2.7.16-alt1 sisyphus+226365.200.2.1 1554143277 installed
<13>Nov 24 03:43:55 rpmi: python-modules-compiler-2.7.16-alt1 sisyphus+226365.200.2.1 1554143277 installed
<13>Nov 24 03:43:55 rpmi: python-modules-email-2.7.16-alt1 sisyphus+226365.200.2.1 1554143277 installed
<13>Nov 24 03:43:55 rpmi: python-modules-unittest-2.7.16-alt1 sisyphus+226365.200.2.1 1554143277 installed
<13>Nov 24 03:43:55 rpmi: python-modules-nis-2.7.16-alt1 sisyphus+226365.200.2.1 1554143277 installed
<13>Nov 24 03:43:55 rpmi: python-modules-2.7.16-alt1 sisyphus+226365.200.2.1 1554143277 installed
<13>Nov 24 03:43:55 rpmi: python-module-six-1.12.0-alt1 sisyphus+219665.100.2.1 1548148570 installed
<13>Nov 24 03:43:55 rpmi: python-modules-ctypes-2.7.16-alt1 sisyphus+226365.200.2.1 1554143277 installed
<13>Nov 24 03:43:55 rpmi: python-modules-xml-2.7.16-alt1 sisyphus+226365.200.2.1 1554143277 installed
<13>Nov 24 03:43:55 rpmi: python-module-pkg_resources-1:40.8.0-alt2 sisyphus+229158.200.2.1 1557735221 installed
<13>Nov 24 03:43:55 rpmi: python-modules-json-2.7.16-alt1 sisyphus+226365.200.2.1 1554143277 installed
<13>Nov 24 03:43:55 rpmi: python-modules-multiprocessing-2.7.16-alt1 sisyphus+226365.200.2.1 1554143277 installed
<13>Nov 24 03:43:55 rpmi: python-modules-logging-2.7.16-alt1 sisyphus+226365.200.2.1 1554143277 installed
<13>Nov 24 03:43:55 rpmi: python-modules-hotshot-2.7.16-alt1 sisyphus+226365.200.2.1 1554143277 installed
<13>Nov 24 03:43:55 rpmi: python-module-py-1.8.0-alt2 sisyphus+228349.1400.4.1 1556631070 installed
<13>Nov 24 03:43:55 rpmi: python-module-chardet-3.0.4-alt1 sisyphus+227476.1700.1.2 1555756717 installed
<13>Nov 24 03:43:55 rpmi: python-tools-2to3-2.7.16-alt1 sisyphus+226365.200.2.1 1554143277 installed
<13>Nov 24 03:43:55 rpmi: python-module-future-0.16.0-alt2 sisyphus+228356.200.3.3 1556645013 installed
<13>Nov 24 03:43:55 rpmi: python-module-pyglet-1.3.0-alt4.a1.hg20150730.1.1.1 1460413686 installed
<13>Nov 24 03:43:55 rpmi: python-module-whoosh-2.7.4-alt1 1527697941 installed
<13>Nov 24 03:43:55 rpmi: python-module-webencodings-0.5.1-alt1.1 1517943573 installed
<13>Nov 24 03:43:55 rpmi: python-module-more-itertools-1:5.0.0-alt2 sisyphus+226536.200.1.1 1554329977 installed
<13>Nov 24 03:43:55 rpmi: python-modules-bsddb-2.7.16-alt1 sisyphus+226365.200.2.1 1554143277 installed
<13>Nov 24 03:43:55 rpmi: python-2.7.16-alt1 sisyphus+226365.200.2.1 1554143277 installed
<13>Nov 24 03:43:55 rpmi: python-strict-2.7.16-alt1 sisyphus+226365.200.2.1 1554143277 installed
<13>Nov 24 03:43:56 rpmi: python-modules-distutils-2.7.16-alt1 sisyphus+226365.200.2.1 1554143277 installed
<13>Nov 24 03:43:56 rpmi: python-module-attrs-19.1.0-alt1 sisyphus+227473.2100.1.2 1555756986 installed
<13>Nov 24 03:43:56 rpmi: python-module-cssselect-0.9.1-alt1.2 sisyphus+227479.1100.1.2 1555757152 installed
<13>Nov 24 03:43:56 rpmi: python-module-html5lib-1:0.999999999-alt4.qa1 sisyphus+227493.600.1.3 1555835341 installed
<13>Nov 24 03:43:56 rpmi: python-module-lxml-4.3.3-alt1.1 sisyphus+225625.33200.91.1 1555315088 installed
<13>Nov 24 03:43:56 rpmi: python-module-docutils-0.14-alt2 1535729778 installed
<13>Nov 24 03:43:56 rpmi: python-module-idna-2.8-alt1 sisyphus+227494.400.1.3 1555838720 installed
<13>Nov 24 03:43:56 rpmi: python-module-pycparser-2.19-alt1 sisyphus+228366.1000.2.3 1556706938 installed
<13>Nov 24 03:43:56 rpmi: python-module-cffi-1.12.3-alt1 sisyphus+229040.200.3.1 1557316502 installed
<13>Nov 24 03:43:56 rpmi: python-module-asn1crypto-0.24.0-alt1 sisyphus+227473.1300.1.2 1555756512 installed
<13>Nov 24 03:43:56 rpmi: python-module-ntlm-1.1.0-alt1.2 sisyphus+228512.100.1.1 1556654575 installed
<13>Nov 24 03:43:56 rpmi: python-module-pytz-1:2016.10-alt1 1484291011 installed
<13>Nov 24 03:43:57 rpmi: python-module-babel-1:2.6.0-alt1 sisyphus+228351.2400.6.2 1556652168 installed
<13>Nov 24 03:43:57 rpmi: python-module-PyStemmer-1.0.1-alt1.2.1 1321387369 installed
<13>Nov 24 03:43:57 rpmi: python-module-snowballstemmer-1.2.0-alt2.1 1457859319 installed
<13>Nov 24 03:43:57 rpmi: python-module-funcsigs-1.0.2-alt2 sisyphus+228355.2600.2.1 1556560236 installed
<13>Nov 24 03:43:57 rpmi: python-module-scandir-1.10.0-alt1 sisyphus+225192.100.1.2 1552968852 installed
<13>Nov 24 03:43:57 rpmi: python-module-pathlib2-2.3.3-alt1 sisyphus+228364.300.4.1 1556886257 installed
<13>Nov 24 03:43:57 rpmi: python-module-atomicwrites-1.3.0-alt1 sisyphus+227473.2000.1.3 1555763467 installed
<13>Nov 24 03:43:57 rpmi: python-module-simplejson-3.15.0-alt1.qa1 sisyphus+225625.16100.91.1 1555293606 installed
<13>Nov 24 03:43:57 rpmi: python-module-ipaddress-1.0.18-alt1.1 sisyphus+227494.1700.1.3 1555839523 installed
<13>Nov 24 03:43:57 rpmi: python-module-cryptography-2.6.1-alt1 sisyphus+225625.24400.91.1 1555299604 installed
<13>Nov 24 03:43:57 rpmi: python-module-OpenSSL-18.0.0-alt1 1532996168 installed
<13>Nov 24 03:43:57 rpmi: python-module-ndg-0.4.2-alt1.qa1 sisyphus+227504.1300.1.2 1555853074 installed
<13>Nov 24 03:43:57 rpmi: python-module-ndg-httpsclient-0.4.2-alt1.qa1 sisyphus+227504.1300.1.2 1555853074 installed
<13>Nov 24 03:43:57 rpmi: python-module-backports-3.5.0.1-alt1.1.1 1517645428 installed
<13>Nov 24 03:43:57 rpmi: python-module-backports.ssl_match_hostname-3.5.0.1-alt1.1.1 1517645428 installed
<13>Nov 24 03:43:57 rpmi: python-module-urllib3-2:1.24.3-alt1 sisyphus+228978.100.1.1 1557126149 installed
<13>Nov 24 03:43:57 rpmi: python-module-requests-2.21.0-alt1 sisyphus+228370.100.2.2 1556711628 installed
<13>Nov 24 03:43:57 rpmi: python-module-typing-3.6.6-alt2 sisyphus+220108.100.1.1 1548749697 installed
<13>Nov 24 03:43:57 rpmi: python-module-markupsafe-0.23-alt1.2.1.1 sisyphus+225625.12200.91.1 1555290677 installed
<13>Nov 24 03:43:57 rpmi: python-module-jinja2-2.10-alt1 1521724576 installed
<13>Nov 24 03:43:57 rpmi: python-modules-sqlite3-2.7.16-alt1 sisyphus+226365.200.2.1 1554143277 installed
<13>Nov 24 03:43:57 rpmi: python-module-SQLAlchemy-1.2.15-alt1 sisyphus+225625.4500.91.1 1555285684 installed
<13>Nov 24 03:43:57 rpmi: python-module-mpmath-0.19-alt1.git20150621.1.1.1.1 sisyphus+227503.2100.1.3 1555860908 installed
<13>Nov 24 03:43:58 rpmi: python-module-sympy-1:1.1.1-alt1.1.1 sisyphus+228334.100.1.1 1556542452 installed
<13>Nov 24 03:43:58 rpmi: python-module-sympy-tests-1:1.1.1-alt1.1.1 sisyphus+228334.100.1.1 1556542452 installed
<13>Nov 24 03:43:58 rpmi: python-module-pluggy-0.11.0-alt1 sisyphus+229116.100.1.1 1557316655 installed
<13>Nov 24 03:43:58 rpmi: python-module-pytest-3.10.1-alt5 sisyphus+228366.2000.2.3 1556707871 installed
<13>Nov 24 03:43:58 rpmi: python-module-numpy-1:1.15.4-alt1 sisyphus+225625.25600.91.1 1555303051 installed
<13>Nov 24 03:43:58 rpmi: python-module-numpy-testing-1:1.15.4-alt1 sisyphus+225625.25600.91.1 1555303051 installed
<13>Nov 24 03:43:58 rpmi: python-module-xapian-1.4.5-alt3 sisyphus+225625.23000.91.1 1555297606 installed
<13>Nov 24 03:43:58 rpmi: python-module-sphinxcontrib-websupport-1.0.1-alt3.qa1 sisyphus+227529.1200.1.2 1555924506 installed
<13>Nov 24 03:43:58 rpmi: python-module-alabaster-0.7.6-alt3 sisyphus+228351.700.4.1 1556637370 installed
<13>Nov 24 03:43:58 rpmi: python-module-Pygments-2.2.0-alt2 1526455576 installed
<13>Nov 24 03:43:59 rpmi: python-module-sphinx-1:1.6.5-alt4 sisyphus+228232.100.1.1 1556298645 installed
<86>Nov 24 03:43:59 groupadd[12365]: group added to /etc/group: name=sasl, GID=498
<86>Nov 24 03:43:59 groupadd[12365]: group added to /etc/gshadow: name=sasl
<86>Nov 24 03:43:59 groupadd[12365]: new group: name=sasl, GID=498
<13>Nov 24 03:43:59 rpmi: libsasl2-3-2.1.27-alt2 sisyphus+228101.100.1.1 1556139861 installed
<13>Nov 24 03:43:59 rpmi: libldap-2.4.48-alt3 p9+238817.100.1.1 1570449030 installed
<13>Nov 24 03:43:59 rpmi: libcurl-7.65.0-alt1 p9+229801.100.1.1 1558513332 installed
<13>Nov 24 03:43:59 rpmi: libpoppler90-0.80.0-alt1 p9+237607.100.1.1 1568643072 installed
<13>Nov 24 03:43:59 rpmi: python3-module-genshi-0.7-alt2 sisyphus+229363.100.1.1 1557847321 installed
<13>Nov 24 03:43:59 rpmi: python3-module-webencodings-0.5.1-alt1.1 1517943573 installed
<13>Nov 24 03:43:59 rpmi: python3-module-html5lib-1:0.999999999-alt4.qa1 sisyphus+227493.600.1.3 1555835341 installed
<13>Nov 24 03:43:59 rpmi: python3-module-lxml-4.3.3-alt1.1 sisyphus+225625.33200.91.1 1555315088 installed
<13>Nov 24 03:43:59 rpmi: python3-module-cssselect-0.9.1-alt1.2 sisyphus+227479.1100.1.2 1555757152 installed
<13>Nov 24 03:43:59 rpmi: python3-module-javapackages-1:5.0.0-alt1_12jpp8 sisyphus+228348.2100.3.3 1556657006 installed
<13>Nov 24 03:43:59 rpmi: rpm-build-java-1:5.0.0-alt1_12jpp8 sisyphus+228348.2100.3.3 1556657006 installed
<13>Nov 24 03:43:59 rpmi: perl-Net-SSLeay-1.86_09-alt2 sisyphus+227568.100.1.1 1555676534 installed
<13>Nov 24 03:43:59 rpmi: perl-IO-Socket-SSL-2.066-alt1 sisyphus+223890.100.1.1 1551873760 installed
<13>Nov 24 03:43:59 rpmi: perl-Net-HTTPS-6.18-alt1 1526560501 installed
<13>Nov 24 03:43:59 rpmi: perl-LWP-Protocol-https-6.07-alt1 1494527383 installed
<13>Nov 24 03:43:59 rpmi: perl-Net-SMTP-SSL-1.04-alt1 1479470835 installed
<13>Nov 24 03:43:59 rpmi: perl-MailTools-2.20-alt1 1517533205 installed
<13>Nov 24 03:43:59 rpmi: perl-MIME-Lite-3.030-alt1 1383865152 installed
<13>Nov 24 03:43:59 rpmi: perl-Log-Dispatch-2.68-alt2 sisyphus.218872.100 1546338428 installed
<13>Nov 24 03:43:59 rpmi: perl-Log-Log4perl-1.49-alt1 1489613295 installed
<13>Nov 24 03:43:59 rpmi: ca-trust-java-0.1.2-alt1 p9+233349.100.1.1 1561655062 installed
<13>Nov 24 03:44:01 rpmi: java-1.8.0-openjdk-headless-0:1.8.0.212.b04-alt2_0jpp8 p9+234508.100.3.1 1563175554 installed
<13>Nov 24 03:44:02 rpmi: java-1.8.0-openjdk-0:1.8.0.212.b04-alt2_0jpp8 p9+234508.100.3.1 1563175554 installed
<13>Nov 24 03:44:03 rpmi: java-1.8.0-openjdk-devel-0:1.8.0.212.b04-alt2_0jpp8 p9+234508.100.3.1 1563175554 installed
<13>Nov 24 03:44:04 rpmi: gambit-4.9.3-alt1 sisyphus+220998.100.1.4 1549742897 installed
<13>Nov 24 03:44:04 rpmi: foomatic-db-engine-4.0.12-alt1 1449527980 installed
<13>Nov 24 03:44:04 rpmi: ghostscript-utils-9.27-alt1 p9+230401.100.1.1 1558957679 installed
<13>Nov 24 03:44:04 rpmi: texlive-2019-alt1_2 p9+238369.100.3.1 1569961493 installed
<13>Nov 24 03:44:15 rpmi: texlive-collection-basic-2018-alt1_5 sisyphus+226263.100.1.1 1554169804 installed
<13>Nov 24 03:44:15 rpmi: texlive-texmf-2018-alt1_5 sisyphus+226263.100.1.1 1554169804 installed
<13>Nov 24 03:45:20 rpmi: texlive-dist-2018-alt1_5 sisyphus+226263.100.1.1 1554169804 installed
<13>Nov 24 03:45:20 rpmi: java-stub-javadoc-0.1-alt1 1229813340 installed
<13>Nov 24 03:45:20 rpmi: java-devel-default-1.7.0-alt1 1454012839 installed
<13>Nov 24 03:45:20 rpmi: libcurl-devel-7.65.0-alt1 p9+229801.100.1.1 1558513332 installed
<13>Nov 24 03:45:20 rpmi: libpango-devel-1.44.6-alt1 p9+237353.700.2.2 1568373865 installed
<13>Nov 24 03:45:20 rpmi: gcc-c++-8-alt1 sisyphus+222164.100.1.1 1550685957 installed
<13>Nov 24 03:45:20 rpmi: gcc-fortran-8-alt1 sisyphus+222164.100.1.1 1550685957 installed
<13>Nov 24 03:45:21 rpmi: tk-devel-8.6.9-alt1 sisyphus+227145.200.1.2 1555606663 installed
<13>Nov 24 03:45:21 rpmi: libXmu-devel-1.1.3-alt1 sisyphus+225206.1200.1.2 1552949629 installed
<13>Nov 24 03:45:21 rpmi: makeinfo-6.5-alt2 sisyphus+220294.200.2.1 1548933637 installed
<13>Nov 24 03:45:21 rpmi: liblapack-devel-1:3.8.0-alt3 sisyphus+221521.100.1.1 1550134909 installed
<13>Nov 24 03:45:21 rpmi: libpcre-devel-8.43-alt1 sisyphus+222771.100.1.1 1551029667 installed
<13>Nov 24 03:45:21 rpmi: libtre-devel-0.8.0-alt2.1 1334590818 installed
<13>Nov 24 03:45:21 rpmi: libtiff-devel-4.0.10.0.57.f9fc01c3-alt1 sisyphus+226958.100.1.1 1554850937 installed
<13>Nov 24 03:45:21 rpmi: texi2dvi-6.5-alt2 sisyphus+220294.200.2.1 1548933637 installed
<13>Nov 24 03:45:21 rpmi: libjpeg-devel-2:2.0.2-alt1 sisyphus+226996.100.1.1 1554902884 installed
<13>Nov 24 03:45:21 rpmi: libreadline-devel-7.0.3-alt3 sisyphus+222164.300.1.1 1550686325 installed
<13>Nov 24 03:45:21 rpmi: liblzma-devel-5.2.4-alt1 sisyphus+221902.5700.4.1 1550600683 installed
<13>Nov 24 03:45:21 rpmi: bzlib-devel-1:1.0.6-alt6 sisyphus+224341.100.1.1 1552254551 installed
Building target platforms: x86_64
Building for target x86_64
Wrote: /usr/src/in/nosrpm/R-base-3.5.3-alt1.nosrc.rpm
Installing R-base-3.5.3-alt1.src.rpm
Building target platforms: x86_64
Building for target x86_64
Executing(%prep): /bin/sh -e /usr/src/tmp/rpm-tmp.11
+ umask 022
+ /bin/mkdir -p /usr/src/RPM/BUILD
+ cd /usr/src/RPM/BUILD
+ cd /usr/src/RPM/BUILD
+ rm -rf R-3.5.3
+ echo 'Source #0 (R-3.5.3.tar):'
Source #0 (R-3.5.3.tar):
+ /bin/tar -xf /usr/src/RPM/SOURCES/R-3.5.3.tar
+ cd R-3.5.3
+ /bin/chmod -c -Rf u+rwX,go-w .
+ echo 'Patch #0 (R-3.5.3-alt1.patch):'
Patch #0 (R-3.5.3-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/9bcb4bdb4dd1185d3f43ac2d1ba0d8a70921a4e0
patching file .gear/tags/a267957eb382565da32225335ac89fb8c75df0da
patching file .gear/tags/a3506a8419eb2903e6d3ce37c465295a254fd1d5
patching file .gear/tags/a8802667f7d1597d2cd5442d00d4d4773505446e
patching file .gear/tags/c7dc0028771e7098f72fe8ac9e9575451d4fb020
patching file .gear/tags/dbe24e8137437d3688e1d77cf1b67279d3099cea
patching file .gear/tags/ebdb5ee7ba9a5499c21aadcfee3318a7d6d52061
patching file .gear/tags/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.77595
+ umask 022
+ /bin/mkdir -p /usr/src/RPM/BUILD
+ cd /usr/src/RPM/BUILD
+ cd R-3.5.3
+ export lt_cv_prog_cc_static_works=no ac_cv_path_R_ZIPCMD=zip ac_cv_path_R_UNZIPCMD=unzip ac_cv_path_R_BROWSER=firefox ac_cv_path_R_PDFVIEWER=evince 'ac_cv_path_PAGER=less -isR' ac_cv_prog_R_PRINTCMD=lpr
+ lt_cv_prog_cc_static_works=no
+ ac_cv_path_R_ZIPCMD=zip
+ ac_cv_path_R_UNZIPCMD=unzip
+ ac_cv_path_R_BROWSER=firefox
+ ac_cv_path_R_PDFVIEWER=evince
+ ac_cv_path_PAGER='less -isR'
+ ac_cv_prog_R_PRINTCMD=lpr
+ CFLAGS='-pipe -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
+ '[' -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 --with-blas=openblas --with-lapack=lapack --with-tcl-config=/usr/lib64/tclConfig.sh --with-tk-config=/usr/lib64/tkConfig.sh '--libdir=${prefix}/lib64' 'rincludedir=${prefix}/include/R' 'rdocdir=${prefix}/share/doc/R-3.5'
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 pkg-config... /usr/bin/pkg-config
checking for x86_64-alt-linux-gcc... x86_64-alt-linux-gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether x86_64-alt-linux-gcc accepts -g... yes
checking for x86_64-alt-linux-gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... x86_64-alt-linux-gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking whether x86_64-alt-linux-gcc needs -traditional... no
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking how to run the C preprocessor... x86_64-alt-linux-gcc -E
checking for f95... f95
checking for x86_64-alt-linux-g77... (cached) f95
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether f95 accepts -g... yes
checking for x86_64-alt-linux-g++... x86_64-alt-linux-g++
checking whether we are using the GNU C++ compiler... yes
checking whether x86_64-alt-linux-g++ accepts -g... yes
checking whether x86_64-alt-linux-g++ -pipe -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 f95 accepts -fvisibility... yes
checking for x86_64-alt-linux-gcc... x86_64-alt-linux-gcc
checking whether we are using the GNU Objective C compiler... no
checking whether x86_64-alt-linux-gcc accepts -g... no
checking for Objective C++ compiler... trying some possibilities
checking whether x86_64-alt-linux-g++ can compile ObjC++... no
no working ObjC++ compiler found
checking how to print strings... printf
checking for a sed that does not truncate output... (cached) /bin/sed
checking for fgrep... /bin/grep -F
checking for ld used by x86_64-alt-linux-gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking the maximum length of command line arguments... 1572864
checking how to convert x86_64-alt-linux-gnu file names to x86_64-alt-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-alt-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for x86_64-alt-linux-objdump... no
checking for objdump... objdump
checking how to recognize dependent libraries... (cached) pass_all
checking for x86_64-alt-linux-dlltool... no
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for x86_64-alt-linux-ar... (cached) ar
checking for archiver @FILE support... @
checking for x86_64-alt-linux-strip... no
checking for strip... strip
checking for x86_64-alt-linux-ranlib... no
checking for ranlib... ranlib
checking for gawk... gawk
checking command to parse /usr/bin/nm -B output from x86_64-alt-linux-gcc object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for x86_64-alt-linux-mt... no
checking for mt... no
checking if : is a manifest tool... no
checking for dlfcn.h... yes
checking for objdir... .libs
checking if x86_64-alt-linux-gcc supports -fno-rtti -fno-exceptions... no
checking for x86_64-alt-linux-gcc option to produce PIC... -fPIC -DPIC
checking if x86_64-alt-linux-gcc PIC flag -fPIC -DPIC works... yes
checking if x86_64-alt-linux-gcc static flag -static works... no
checking if x86_64-alt-linux-gcc supports -c -o file.o... yes
checking if x86_64-alt-linux-gcc supports -c -o file.o... (cached) yes
checking whether the x86_64-alt-linux-gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking how to run the C++ preprocessor... x86_64-alt-linux-g++ -E
checking for ld used by x86_64-alt-linux-g++... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the x86_64-alt-linux-g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for x86_64-alt-linux-g++ option to produce PIC... -fPIC -DPIC
checking if x86_64-alt-linux-g++ PIC flag -fPIC -DPIC works... yes
checking if x86_64-alt-linux-g++ static flag -static works... no
checking if x86_64-alt-linux-g++ supports -c -o file.o... yes
checking if x86_64-alt-linux-g++ supports -c -o file.o... (cached) yes
checking whether the x86_64-alt-linux-g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for f95 option to produce PIC... -fPIC
checking if f95 PIC flag -fPIC works... yes
checking if f95 static flag -static works... no
checking if f95 supports -c -o file.o... yes
checking if f95 supports -c -o file.o... (cached) yes
checking whether the f95 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for cos in -lm... yes
checking for sin in -lm... yes
checking for dlopen in -ldl... yes
checking readline/history.h usability... yes
checking readline/history.h presence... yes
checking for readline/history.h... yes
checking readline/readline.h usability... yes
checking readline/readline.h presence... yes
checking for readline/readline.h... yes
checking for rl_callback_read_char in -lreadline... yes
checking for history_truncate_file... yes
checking whether rl_callback_sigcleanup exists and is declared... 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 dl.h usability... no
checking dl.h presence... no
checking for dl.h... no
checking elf.h usability... yes
checking elf.h presence... yes
checking for elf.h... yes
checking features.h usability... yes
checking features.h presence... yes
checking for features.h... yes
checking floatingpoint.h usability... no
checking floatingpoint.h presence... no
checking for floatingpoint.h... no
checking langinfo.h usability... yes
checking langinfo.h presence... yes
checking for langinfo.h... yes
checking netdb.h usability... yes
checking netdb.h presence... yes
checking for netdb.h... yes
checking netinet/in.h usability... yes
checking netinet/in.h presence... yes
checking for netinet/in.h... yes
checking sys/param.h usability... yes
checking sys/param.h presence... yes
checking for sys/param.h... yes
checking stdalign.h usability... yes
checking stdalign.h presence... yes
checking for stdalign.h... yes
checking errno.h usability... yes
checking errno.h presence... yes
checking for errno.h... yes
checking for inttypes.h... (cached) yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking locale.h usability... yes
checking locale.h presence... yes
checking for locale.h... yes
checking stdarg.h usability... yes
checking stdarg.h presence... yes
checking for stdarg.h... yes
checking stdbool.h usability... yes
checking stdbool.h presence... yes
checking for stdbool.h... yes
checking for stdint.h... (cached) yes
checking for string.h... (cached) yes
checking whether setjmp.h is POSIX.1 compatible... yes
checking whether sigsetjmp is declared... yes
checking whether siglongjmp is declared... yes
checking for GNU C library with version >= 2... yes
checking return type of signal handlers... void
checking for uint64_t... yes
checking for int64_t... yes
checking for int_fast64_t... yes
checking for pid_t... yes
checking for size_t... yes
checking whether SIZE_MAX is declared... yes
checking for blkcnt_t... yes
checking for type of socket length... socklen_t *
checking for stack_t... yes
checking for intptr_t... yes
checking for uintptr_t... yes
checking whether byte ordering is bigendian... no
checking for an ANSI C-conforming const... yes
checking for x86_64-alt-linux-gcc option to accept ISO C99... none needed
checking for x86_64-alt-linux-gcc option to accept ISO Standard C... (cached) none needed
checking for inline... inline
checking size of int... 4
checking size of long... 8
checking size of long long... 8
checking size of double... 8
checking size of size_t... 8
checking size of long double... 16
checking whether we can compute C Make dependencies... yes, using $(CC) -MM
checking whether x86_64-alt-linux-gcc supports -c -o FILE.lo... yes
checking for x86_64-alt-linux-gcc option to support OpenMP... unsupported
checking how to get verbose linking output from f95... -v
checking for Fortran 77 libraries of f95... -L/usr/local/lib64 -L/usr/lib64/gcc/x86_64-alt-linux/8 -L/usr/lib64/gcc/x86_64-alt-linux/8/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib64/gcc/x86_64-alt-linux/8/../../.. -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/8 -L/usr/lib64/gcc/x86_64-alt-linux/8/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib64/gcc/x86_64-alt-linux/8/../../.. -lgcc_s
checking for dummy main to link with Fortran 77 libraries... none
checking for Fortran 77 name-mangling scheme... lower case, underscore, no extra underscore
checking whether f95 appends underscores to external names... yes
checking whether f95 appends extra underscores to external names... no
checking whether mixed C/Fortran code can be run... yes
checking whether f95 and x86_64-alt-linux-gcc agree on int and double... yes
checking whether f95 and x86_64-alt-linux-gcc agree on double complex... yes
checking for f95 option to support OpenMP... unsupported
checking whether x86_64-alt-linux-g++ accepts -M for generating dependencies... yes
checking for x86_64-alt-linux-g++ option to support OpenMP... unsupported
checking whether we can compute ObjC Make dependencies... no
checking for ObjC runtime library...
checking whether x86_64-alt-linux-gcc accepts -fobjc-exceptions... no
checking whether C runtime needs -D__NO_MATH_INLINES... no
checking for xmkmf... no
checking whether x86_64-alt-linux-g++ supports C++98 features with -std=gnu++98... yes
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 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 for pcre_fullinfo in -lpcre... yes
checking pcre.h usability... no
checking pcre.h presence... no
checking for pcre.h... no
checking pcre/pcre.h usability... yes
checking pcre/pcre.h presence... yes
checking for pcre/pcre.h... yes
checking if PCRE version >= 8.20, < 10.0 and has UTF-8 support... yes
checking if PCRE version >= 8.32... yes
checking whether PCRE support suffices... yes
checking for pcre2-config... no
checking for tre_regncompb in -ltre... no
checking for curl-config... /usr/bin/curl-config
checking libcurl version ... 7.65.0-DEV
checking curl/curl.h usability... yes
checking curl/curl.h presence... yes
checking for curl/curl.h... yes
checking if libcurl is version 7 and >= 7.22.0... yes
checking if libcurl supports https... yes
checking if jpeglib version >= 6b... yes
checking for jpeg_destroy_compress in -ljpeg... yes
checking if libpng version >= 1.2.7... yes
checking for png_create_write_struct in -lpng... yes
checking tiffio.h usability... yes
checking tiffio.h presence... yes
checking for tiffio.h... yes
checking for TIFFOpen in -ltiff... yes
checking whether leap seconds are treated according to POSIX... yes
checking for inline... inline
checking for sys/time.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... (cached) yes
checking for struct stat.st_atim.tv_nsec... yes
checking whether struct stat.st_atim is of type struct timespec... yes
checking for setitimer... yes
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for _LARGEFILE_SOURCE value needed for large files... no
checking whether KERN_USRSTACK sysctl is supported... no
checking for visible __lib_stack_end... yes
checking for lpr... (cached) lpr
checking for paperconf... /usr/bin/paperconf
checking for x86_64-alt-linux-gfortran... x86_64-alt-linux-gfortran
checking whether we are using the GNU Fortran compiler... yes
checking whether x86_64-alt-linux-gfortran accepts -g... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for x86_64-alt-linux-gfortran option to produce PIC... -fPIC
checking if x86_64-alt-linux-gfortran PIC flag -fPIC works... yes
checking if x86_64-alt-linux-gfortran static flag -static works... no
checking if x86_64-alt-linux-gfortran supports -c -o file.o... yes
checking if x86_64-alt-linux-gfortran supports -c -o file.o... (cached) yes
checking whether the x86_64-alt-linux-gfortran linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for Fortran flag to compile .f90 files... none
checking for Fortran flag to compile .f95 files... none
checking for x86_64-alt-linux-gfortran option to support OpenMP... unsupported
checking for recommended packages... yes
checking whether NLS is requested... yes
Configuring src/extra/intl directory
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking whether we are using the GNU C Library 2 or newer... yes
checking for x86_64-alt-linux-ranlib... ranlib
checking for simple visibility declarations... yes
checking for stdint.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking whether integer division by zero raises SIGFPE... yes
checking for inttypes.h... yes
checking for unsigned long long int... yes
checking for inttypes.h... (cached) yes
checking whether the inttypes.h PRIxNN macros are broken... no
checking for ld used by x86_64-alt-linux-gcc... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking for shared library run path origin... done
checking whether imported symbols can be declared weak... yes
checking for multithread API to use... none
checking argz.h usability... yes
checking argz.h presence... yes
checking for argz.h... yes
checking for inttypes.h... (cached) yes
checking for limits.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... (cached) yes
checking for getcwd... yes
checking for getegid... yes
checking for geteuid... yes
checking for getgid... yes
checking for getuid... yes
checking for mempcpy... (cached) yes
checking for munmap... yes
checking for stpcpy... yes
checking for strcasecmp... yes
checking for strdup... (cached) yes
checking for strtoul... yes
checking for tsearch... yes
checking for argz_count... yes
checking for argz_stringify... yes
checking for argz_next... yes
checking for __fsetlocking... yes
checking whether feof_unlocked is declared... yes
checking whether fgets_unlocked is declared... yes
checking for iconv... (cached) yes
checking for iconv declaration... (cached)
extern size_t iconv (iconv_t cd, char * *inbuf, size_t *inbytesleft, char * *outbuf, size_t *outbytesleft);
checking for NL_LOCALE_NAME macro... yes
checking for bison... bison
checking version of bison... 3.0.5, 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
config.status: creating Makeconf
config.status: creating Makefile
config.status: creating doc/Makefile
config.status: creating doc/html/Makefile
config.status: creating doc/manual/Makefile
config.status: creating etc/Makefile
config.status: creating etc/Makeconf
config.status: creating etc/Renviron
config.status: creating etc/javaconf
config.status: creating etc/ldpaths
config.status: creating m4/Makefile
config.status: creating po/Makefile
config.status: creating share/Makefile
config.status: creating src/Makefile
config.status: creating src/appl/Makefile
config.status: creating src/extra/Makefile
config.status: creating src/extra/blas/Makefile
config.status: creating src/extra/intl/Makefile
config.status: creating src/extra/tre/Makefile
config.status: creating src/extra/tzone/Makefile
config.status: creating src/extra/xdr/Makefile
config.status: creating src/include/Makefile
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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 77 compiler: f95 -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing
Default C++ compiler: x86_64-alt-linux-g++ -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing
C++98 compiler: x86_64-alt-linux-g++ -std=gnu++98 -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing
C++11 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
Fortran 90/95 compiler: x86_64-alt-linux-gfortran -g -O2
Obj-C compiler: x86_64-alt-linux-gcc
Interfaces supported: X11, tcltk
External libraries: readline, BLAS(OpenBLAS), LAPACK(generic), curl
Additional capabilities: PNG, JPEG, TIFF, NLS, cairo, ICU
Options enabled: shared R library, R profiling, static HTML
Capabilities skipped:
Options not enabled: shared BLAS, memory profiling
Recommended packages: yes
configure: WARNING: neither inconsolata.sty nor zi4.sty found: PDF vignettes and package manuals will not be rendered optimally
+ 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-3.5.3/src/scripts'
creating src/scripts/R.fe
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/scripts'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/scripts'
mkdir -p -- ../../bin
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/scripts'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/include'
mkdir -p -- ../../include
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/include'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/include/R_ext'
mkdir -p -- ../../../include/R_ext
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/include/R_ext'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre'
making regcomp.d from regcomp.c
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre'
making regerror.d from regerror.c
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre'
making regexec.d from regexec.c
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre'
making tre-match-approx.d from tre-match-approx.c
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre'
making tre-compile.d from tre-compile.c
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre'
making tre-ast.d from tre-ast.c
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre'
making tre-match-backtrack.d from tre-match-backtrack.c
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre'
making tre-match-parallel.d from tre-match-parallel.c
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre'
making tre-mem.d from tre-mem.c
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre'
making tre-parse.d from tre-parse.c
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre'
making tre-stack.d from tre-stack.c
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre'
making xmalloc.d from xmalloc.c
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre'
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -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-3.5.3/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre'
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -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-3.5.3/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre'
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -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-3.5.3/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre'
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -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-3.5.3/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre'
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -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-3.5.3/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre'
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -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-3.5.3/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre'
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -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-3.5.3/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre'
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -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-3.5.3/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre'
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -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-3.5.3/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre'
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -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-3.5.3/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre'
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -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-3.5.3/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre'
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -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-3.5.3/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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-3.5.3/src/extra/tre'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl'
making integrate.d from integrate.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl'
making interv.d from interv.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl'
making maxcol.d from maxcol.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl'
making pretty.d from pretty.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl'
making uncmin.d from uncmin.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl'
making optim.d from optim.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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-3.5.3/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl'
f95 -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-3.5.3/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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-3.5.3/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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-3.5.3/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl'
f95 -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-3.5.3/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl'
f95 -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-3.5.3/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl'
f95 -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-3.5.3/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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-3.5.3/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl'
f95 -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-3.5.3/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl'
f95 -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-3.5.3/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl'
f95 -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-3.5.3/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl'
f95 -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-3.5.3/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl'
f95 -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-3.5.3/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl'
f95 -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-3.5.3/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl'
f95 -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-3.5.3/src/appl'
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f95 -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-3.5.3/src/appl'
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f95 -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-3.5.3/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl'
f95 -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-3.5.3/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl'
f95 -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-3.5.3/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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-3.5.3/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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-3.5.3/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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-3.5.3/src/appl'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
making mlutils.d from mlutils.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
making d1mach.d from d1mach.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making fmax2.d from fmax2.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making fprec.d from fprec.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
making i1mach.d from i1mach.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making ftrunc.d from ftrunc.c
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make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
making sign.d from sign.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
making fsign.d from fsign.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
making fmin2.d from fmin2.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
making fround.d from fround.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
making imax2.d from imax2.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
making imin2.d from imin2.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making chebyshev.d from chebyshev.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making log1p.d from log1p.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
making lgammacor.d from lgammacor.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
making stirlerr.d from stirlerr.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
making gamma_cody.d from gamma_cody.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
making lbeta.d from lbeta.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making gammalims.d from gammalims.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making lgamma.d from lgamma.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
making gamma.d from gamma.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
making beta.d from beta.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
making bd0.d from bd0.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
making polygamma.d from polygamma.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
making bessel_i.d from bessel_i.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
making cospi.d from cospi.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
making bessel_j.d from bessel_j.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making bessel_k.d from bessel_k.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
making choose.d from choose.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making snorm.d from snorm.c
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making sexp.d from sexp.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making bessel_y.d from bessel_y.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
making pgamma.d from pgamma.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
making dgamma.d from dgamma.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
making rbeta.d from rbeta.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
making qbeta.d from qbeta.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
making dunif.d from dunif.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
making dbeta.d from dbeta.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
making punif.d from punif.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
making rgamma.d from rgamma.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
making pbeta.d from pbeta.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
making qunif.d from qunif.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making rnorm.d from rnorm.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
making qgamma.d from qgamma.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
making runif.d from runif.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making dlnorm.d from dlnorm.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making plnorm.d from plnorm.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
making df.d from df.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
making dnorm.d from dnorm.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making rlnorm.d from rlnorm.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making pnorm.d from pnorm.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making qnorm.d from qnorm.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making dnf.d from dnf.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making dt.d from dt.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making rt.d from rt.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
making qt.d from qt.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making qlnorm.d from qlnorm.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making dnt.d from dnt.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making pf.d from pf.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
making qf.d from qf.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making rchisq.d from rchisq.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making qchisq.d from qchisq.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making pchisq.d from pchisq.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making rf.d from rf.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making pt.d from pt.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making rbinom.d from rbinom.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
making dchisq.d from dchisq.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
making rmultinom.d from rmultinom.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making pbinom.d from pbinom.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
making dbinom.d from dbinom.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making qbinom.d from qbinom.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making rnchisq.d from rnchisq.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making pcauchy.d from pcauchy.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making dcauchy.d from dcauchy.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making pexp.d from pexp.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making qcauchy.d from qcauchy.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making qexp.d from qexp.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making rcauchy.d from rcauchy.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making dgeom.d from dgeom.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making rexp.d from rexp.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making dexp.d from dexp.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making pgeom.d from pgeom.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making qgeom.d from qgeom.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making qhyper.d from qhyper.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making qnbinom.d from qnbinom.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making pnbinom.d from pnbinom.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making dhyper.d from dhyper.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making dpois.d from dpois.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making rgeom.d from rgeom.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making phyper.d from phyper.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making dnbinom.d from dnbinom.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making rnbinom.d from rnbinom.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making rhyper.d from rhyper.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making qpois.d from qpois.c
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making rpois.d from rpois.c
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making ppois.d from ppois.c
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making qweibull.d from qweibull.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making rlogis.d from rlogis.c
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making dweibull.d from dweibull.c
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making pweibull.d from pweibull.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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making rweibull.d from rweibull.c
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making plogis.d from plogis.c
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making qlogis.d from qlogis.c
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making dlogis.d from dlogis.c
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making dnchisq.d from dnchisq.c
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making pnchisq.d from pnchisq.c
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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 fround.c -o fround.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c d1mach.c -o d1mach.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qnchisq.c -o qnchisq.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 rpois.c -o rpois.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 qnbeta.c -o qnbeta.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 dnchisq.c -o dnchisq.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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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 pnf.c -o pnf.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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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 dnbeta.c -o dnbeta.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 pnchisq.c -o pnchisq.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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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 qtukey.c -o qtukey.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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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 ptukey.c -o ptukey.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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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 pnt.c -o pnt.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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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 qnf.c -o qnf.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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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 pnbeta.c -o pnbeta.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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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
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
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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 signrank.c -o signrank.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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-3.5.3/src/nmath'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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-3.5.3/src/nmath'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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-3.5.3/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/unix'
config.status: creating src/unix/Makefile
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making dynload.d from dynload.c
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making X11.d from X11.c
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making Rembedded.d from Rembedded.c
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making sys-std.d from sys-std.c
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making sys-unix.d from sys-unix.c
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making system.d from system.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/unix'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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-3.5.3/src/unix'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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-3.5.3/src/unix'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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-3.5.3/src/unix'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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-3.5.3/src/unix'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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-3.5.3/src/unix'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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-3.5.3/src/unix'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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-3.5.3/src/unix'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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-3.5.3"' \
-o Rscript ./Rscript.c
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config.status: creating src/main/Makefile
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making altrep.d from altrep.c
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making Renviron.d from Renviron.c
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making RNG.d from RNG.c
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making arithmetic.d from arithmetic.c
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making apply.d from apply.c
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making agrep.d from agrep.c
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making CommandLineArgs.d from CommandLineArgs.c
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making attrib.d from attrib.c
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making coerce.d from coerce.c
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making bind.d from bind.c
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making colors.d from colors.c
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making Rdynload.d from Rdynload.c
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making cum.d from cum.c
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making array.d from array.c
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making builtin.d from builtin.c
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making complex.d from complex.c
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making character.d from character.c
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making context.d from context.c
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making datetime.d from datetime.c
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making debug.d from debug.c
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making devices.d from devices.c
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making dstruct.d from dstruct.c
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making connections.d from connections.c
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making dounzip.d from dounzip.c
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making duplicate.d from duplicate.c
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making dcf.d from dcf.c
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making edit.d from edit.c
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making engine.d from engine.c
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making format.d from format.c
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making eval.d from eval.c
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making errors.d from errors.c
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making gram.d from gram.c
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making inlined.d from inlined.c
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making inspect.d from inspect.c
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making dotcode.d from dotcode.c
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making iosupport.d from iosupport.c
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making identical.d from identical.c
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making graphics.d from graphics.c
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making logic.d from logic.c
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making grep.d from grep.c
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making internet.d from internet.c
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make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
making mapply.d from mapply.c
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make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
making names.d from names.c
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make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
making platform.d from platform.c
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make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
making plotmath.d from plotmath.c
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making objects.d from objects.c
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make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
making match.d from match.c
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make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
making print.d from print.c
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make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
making options.d from options.c
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make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
making printarray.d from printarray.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
making printutils.d from printutils.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
making printvector.d from printvector.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
making memory.d from memory.c
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make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
making paste.d from paste.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
making plot.d from plot.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
making plot3d.d from plot3d.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
making radixsort.d from radixsort.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
making random.d from random.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
making qsort.d from qsort.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
making registration.d from registration.c
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make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
making relop.d from relop.c
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make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
making rlocale.d from rlocale.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
making raw.d from raw.c
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make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
making scan.d from scan.c
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making source.d from source.c
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make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
making saveload.d from saveload.c
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making seq.d from seq.c
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make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
making sort.d from sort.c
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make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
making sprintf.d from sprintf.c
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making split.d from split.c
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making startup.d from startup.c
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make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
making subscript.d from subscript.c
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make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
making serialize.d from serialize.c
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making summary.d from summary.c
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making subassign.d from subassign.c
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making subset.d from subset.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 g_fontdb.d from g_fontdb.c
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make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
making alloca.d from alloca.c
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making version.d from version.c
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making util.d from util.c
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making strncasecmp.d from strncasecmp.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
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making Rmain.d from Rmain.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
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making strdup.d from strdup.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
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making g_alab_her.d from g_alab_her.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
making g_cntrlify.d from g_cntrlify.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
making g_her_glyph.d from g_her_glyph.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
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making mkdtemp.d from mkdtemp.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c CommandLineArgs.c -o CommandLineArgs.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c Renviron.c -o Renviron.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c Rdynload.c -o Rdynload.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c agrep.c -o agrep.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c RNG.c -o RNG.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
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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
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c apply.c -o apply.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c colors.c -o colors.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
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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
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
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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
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
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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
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
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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
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
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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
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c character.c -o character.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
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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
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
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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
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
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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
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dcf.c -o dcf.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c context.c -o context.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dstruct.c -o dstruct.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c duplicate.c -o duplicate.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dounzip.c -o dounzip.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c edit.c -o edit.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c datetime.c -o datetime.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c devices.c -o devices.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c deparse.c -o deparse.o
deparse.c: In function 'deparse2buff':
deparse.c:1443:8: warning: 'doquote' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(doquote)
^
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main'
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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 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 times.c -o times.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 sort.c -o sort.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 g_alab_her.c -o g_alab_her.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 g_cntrlify.c -o g_cntrlify.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 version.c -o version.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 g_fontdb.c -o g_fontdb.o
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f95 -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 g_her_glyph.c -o g_her_glyph.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 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 summary.c -o summary.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 -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 sysutils.c -o sysutils.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 -shared -pthread -L/usr/local/lib64 -o libR.so CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.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 -lpcre -llzma -lbz2 -lz -lrt -ldl -lm -licuuc -licui18n
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mkdir -p -- /usr/src/RPM/BUILD/R-3.5.3/bin/exec
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mkdir -p -- /usr/src/RPM/BUILD/R-3.5.3/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 Lapack.d from Lapack.c
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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 nanoftp.d from nanoftp.c
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making sock.d from sock.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 internet.d from internet.c
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making sockconn.d from sockconn.c
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making libcurl.d from libcurl.c
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making nanohttp.d from nanohttp.c
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making devX11.d from devX11.c
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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 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 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 internet.c -o internet.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/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/pcre -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 -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 -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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mkdir -p -- /usr/src/RPM/BUILD/R-3.5.3/modules
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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/pcre -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 internet.so Rhttpd.o Rsock.o internet.o libcurl.o nanoftp.o nanohttp.o sock.o sockconn.o -lcurl -lR
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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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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/pcre -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/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/pcre -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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mkdir -p -- ../../library
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building system startup profile
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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 init.d from init.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 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/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 stubs.c -o stubs.o
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c devCairo.c -o devCairo.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 devPicTeX.c -o devPicTeX.o
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -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 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 devQuartz.c -o devQuartz.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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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 chull.c -o chull.o
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x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o grDevices.so axis_scales.o chull.o devices.o init.o stubs.o colors.o devCairo.o devPicTeX.o devPS.o devQuartz.o -lz -L../../../../lib -lR
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src'
make[6]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src'
mkdir -p -- ../../../../library/grDevices/libs
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make[7]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src/cairo'
making cairoBM.d from cairoBM.c
make[7]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src/cairo'
make[9]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src/cairo'
x86_64-alt-linux-gcc -I. -I../../../../../src/include -I../../../../../src/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/pcre -I/usr/include/libpng16 -I../../../../../src/modules/X11 -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c cairoBM.c -o cairoBM.o
make[9]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src/cairo'
make[9]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src/cairo'
x86_64-alt-linux-gcc -shared -L"../../../../../lib" -L/usr/local/lib64 -o cairo.so cairoBM.o ../../../../../src/modules/X11/rbitmap.o -ltiff -ljpeg -lpng16 -lz -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lharfbuzz -lpng16 -lz -lcairo -L"../../../../../lib" -lR -lm
make[9]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src/cairo'
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byte-compiling package 'grDevices'
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make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/graphics'
building package 'graphics'
mkdir -p -- ../../../library/graphics
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make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/graphics'
mkdir -p -- ../../../library/graphics/R
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/graphics'
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making init.d from init.c
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making plot.d from plot.c
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making base.d from base.c
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making par.d from par.c
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making plot3d.d from plot3d.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/graphics/src'
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making graphics.d from graphics.c
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making stem.d from stem.c
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make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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-3.5.3/src/library/graphics/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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-3.5.3/src/library/graphics/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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-3.5.3/src/library/graphics/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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-3.5.3/src/library/graphics/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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-3.5.3/src/library/graphics/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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-3.5.3/src/library/graphics/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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-3.5.3/src/library/graphics/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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-3.5.3/src/library/graphics/src'
make[6]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/graphics/src'
mkdir -p -- ../../../../library/graphics/libs
make[6]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/graphics/src'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/graphics'
byte-compiling package 'graphics'
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/graphics'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats'
building package 'stats'
mkdir -p -- ../../../library/stats
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mkdir -p -- ../../../library/stats/R
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making kmeans.d from kmeans.c
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making init.d from init.c
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make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src'
making chisqsim.d from chisqsim.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src'
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making ansari.d from ansari.c
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making bandwidths.d from bandwidths.c
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making kendall.d from kendall.c
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making d2x2xk.d from d2x2xk.c
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making fexact.d from fexact.c
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making prho.d from prho.c
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making ks.d from ks.c
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making line.d from line.c
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making swilk.d from swilk.c
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making ksmooth.d from ksmooth.c
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making loessc.d from loessc.c
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making smooth.d from smooth.c
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making monoSpl.d from monoSpl.c
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making isoreg.d from isoreg.c
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making Srunmed.d from Srunmed.c
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making dblcen.d from dblcen.c
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making HoltWinters.d from HoltWinters.c
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making arima.d from arima.c
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making hclust-utils.d from hclust-utils.c
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making filter.d from filter.c
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making burg.d from burg.c
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making mAR.d from mAR.c
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making nls.d from nls.c
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making distance.d from distance.c
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making PPsum.d from PPsum.c
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making pacf.d from pacf.c
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making rWishart.d from rWishart.c
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making starma.d from starma.c
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making sbart.d from sbart.c
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making port.d from port.c
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making loglin.d from loglin.c
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making family.d from family.c
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making approx.d from approx.c
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making lowess.d from lowess.c
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making fft.d from fft.c
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making massdist.d from massdist.c
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making lm.d from lm.c
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making splines.d from splines.c
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making complete_cases.d from complete_cases.c
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making cov.d from cov.c
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making deriv.d from deriv.c
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making fourier.d from fourier.c
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making integrate.d from integrate.c
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making rcont.d from rcont.c
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making zeroin.d from zeroin.c
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making optim.d from optim.c
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making model.d from model.c
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making influence.d from influence.c
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making optimize.d from optimize.c
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making distn.d from distn.c
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making random.d from random.c
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -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-3.5.3/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 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 -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c d2x2xk.c -o d2x2xk.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 rcont.c -o rcont.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 fft.c -o fft.o
fft.c: In function 'fft_work':
fft.c:148:9: warning: array subscript -1 is below array bounds of 'int[20]' [-Warray-bounds]
nfac--;/*the global one!*/
~~~~^~
fft.c:148:9: warning: array subscript -1 is below array bounds of 'int[20]' [-Warray-bounds]
fft.c:148:9: warning: array subscript -1 is below array bounds of 'int[20]' [-Warray-bounds]
fft.c:148:9: warning: array subscript -1 is below array bounds of 'int[20]' [-Warray-bounds]
fft.c:148:9: warning: array subscript -1 is below array bounds of 'int[20]' [-Warray-bounds]
fft.c:148:9: warning: array subscript -1 is below array bounds of 'int[20]' [-Warray-bounds]
fft.c:148:9: warning: array subscript -1 is below array bounds of 'int[20]' [-Warray-bounds]
fft.c:148:9: warning: array subscript -1 is below array bounds of 'int[20]' [-Warray-bounds]
fft.c:148:9: warning: array subscript -1 is below array bounds of 'int[20]' [-Warray-bounds]
fft.c:148:9: warning: array subscript -1 is below array bounds of 'int[20]' [-Warray-bounds]
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f95 -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c bsplvd.f -o bsplvd.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src'
f95 -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c bvalus.f -o bvalus.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src'
f95 -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c bvalue.f -o bvalue.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src'
f95 -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qsbart.f -o qsbart.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 model.c -o model.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src'
f95 -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c sinerp.f -o sinerp.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src'
f95 -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c sgram.f -o sgram.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src'
f95 -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c stxwx.f -o stxwx.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src'
f95 -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c sslvrg.f -o sslvrg.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src'
f95 -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c hclust.f -o hclust.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src'
f95 -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c eureka.f -o eureka.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src'
f95 -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c kmns.f -o kmns.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 deriv.c -o deriv.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src'
f95 -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c lminfl.f -o lminfl.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 random.c -o random.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 cov.c -o cov.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src'
f95 -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c stl.f -o stl.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 optimize.c -o optimize.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src'
f95 -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c loessf.f -o loessf.o
loessf.f:59:14:
j=DBLE(j)/2.D0
1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
loessf.f:1893:14:
m=DBLE(l+u)/2.D0
1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
loessf.f:1398:20:
i=phi(pi(ii))
1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
loessf.f:927:12:
lg=DBLE(lg)/2.D0
1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
loessf.f:522:22:
if(deg.eq.2) dk=dble((d+2)*(d+1))/2.d0
1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
loessf.f:1204:13:
ifloor=x
1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
loessf.f:834:22:
if(deg.eq.2) dk=dble((d+2)*(d+1))/2.d0
1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
loessf.f:1582:18:
i1=dble((d+2)*(d+1))/2.d0
1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
loessf.f:472:25:
subroutine ehg133(n,d,vc,nvmax,nc,ncmax,a,c,hi,lo,v,vval,xi,m,z,s)
1
Warning: Unused dummy argument 'n' at (1) [-Wunused-dummy-argument]
loessf.f:472:39:
subroutine ehg133(n,d,vc,nvmax,nc,ncmax,a,c,hi,lo,v,vval,xi,m,z,s)
1
Warning: Unused dummy argument 'nc' at (1) [-Wunused-dummy-argument]
loessf.f:827:31:
subroutine ehg197(deg,tau,d,f,dk,trl)
1
Warning: Unused dummy argument 'tau' at (1) [-Wunused-dummy-argument]
loessf.f:1984:31:
subroutine ehg137(z,kappa,leaf,nleaf,d,nv,nvmax,ncmax,a,xi,lo,hi)
1
Warning: Unused dummy argument 'kappa' at (1) [-Wunused-dummy-argument]
loessf.f:1984:47:
subroutine ehg137(z,kappa,leaf,nleaf,d,nv,nvmax,ncmax,a,xi,lo,hi)
1
Warning: Unused dummy argument 'nv' at (1) [-Wunused-dummy-argument]
loessf.f:1984:53:
subroutine ehg137(z,kappa,leaf,nleaf,d,nv,nvmax,ncmax,a,xi,lo,hi)
1
Warning: Unused dummy argument 'nvmax' at (1) [-Wunused-dummy-argument]
loessf.f:1497:50:
subroutine lowesb(xx,yy,ww,diagl,infl,iv,liv,lv,wv)
1
Warning: Unused dummy argument 'liv' at (1) [-Wunused-dummy-argument]
loessf.f:1497:53:
subroutine lowesb(xx,yy,ww,diagl,infl,iv,liv,lv,wv)
1
Warning: Unused dummy argument 'lv' at (1) [-Wunused-dummy-argument]
loessf.f:1648:30:
subroutine lowese(iv,liv,lv,wv,m,z,s)
1
Warning: Unused dummy argument 'liv' at (1) [-Wunused-dummy-argument]
loessf.f:1648:33:
subroutine lowese(iv,liv,lv,wv,m,z,s)
1
Warning: Unused dummy argument 'lv' at (1) [-Wunused-dummy-argument]
loessf.f:1667:39:
subroutine lowesf(xx,yy,ww,iv,liv,lv,wv,m,z,l,ihat,s)
1
Warning: Unused dummy argument 'liv' at (1) [-Wunused-dummy-argument]
loessf.f:1667:42:
subroutine lowesf(xx,yy,ww,iv,liv,lv,wv,m,z,l,ihat,s)
1
Warning: Unused dummy argument 'lv' at (1) [-Wunused-dummy-argument]
loessf.f:1699:30:
subroutine lowesl(iv,liv,lv,wv,m,z,l)
1
Warning: Unused dummy argument 'liv' at (1) [-Wunused-dummy-argument]
loessf.f:1699:33:
subroutine lowesl(iv,liv,lv,wv,m,z,l)
1
Warning: Unused dummy argument 'lv' at (1) [-Wunused-dummy-argument]
loessf.f:1721:33:
subroutine lowesr(yy,iv,liv,lv,wv)
1
Warning: Unused dummy argument 'liv' at (1) [-Wunused-dummy-argument]
loessf.f:1721:36:
subroutine lowesr(yy,iv,liv,lv,wv)
1
Warning: Unused dummy argument 'lv' at (1) [-Wunused-dummy-argument]
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src'
f95 -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ppr.f -o ppr.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src'
f95 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -msse2 -mfpmath=sse -c portsrc.f -o portsrc.o
portsrc.f:6446:0:
NCOMP = NCOMP + 1
Warning: 'ncomp' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:6357:0:
INTEGER DEG,HEAD,IC,IP,IPL,IPU,IR,JCOL,JP,JPL,JPU,L,MAXINC,
Warning: 'jcol' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:5340:0:
IF (ALPHAK .LE. ZERO .OR. ALPHAK .LT. LK .OR. ALPHAK .GE. UK)
Warning: 'alphak' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:5477:0:
IF (ALPHAK .GE. TWOPSI*PSIFAC) GO TO 310
Warning: 'psifac' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:10115:0:
V(PREDUC) = HALF * (DABS(ALPHAK)*DST*DST + GTSTA)
Warning: 'gtsta' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:10032:0:
IF (-V(DST0) .GE. ALPHAK .OR. ALPHAK .LT. LK .OR. ALPHAK .GE. UK)
Warning: 'alphak' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:10027:0:
LK = DMAX1(LK, PHI*W(PHIPIN))
Warning: 'phi' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:10169:0:
IF (KA .GE. KAMIN) GO TO 340
Warning: 'kamin' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:11936:0:
V(NREDUC) = NRED
Warning: 'nred' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:11939:0:
V(DST0) = DNWTST
Warning: 'dnwtst' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:2392:0:
V(NREDUC) = NRED
Warning: 'nred' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:2391:0:
60 V(DST0) = DS0
Warning: 'ds0' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:7913:0:
V(NREDUC) = NRED
Warning: 'nred' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:7912:0:
90 V(DST0) = DS0
Warning: 'ds0' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:8391:0:
210 IV(FDH) = HES
Warning: 'hes' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:3464:0:
IF (LIV .LT. MIV2) GO TO 300
Warning: 'miv2' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:11772:0:
270 CALL DITSUM(D, V(G1), IV, LIV, LV, P, V, X)
Warning: 'g1' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:440:0:
300 CALL DITSUM(D, V(G1), IV, LIV, LV, P, V, X)
Warning: 'g1' may be used uninitialized in this function [-Wmaybe-uninitialized]
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src'
x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o stats.so init.o kmeans.o ansari.o bandwidths.o chisqsim.o d2x2xk.o fexact.o kendall.o ks.o line.o smooth.o prho.o swilk.o ksmooth.o loessc.o monoSpl.o isoreg.o Srunmed.o dblcen.o distance.o hclust-utils.o nls.o rWishart.o HoltWinters.o PPsum.o arima.o burg.o filter.o mAR.o pacf.o starma.o port.o family.o sbart.o approx.o loglin.o lowess.o massdist.o splines.o lm.o complete_cases.o cov.o deriv.o fft.o fourier.o model.o optim.o optimize.o integrate.o random.o distn.o zeroin.o rcont.o influence.o bsplvd.o bvalue.o bvalus.o loessf.o ppr.o qsbart.o sgram.o sinerp.o sslvrg.o stxwx.o hclust.o kmns.o eureka.o stl.o portsrc.o lminfl.o -llapack -lopenblas -lgfortran -lm -lquadmath -L../../../../lib -lR
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src'
make[6]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src'
mkdir -p -- ../../../../library/stats/libs
make[6]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats'
byte-compiling package 'stats'
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/datasets'
building package 'datasets'
mkdir -p -- ../../../library/datasets
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/datasets'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/datasets'
mkdir -p -- ../../../library/datasets/data
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/datasets'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods'
building package 'methods'
mkdir -p -- ../../../library/methods
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods'
mkdir -p -- ../../../library/methods/R
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src'
making do_substitute_direct.d from do_substitute_direct.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src'
making init.d from init.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src'
making utils.d from utils.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src'
making tests.d from tests.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src'
making slot.d from slot.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src'
making class_support.d from class_support.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src'
making methods_list_dispatch.d from methods_list_dispatch.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/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-3.5.3/src/library/methods/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/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 tests.c -o tests.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/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 utils.c -o utils.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/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 class_support.c -o class_support.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/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 slot.c -o slot.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/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 do_substitute_direct.c -o do_substitute_direct.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/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 methods_list_dispatch.c -o methods_list_dispatch.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src'
x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o methods.so do_substitute_direct.o init.o methods_list_dispatch.o slot.o class_support.o tests.o utils.o -L../../../../lib -lR
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initializing class and method definitions ... done
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building package 'grid'
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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 register.c -o register.o
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c just.c -o just.o
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c util.c -o util.o
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c matrix.c -o matrix.o
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c state.c -o state.o
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c layout.c -o layout.o
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c gpar.c -o gpar.o
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c unit.c -o unit.o
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c viewport.c -o viewport.o
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c grid.c -o grid.o
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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/include -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c tcltk.c -o tcltk.o
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x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o tcltk.so init.o tcltk.o tcltk_unix.o -L/usr/lib64 -ltcl8.6 -lpthread -L/usr/lib64 -ltk8.6 -lX11 -lm -L../../../../lib -lR
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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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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 rngstream.c -o rngstream.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 fork.c -o fork.o
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x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o parallel.so init.o rngstream.o fork.o -L../../../../lib -lR
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you should 'make docs' now ...
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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 -shared -L/usr/src/RPM/BUILD/R-3.5.3/lib -L/usr/local/lib64 -o conftest.so conftest.o -L/usr/lib/jvm/java/jre/lib/amd64/server -ljvm -L/usr/src/RPM/BUILD/R-3.5.3/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-3.5.3
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utils
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vcov html
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weights html
wilcox.test html
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xtabs html
zC html
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EuStockMarkets html
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HairEyeColor html
Harman23.cor html
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Indometh html
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airquality html
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faithful html
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infert html
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trees html
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women html
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converting help for package 'grid'
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converting help for package 'splines'
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converting help for package 'stats4'
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converting help for package 'compiler'
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converting help for package 'parallel'
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make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library'
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begin installing recommended package nnet
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begin installing recommended package spatial
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begin installing recommended package KernSmooth
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begin installing recommended package rpart
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* installing *source* package 'codetools' ...
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** R
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converting help for package 'codetools'
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** building package indices
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Making 'packages.html' ... done
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* installing *source* package 'spatial' ...
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** libs
make[3]: Entering directory '/usr/src/tmp/RtmpGcHEVh/R.INSTALL1ffc563a6bab4/spatial/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpGcHEVh/R.INSTALL1ffc563a6bab4/spatial/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpGcHEVh/R.INSTALL1ffc563a6bab4/spatial/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpGcHEVh/R.INSTALL1ffc563a6bab4/spatial/src'
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x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.5.3/lib -L/usr/local/lib64 -o spatial.so init.o krc.o pps.o -L/usr/src/RPM/BUILD/R-3.5.3/lib -lR
make[3]: Leaving directory '/usr/src/tmp/RtmpGcHEVh/R.INSTALL1ffc563a6bab4/spatial/src'
installing to /usr/src/RPM/BUILD/R-3.5.3/library/spatial/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'spatial'
finding HTML links ... done
Kaver html
Kenvl html
Kfn html
Psim html
SSI html
Strauss html
anova.trls html
correlogram html
expcov html
ppgetregion html
ppinit html
pplik html
ppregion html
predict.trls html
prmat html
semat html
surf.gls html
surf.ls html
trls.influence html
trmat html
variogram html
** building package indices
** testing if installed package can be loaded
* DONE (spatial)
Making 'packages.html' ... done
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended'
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* installing *source* package 'nnet' ...
** package 'nnet' successfully unpacked and MD5 sums checked
** libs
make[3]: Entering directory '/usr/src/tmp/RtmpGvAd78/R.INSTALL1ff7b512f2060/nnet/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c nnet.c -o nnet.o
make[3]: Leaving directory '/usr/src/tmp/RtmpGvAd78/R.INSTALL1ff7b512f2060/nnet/src'
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x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.5.3/lib -L/usr/local/lib64 -o nnet.so nnet.o -L/usr/src/RPM/BUILD/R-3.5.3/lib -lR
make[3]: Leaving directory '/usr/src/tmp/RtmpGvAd78/R.INSTALL1ff7b512f2060/nnet/src'
installing to /usr/src/RPM/BUILD/R-3.5.3/library/nnet/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'nnet'
finding HTML links ... done
class.ind html
multinom html
nnet.Hess html
nnet html
predict.nnet html
which.is.max html
** building package indices
** testing if installed package can be loaded
* DONE (nnet)
Making 'packages.html' ... done
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended'
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* installing *source* package 'KernSmooth' ...
** package 'KernSmooth' successfully unpacked and MD5 sums checked
** libs
make[3]: Entering directory '/usr/src/tmp/Rtmp3GmWgg/R.INSTALL1ff93115200c0/KernSmooth/src'
f95 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c blkest.f -o blkest.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp3GmWgg/R.INSTALL1ff93115200c0/KernSmooth/src'
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f95 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c cp.f -o cp.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp3GmWgg/R.INSTALL1ff93115200c0/KernSmooth/src'
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f95 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dgesl.f -o dgesl.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp3GmWgg/R.INSTALL1ff93115200c0/KernSmooth/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp3GmWgg/R.INSTALL1ff93115200c0/KernSmooth/src'
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f95 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c linbin.f -o linbin.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp3GmWgg/R.INSTALL1ff93115200c0/KernSmooth/src'
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f95 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rlbin.f -o rlbin.o
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f95 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c locpoly.f -o locpoly.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp3GmWgg/R.INSTALL1ff93115200c0/KernSmooth/src'
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f95 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c sdiag.f -o sdiag.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp3GmWgg/R.INSTALL1ff93115200c0/KernSmooth/src'
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f95 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c sstdiag.f -o sstdiag.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp3GmWgg/R.INSTALL1ff93115200c0/KernSmooth/src'
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x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.5.3/lib -L/usr/local/lib64 -o KernSmooth.so blkest.o cp.o dgedi.o dgefa.o dgesl.o init.o linbin.o linbin2D.o locpoly.o rlbin.o sdiag.o sstdiag.o -lopenblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/usr/src/RPM/BUILD/R-3.5.3/lib -lR
make[3]: Leaving directory '/usr/src/tmp/Rtmp3GmWgg/R.INSTALL1ff93115200c0/KernSmooth/src'
installing to /usr/src/RPM/BUILD/R-3.5.3/library/KernSmooth/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'KernSmooth'
finding HTML links ... done
bkde html
bkde2D html
bkfe html
dpih html
dpik html
dpill html
locpoly html
** building package indices
** testing if installed package can be loaded
* DONE (KernSmooth)
Making 'packages.html' ... done
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended'
* installing *source* package 'MASS' ...
** package 'MASS' successfully unpacked and MD5 sums checked
** libs
make[3]: Entering directory '/usr/src/tmp/RtmphLoA67/R.INSTALL1ff423791373/MASS/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmphLoA67/R.INSTALL1ff423791373/MASS/src'
make[3]: Entering directory '/usr/src/tmp/RtmphLoA67/R.INSTALL1ff423791373/MASS/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmphLoA67/R.INSTALL1ff423791373/MASS/src'
make[3]: Entering directory '/usr/src/tmp/RtmphLoA67/R.INSTALL1ff423791373/MASS/src'
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.5.3/lib -L/usr/local/lib64 -o MASS.so MASS.o lqs.o -L/usr/src/RPM/BUILD/R-3.5.3/lib -lR
make[3]: Leaving directory '/usr/src/tmp/RtmphLoA67/R.INSTALL1ff423791373/MASS/src'
installing to /usr/src/RPM/BUILD/R-3.5.3/library/MASS/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'MASS'
finding HTML links ... done
Aids2 html
Animals html
Boston html
Cars93 html
Cushings html
DDT html
GAGurine html
Insurance html
MASS-internal html
Melanoma html
Null html
OME html
Pima.tr html
Rabbit html
Rubber html
SP500 html
Sitka html
Sitka89 html
Skye html
Traffic html
UScereal html
UScrime html
VA html
abbey html
accdeaths html
addterm html
anorexia html
anova.negbin html
area html
bacteria html
bandwidth.nrd html
bcv html
beav1 html
beav2 html
biopsy html
birthwt html
boxcox html
cabbages html
caith html
cats html
cement html
chem html
con2tr html
confint html
contr.sdif html
coop html
corresp html
cov.rob html
cov.trob html
cpus html
crabs html
deaths html
denumerate html
dose.p html
drivers html
dropterm html
eagles html
epil html
eqscplot html
farms html
fgl html
fitdistr html
forbes html
fractions html
galaxies html
gamma.dispersion html
gamma.shape.glm html
gehan html
genotype html
geyser html
gilgais html
ginv html
glm.convert html
glm.nb html
glmmPQL html
hills html
hist.scott html
housing html
huber html
hubers html
immer html
isoMDS html
kde2d html
lda html
ldahist html
leuk html
lm.gls html
lm.ridge html
loglm html
loglm1 html
logtrans html
lqs html
mammals html
mca html
mcycle html
menarche html
michelson html
minn38 html
motors html
muscle html
mvrnorm html
negative.binomial html
newcomb html
nlschools html
npk html
npr1 html
oats html
painters html
pairs.lda html
Rd warning: /usr/src/tmp/RtmphLoA67/R.INSTALL1ff423791373/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-3.5.3/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended'
begin installing recommended package cluster
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended'
begin installing recommended package class
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended'
* installing *source* package 'rpart' ...
** package 'rpart' successfully unpacked and MD5 sums checked
** libs
make[3]: Entering directory '/usr/src/tmp/RtmpYHbfWc/R.INSTALL1ff9965dc8ace/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpYHbfWc/R.INSTALL1ff9965dc8ace/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpYHbfWc/R.INSTALL1ff9965dc8ace/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpYHbfWc/R.INSTALL1ff9965dc8ace/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpYHbfWc/R.INSTALL1ff9965dc8ace/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpYHbfWc/R.INSTALL1ff9965dc8ace/rpart/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c bsplit.c -o bsplit.o
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpYHbfWc/R.INSTALL1ff9965dc8ace/rpart/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c gini.c -o gini.o
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c graycode.c -o graycode.o
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -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"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c nodesplit.c -o nodesplit.o
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c xpred.c -o xpred.o
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x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.5.3/lib -L/usr/local/lib64 -o rpart.so anova.o anovapred.o branch.o bsplit.o choose_surg.o fix_cp.o free_tree.o gini.o graycode.o init.o insert_split.o make_cp_list.o make_cp_table.o mysort.o nodesplit.o partition.o poisson.o pred_rpart.o print_tree.o rpart.o rpart_callback.o rpartexp.o rpartexp2.o rpcountup.o rpmatrix.o rundown.o rundown2.o surrogate.o usersplit.o xpred.o xval.o -L/usr/src/RPM/BUILD/R-3.5.3/lib -lR
make[3]: Leaving directory '/usr/src/tmp/RtmpYHbfWc/R.INSTALL1ff9965dc8ace/rpart/src'
installing to /usr/src/RPM/BUILD/R-3.5.3/library/rpart/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'rpart'
finding HTML links ... done
car.test.frame html
car90 html
cu.summary html
kyphosis html
labels.rpart html
meanvar.rpart html
na.rpart html
path.rpart html
plot.rpart html
plotcp html
post.rpart html
predict.rpart html
print.rpart html
printcp html
prune.rpart html
residuals.rpart html
rpart-internal html
rpart html
rpart.control html
rpart.exp html
rpart.object html
rsq.rpart html
snip.rpart html
solder html
stagec html
summary.rpart html
text.rpart html
xpred.rpart html
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rpart)
Making 'packages.html' ... done
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* installing *source* package 'foreign' ...
** package 'foreign' successfully unpacked and MD5 sums checked
** libs
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x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.5.3/lib -L/usr/local/lib64 -o foreign.so R_systat.o Rdbfread.o Rdbfwrite.o SASxport.o avl.o dbfopen.o file-handle.o format.o init.o minitab.o pfm-read.o sfm-read.o spss.o stataread.o -L/usr/src/RPM/BUILD/R-3.5.3/lib -lR
make[3]: Leaving directory '/usr/src/tmp/RtmpUNv2Cf/R.INSTALL1ff815d8a7f0d/foreign/src'
installing to /usr/src/RPM/BUILD/R-3.5.3/library/foreign/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'foreign'
finding HTML links ... done
lookup.xport html
read.S html
read.arff html
read.dbf html
read.dta html
read.epiinfo html
read.mtp html
read.octave html
read.spss html
read.ssd html
read.systat html
read.xport html
write.arff html
write.dbf html
write.dta html
write.foreign html
** building package indices
** testing if installed package can be loaded
* DONE (foreign)
Making 'packages.html' ... done
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended'
* installing *source* package 'class' ...
** package 'class' successfully unpacked and MD5 sums checked
** libs
make[3]: Entering directory '/usr/src/tmp/RtmpCJnBp0/R.INSTALL78c42460a37/class/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpCJnBp0/R.INSTALL78c42460a37/class/src'
make[3]: Entering directory '/usr/src/tmp/RtmpCJnBp0/R.INSTALL78c42460a37/class/src'
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.5.3/lib -L/usr/local/lib64 -o class.so class.o -L/usr/src/RPM/BUILD/R-3.5.3/lib -lR
make[3]: Leaving directory '/usr/src/tmp/RtmpCJnBp0/R.INSTALL78c42460a37/class/src'
installing to /usr/src/RPM/BUILD/R-3.5.3/library/class/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'class'
finding HTML links ... done
SOM html
batchSOM html
condense html
knn html
knn.cv html
knn1 html
lvq1 html
lvq2 html
lvq3 html
lvqinit html
lvqtest html
multiedit html
olvq1 html
reduce.nn html
somgrid html
** building package indices
** testing if installed package can be loaded
* DONE (class)
Making 'packages.html' ... done
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended'
* installing *source* package 'lattice' ...
** package 'lattice' successfully unpacked and MD5 sums checked
** libs
make[3]: Entering directory '/usr/src/tmp/RtmpCbv3hd/R.INSTALL1ff6378092acd/lattice/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpCbv3hd/R.INSTALL1ff6378092acd/lattice/src'
make[3]: Entering directory '/usr/src/tmp/RtmpCbv3hd/R.INSTALL1ff6378092acd/lattice/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpCbv3hd/R.INSTALL1ff6378092acd/lattice/src'
make[3]: Entering directory '/usr/src/tmp/RtmpCbv3hd/R.INSTALL1ff6378092acd/lattice/src'
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.5.3/lib -L/usr/local/lib64 -o lattice.so init.o threeDplot.o -L/usr/src/RPM/BUILD/R-3.5.3/lib -lR
make[3]: Leaving directory '/usr/src/tmp/RtmpCbv3hd/R.INSTALL1ff6378092acd/lattice/src'
installing to /usr/src/RPM/BUILD/R-3.5.3/library/lattice/libs
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'lattice'
finding HTML links ... done
Lattice html
Rows html
USMortality html
axis.default html
banking html
barchart.table html
barley html
cloud html
draw.colorkey html
draw.key html
environmental html
ethanol html
histogram html
interaction html
lattice.options html
latticeParseFormula html
level.colors html
levelplot html
llines html
lset html
make.groups html
melanoma html
oneway html
packet.panel.default html
panel.axis html
panel.barchart html
panel.bwplot html
panel.cloud html
panel.densityplot html
panel.dotplot html
panel.functions html
panel.histogram html
panel.levelplot html
panel.loess html
panel.number html
panel.pairs html
panel.parallel html
panel.qqmath html
panel.qqmathline html
panel.smoothScatter html
panel.spline html
panel.stripplot html
panel.superpose html
panel.violin html
panel.xyplot html
prepanel.default html
prepanel.functions html
print.trellis html
qq html
qqmath html
rfs html
shingles html
simpleKey html
simpleTheme html
singer html
splom html
strip.default html
tmd html
trellis.device html
trellis.object html
trellis.par.get html
update.trellis html
utilities.3d html
xyplot html
xyplot.ts html
** building package indices
** testing if installed package can be loaded
* DONE (lattice)
Making 'packages.html' ... done
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended'
begin installing recommended package Matrix
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended'
begin installing recommended package nlme
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended'
* installing *source* package 'cluster' ...
** package 'cluster' successfully unpacked and MD5 sums checked
** libs
make[3]: Entering directory '/usr/src/tmp/Rtmpfi84UZ/R.INSTALL787d4b42f8/cluster/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmpfi84UZ/R.INSTALL787d4b42f8/cluster/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpfi84UZ/R.INSTALL787d4b42f8/cluster/src'
f95 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dysta.f -o dysta.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpfi84UZ/R.INSTALL787d4b42f8/cluster/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpfi84UZ/R.INSTALL787d4b42f8/cluster/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmpfi84UZ/R.INSTALL787d4b42f8/cluster/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpfi84UZ/R.INSTALL787d4b42f8/cluster/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmpfi84UZ/R.INSTALL787d4b42f8/cluster/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpfi84UZ/R.INSTALL787d4b42f8/cluster/src'
f95 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c daisy.f -o daisy.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpfi84UZ/R.INSTALL787d4b42f8/cluster/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpfi84UZ/R.INSTALL787d4b42f8/cluster/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmpfi84UZ/R.INSTALL787d4b42f8/cluster/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpfi84UZ/R.INSTALL787d4b42f8/cluster/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c mona.c -o mona.o
mona.c: In function 'clmona_':
mona.c:261:10: warning: 'nelbb' may be used uninitialized in this function [-Wmaybe-uninitialized]
ner[k] = nelbb;
~~~~~~~^~~~~~~
mona.c:248:7: warning: 'lcc' may be used uninitialized in this function [-Wmaybe-uninitialized]
int lcc, nelbb;
^~~
mona.c:234:6: warning: 'jtelz' may be used uninitialized in this function [-Wmaybe-uninitialized]
int jres = kb - ka + 1 - jtel2,
^~~~
mona.c:234:6: warning: 'jtel' may be used uninitialized in this function [-Wmaybe-uninitialized]
mona.c:227:18: warning: 'jma' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (x[nel + jma * x_dim1] == 1) {
~~~~^~~~~~~~
mona.c:211:8: warning: 'd' may be used uninitialized in this function [-Wmaybe-uninitialized]
jtel = c + d;
~~~~~^~~~~~~
mona.c:211:8: warning: 'c' may be used uninitialized in this function [-Wmaybe-uninitialized]
mona.c:212:9: warning: 'b' may be used uninitialized in this function [-Wmaybe-uninitialized]
jtelz = a + b;
~~~~~~^~~~~~~
mona.c:212:9: warning: 'a' may be used uninitialized in this function [-Wmaybe-uninitialized]
make[3]: Leaving directory '/usr/src/tmp/Rtmpfi84UZ/R.INSTALL787d4b42f8/cluster/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpfi84UZ/R.INSTALL787d4b42f8/cluster/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmpfi84UZ/R.INSTALL787d4b42f8/cluster/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpfi84UZ/R.INSTALL787d4b42f8/cluster/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmpfi84UZ/R.INSTALL787d4b42f8/cluster/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpfi84UZ/R.INSTALL787d4b42f8/cluster/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmpfi84UZ/R.INSTALL787d4b42f8/cluster/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpfi84UZ/R.INSTALL787d4b42f8/cluster/src'
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.5.3/lib -L/usr/local/lib64 -o cluster.so clara.o daisy.o dysta.o fanny.o init.o mona.o pam.o sildist.o spannel.o twins.o -lgfortran -lm -lquadmath -L/usr/src/RPM/BUILD/R-3.5.3/lib -lR
make[3]: Leaving directory '/usr/src/tmp/Rtmpfi84UZ/R.INSTALL787d4b42f8/cluster/src'
installing to /usr/src/RPM/BUILD/R-3.5.3/library/cluster/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'cluster'
finding HTML links ... done
agnes html
agnes.object html
agriculture html
animals html
bannerplot html
chorSub html
clara html
clara.object html
clusGap html
clusplot.default html
Rd warning: /usr/src/tmp/Rtmpfi84UZ/R.INSTALL787d4b42f8/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/Rtmpfi84UZ/R.INSTALL787d4b42f8/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/Rtmpfi84UZ/R.INSTALL787d4b42f8/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/Rtmpfi84UZ/R.INSTALL787d4b42f8/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/Rtmpfi84UZ/R.INSTALL787d4b42f8/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-3.5.3/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended'
* installing *source* package 'nlme' ...
** package 'nlme' successfully unpacked and MD5 sums checked
** libs
make[3]: Entering directory '/usr/src/tmp/Rtmp0HSGMm/R.INSTALL1470731902dd/nlme/src'
f95 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c chol.f -o chol.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp0HSGMm/R.INSTALL1470731902dd/nlme/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp0HSGMm/R.INSTALL1470731902dd/nlme/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp0HSGMm/R.INSTALL1470731902dd/nlme/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp0HSGMm/R.INSTALL1470731902dd/nlme/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp0HSGMm/R.INSTALL1470731902dd/nlme/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp0HSGMm/R.INSTALL1470731902dd/nlme/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp0HSGMm/R.INSTALL1470731902dd/nlme/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp0HSGMm/R.INSTALL1470731902dd/nlme/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp0HSGMm/R.INSTALL1470731902dd/nlme/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp0HSGMm/R.INSTALL1470731902dd/nlme/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp0HSGMm/R.INSTALL1470731902dd/nlme/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp0HSGMm/R.INSTALL1470731902dd/nlme/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp0HSGMm/R.INSTALL1470731902dd/nlme/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp0HSGMm/R.INSTALL1470731902dd/nlme/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp0HSGMm/R.INSTALL1470731902dd/nlme/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp0HSGMm/R.INSTALL1470731902dd/nlme/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp0HSGMm/R.INSTALL1470731902dd/nlme/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp0HSGMm/R.INSTALL1470731902dd/nlme/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp0HSGMm/R.INSTALL1470731902dd/nlme/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp0HSGMm/R.INSTALL1470731902dd/nlme/src'
f95 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rs.f -o rs.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp0HSGMm/R.INSTALL1470731902dd/nlme/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp0HSGMm/R.INSTALL1470731902dd/nlme/src'
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.5.3/lib -L/usr/local/lib64 -o nlme.so chol.o corStruct.o gnls.o init.o matrix.o nlOptimizer.o nlme.o nlmefit.o pdMat.o pythag.o rs.o -lgfortran -lm -lquadmath -L/usr/src/RPM/BUILD/R-3.5.3/lib -lR
make[3]: Leaving directory '/usr/src/tmp/Rtmp0HSGMm/R.INSTALL1470731902dd/nlme/src'
installing to /usr/src/RPM/BUILD/R-3.5.3/library/nlme/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'nlme'
finding HTML links ... done
ACF html
ACF.gls html
ACF.lme html
Alfalfa html
Assay html
BodyWeight html
Cefamandole html
Coef html
Covariate html
Covariate.varFunc html
Dialyzer html
Dim html
Dim.corSpatial html
Dim.corStruct html
Dim.pdMat html
Earthquake html
Extract.pdMat html
Fatigue html
Gasoline html
Glucose html
Glucose2 html
Gun html
IGF html
Initialize html
Initialize.corStruct html
Initialize.glsStruct html
Initialize.lmeStruct html
Initialize.reStruct html
Initialize.varFunc html
LDEsysMat html
Machines html
MathAchSchool html
MathAchieve html
Matrix html
Matrix.pdMat html
Matrix.reStruct html
Meat html
Milk html
Muscle html
Names html
Names.formula html
Names.pdBlocked html
Names.pdMat html
Names.reStruct html
Nitrendipene html
Oats html
Orthodont html
Ovary html
Oxboys html
Oxide html
PBG html
Phenobarb html
Pixel html
Quinidine html
Rail html
RatPupWeight html
Relaxin html
Remifentanil html
Soybean html
Spruce html
Tetracycline1 html
Tetracycline2 html
VarCorr html
Variogram html
Variogram.corExp html
Variogram.corGaus html
Variogram.corLin html
Variogram.corRatio html
Variogram.corSpatial html
Variogram.corSpher html
Variogram.default html
Variogram.gls html
Variogram.lme html
Wafer html
Wheat html
Wheat2 html
allCoef html
anova.gls html
anova.lme html
as.matrix.corStruct html
as.matrix.pdMat html
as.matrix.reStruct html
asOneFormula html
asTable html
augPred html
balancedGrouped html
bdf html
coef.corStruct html
coef.gnls html
coef.lmList html
coef.lme html
coef.modelStruct html
coef.pdMat html
coef.reStruct html
coef.varFunc html
collapse html
collapse.groupedData html
compareFits html
comparePred html
corAR1 html
corARMA html
corCAR1 html
corClasses html
corCompSymm html
corExp html
corFactor html
corFactor.corStruct html
corGaus html
corLin html
corMatrix html
corMatrix.corStruct html
corMatrix.pdMat html
corMatrix.reStruct html
corNatural html
corRatio html
corSpatial html
corSpher html
corSymm html
ergoStool html
fdHess html
fitted.glsStruct html
fitted.gnlsStruct html
fitted.lmList html
fitted.lme html
fitted.lmeStruct html
fitted.nlmeStruct html
fixed.effects html
fixef.lmList html
formula.pdBlocked html
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** 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-3.5.3/src/library/Recommended'
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* installing *source* package 'Matrix' ...
** package 'Matrix' successfully unpacked and MD5 sums checked
** libs
make[3]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src'
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make[3]: Leaving directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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
make[3]: Leaving directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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
make[3]: Leaving directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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
make[3]: Leaving directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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-3.5.3/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
make[3]: Leaving directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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
make[3]: Leaving directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dppMatrix.c -o dppMatrix.o
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dsCMatrix.c -o dsCMatrix.o
make[3]: Leaving directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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-3.5.3/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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dsyMatrix.c -o dsyMatrix.o
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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-3.5.3/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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src'
( cd Lib ; make clean )
( cd Source ; make clean )
make[3]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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]
csi i, k, p, m, n, vnz, p1, top, m2, len, col, rnz, *s, *leftmost, *Ap, *Ai,
^
make[3]: Leaving directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src'
( cd Source ; make clean )
make[3]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src'
( cd Lib ; make -f "/usr/src/RPM/BUILD/R-3.5.3/etc/Makeconf" -f Makefile )
make[3]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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-3.5.3/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-3.5.3/include/R_ext/RS.h:74:25: warning: 'x' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define Free(p) (R_chk_free( (void *)(p) ), (p) = NULL)
^~~~~~~~~~
sparseQR.c:172:53: note: 'x' was declared here
double *ax = REAL(GET_SLOT(ans, Matrix_xSym)), *x;
^
make[3]: Leaving directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_complex.c -o cholmod_complex.o
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_common.c -o cholmod_common.o
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_add.c -o cholmod_add.o
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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]
Int p, pend, j, ncol, packed, nzmax, nz, xtype ;
^~~~~
make[5]: Leaving directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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]
double *Ax, *Xx, *Az, *Xz ;
^~
../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Xx, *Az, *Xz ;
^~
../Core/t_cholmod_dense.c:30:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
double *Ax, *Xx, *Az, *Xz ;
^~
In file included from ../Core/cholmod_dense.c:50:
../Core/t_cholmod_dense.c: In function 'r_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
double *Ax, *Xx, *Az, *Xz ;
^~
../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Xx, *Az, *Xz ;
^~
../Core/t_cholmod_dense.c: In function 'r_cholmod_dense_to_sparse':
../Core/t_cholmod_dense.c:136:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable]
double *Xx, *Cx, *Xz, *Cz ;
^~
../Core/t_cholmod_dense.c:136:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
double *Xx, *Cx, *Xz, *Cz ;
^~
../Core/t_cholmod_dense.c: In function 'r_cholmod_copy_dense2':
../Core/t_cholmod_dense.c:229:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
double *Xx, *Xz, *Yx, *Yz ;
^~
../Core/t_cholmod_dense.c:229:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
double *Xx, *Xz, *Yx, *Yz ;
^~
In file included from ../Core/cholmod_dense.c:52:
../Core/t_cholmod_dense.c: In function 'c_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
double *Ax, *Xx, *Az, *Xz ;
^~
../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Xx, *Az, *Xz ;
^~
../Core/t_cholmod_dense.c: In function 'c_cholmod_dense_to_sparse':
../Core/t_cholmod_dense.c:136:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable]
double *Xx, *Cx, *Xz, *Cz ;
^~
../Core/t_cholmod_dense.c:136:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
double *Xx, *Cx, *Xz, *Cz ;
^~
../Core/t_cholmod_dense.c: In function 'c_cholmod_copy_dense2':
../Core/t_cholmod_dense.c:229:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
double *Xx, *Xz, *Yx, *Yz ;
^~
../Core/t_cholmod_dense.c:229:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
double *Xx, *Xz, *Yx, *Yz ;
^~
../Core/cholmod_dense.c: In function 'cholmod_eye':
../Core/cholmod_dense.c:303:15: warning: variable 'nz' set but not used [-Wunused-but-set-variable]
Int i, n, nz ;
^~
../Core/cholmod_dense.c:302:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
double *Xx, *Xz ;
^~
make[5]: Leaving directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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]
Int nrow, ncol, up, lo, values, diag, astype ;
^~
../Core/cholmod_copy.c:278:21: warning: variable 'up' set but not used [-Wunused-but-set-variable]
Int nrow, ncol, up, lo, values, diag, astype ;
^~
make[5]: Leaving directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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]
double *Rx, *Rz, *Tx, *Tz ;
^~
../Core/t_cholmod_triplet.c:31:23: warning: variable 'Tx' set but not used [-Wunused-but-set-variable]
double *Rx, *Rz, *Tx, *Tz ;
^~
../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
double *Rx, *Rz, *Tx, *Tz ;
^~
../Core/t_cholmod_triplet.c:31:13: warning: variable 'Rx' set but not used [-Wunused-but-set-variable]
double *Rx, *Rz, *Tx, *Tz ;
^~
In file included from ../Core/cholmod_triplet.c:110:
../Core/t_cholmod_triplet.c: In function 'r_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
double *Rx, *Rz, *Tx, *Tz ;
^~
../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
double *Rx, *Rz, *Tx, *Tz ;
^~
In file included from ../Core/cholmod_triplet.c:112:
../Core/t_cholmod_triplet.c: In function 'c_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
double *Rx, *Rz, *Tx, *Tz ;
^~
../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
double *Rx, *Rz, *Tx, *Tz ;
^~
../Core/cholmod_triplet.c: In function 'cholmod_triplet_to_sparse':
../Core/cholmod_triplet.c:345:44: warning: variable 'ok' set but not used [-Wunused-but-set-variable]
Int i, j, p, k, stype, nrow, ncol, nz, ok ;
^~
../Core/cholmod_triplet.c:344:20: warning: variable 'Ri' set but not used [-Wunused-but-set-variable]
Int *Wj, *Rp, *Ri, *Rnz, *Ti, *Tj ;
^~
make[5]: Leaving directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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]
Int k, n, ordering, method, nmethods, status, default_strategy, ncol, uncol,
^~~~
../Cholesky/cholmod_analyze.c:419:45: warning: variable 'CParent' set but not used [-Wunused-but-set-variable]
Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent,
^~~~~~~
../Cholesky/cholmod_analyze.c:419:35: warning: variable 'Cmember' set but not used [-Wunused-but-set-variable]
Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent,
^~~~~~~
make[5]: Leaving directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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]
Int nrow, ncol, stype, convert, n, nsuper, grow2, status ;
^
make[5]: Leaving directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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]
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]
double *Lx, *Lz ;
^~
../Core/cholmod_change_factor.c: In function 'simplicial_symbolic_to_super_symbolic':
../Core/cholmod_change_factor.c:265:17: warning: variable 'xsize' set but not used [-Wunused-but-set-variable]
Int nsuper, xsize, ssize ;
^~~~~
../Core/cholmod_change_factor.c: In function 'change_simplicial_numeric':
../Core/cholmod_change_factor.c:680:15: warning: variable 'Li' set but not used [-Wunused-but-set-variable]
Int *Lp, *Li, *Lnz ;
^~
../Core/cholmod_change_factor.c:680:10: warning: variable 'Lp' set but not used [-Wunused-but-set-variable]
Int *Lp, *Li, *Lnz ;
^~
../Core/cholmod_change_factor.c:679:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
double *Lx, *Lz ;
^~
../Core/cholmod_change_factor.c:679:13: warning: variable 'Lx' set but not used [-Wunused-but-set-variable]
double *Lx, *Lz ;
^~
../Core/cholmod_change_factor.c: In function 'll_super_to_simplicial_numeric':
../Core/cholmod_change_factor.c:827:9: warning: variable 'n' set but not used [-Wunused-but-set-variable]
Int n, lnz, s, nsuper, psi, psend, nsrow, nscol, k1, k2, erows ;
^
../Core/cholmod_change_factor.c:826:21: warning: variable 'Lpx' set but not used [-Wunused-but-set-variable]
Int *Ls, *Lpi, *Lpx, *Super, *Li ;
^~~
../Core/cholmod_change_factor.c:826:10: warning: variable 'Ls' set but not used [-Wunused-but-set-variable]
Int *Ls, *Lpi, *Lpx, *Super, *Li ;
^~
make[5]: Leaving directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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]
Int nrow, ncol, is_complex, symmetry, i, j, q, iz, p, nz, is_binary, stype,
^~~~~~~~
make[5]: Leaving directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^~~~~~~
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^~~~~~~
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^~~~
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
^~~
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
^~
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^~
../Core/t_cholmod_transpose.c:45:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^~
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^~
../Core/t_cholmod_transpose.c:45:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^~
../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
^~
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^~
../Core/t_cholmod_transpose.c:142:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^~
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^~
../Core/t_cholmod_transpose.c:142:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^~
In file included from ../Core/cholmod_transpose.c:126:
../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^~~~~~~
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^~~~~~~
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^~~~
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
^~~
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
^~
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^~
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^~
../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
^~
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^~
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^~
In file included from ../Core/cholmod_transpose.c:128:
../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^~~~~~~
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^~~~~~~
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^~~~
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
^~~
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
^~
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^~
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^~
../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
^~
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^~
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^~
In file included from ../Core/cholmod_transpose.c:131:
../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^~~~~~~
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^~~~~~~
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^~~~
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
^~~
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
^~
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^~
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^~
../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
^~
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^~
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^~
In file included from ../Core/cholmod_transpose.c:133:
../Core/t_cholmod_transpose.c: In function 'z_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^~~~~~~
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^~~~~~~
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^~~~
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
^~~
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
^~
../Core/t_cholmod_transpose.c: In function 'z_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
^~
In file included from ../Core/cholmod_transpose.c:136:
../Core/t_cholmod_transpose.c: In function 'zt_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^~~~~~~
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^~~~~~~
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^~~~
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
^~~
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
^~
../Core/t_cholmod_transpose.c: In function 'zt_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
^~
make[5]: Leaving directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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]
Int i, nrow, nmethods, ordering, xworksize, amd_backup, init_print ;
^~~~~~~~~~
../Check/cholmod_check.c: In function 'check_dense':
../Check/cholmod_check.c:961:37: warning: variable 'nz' set but not used [-Wunused-but-set-variable]
Int i, j, d, nrow, ncol, nzmax, nz, init_print, count, xtype ;
^~
../Check/cholmod_check.c: In function 'check_factor':
../Check/cholmod_check.c:1508:2: warning: variable 'ps2' set but not used [-Wunused-but-set-variable]
ps2, psxend, ssize, xsize, maxcsize, maxesize, nsrow2, jj, ii, xtype ;
^~~
../Check/cholmod_check.c:1506:9: warning: variable 'precise' set but not used [-Wunused-but-set-variable]
count, precise, init_print, ilast, lnz, head, tail, jprev, plast,
^~~~~~~
../Check/cholmod_check.c:1505:38: warning: variable 'ordering' set but not used [-Wunused-but-set-variable]
Int n, nzmax, j, p, pend, i, nz, ordering, space, is_monotonic, minor,
^~~~~~~~
../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]
jnext, examine_super, nsuper, s, k1, k2, psi, psend, psx, nsrow, nscol,
^~~
make[5]: Leaving directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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]
use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
^~~~~
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^~
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^~
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^~
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^~
In file included from ../Cholesky/cholmod_rowfac.c:166:
../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
^~~~~
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^~
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^~
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^~
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^~
In file included from ../Cholesky/cholmod_rowfac.c:168:
../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
^~~~~
In file included from ../Cholesky/cholmod_rowfac.c:172:
../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
^~~~~
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^~
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^~
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^~
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^~
In file included from ../Cholesky/cholmod_rowfac.c:174:
../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
^~~~~
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^~
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^~
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^~
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^~
In file included from ../Cholesky/cholmod_rowfac.c:176:
../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
^~~~~
make[5]: Leaving directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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]
Int totsize ;
^~~~~~~
make[5]: Leaving directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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]
nsrow2, n, ps2, j, i, d, nrhs ;
^
../Supernodal/t_cholmod_super_solve.c: In function 'r_cholmod_super_ltsolve':
../Supernodal/t_cholmod_super_solve.c:241:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
nsrow2, n, ps2, j, i, d, nrhs ;
^
In file included from ../Supernodal/cholmod_super_solve.c:30:
../Supernodal/t_cholmod_super_solve.c: In function 'c_cholmod_super_lsolve':
../Supernodal/t_cholmod_super_solve.c:33:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
nsrow2, n, ps2, j, i, d, nrhs ;
^
../Supernodal/t_cholmod_super_solve.c: In function 'c_cholmod_super_ltsolve':
../Supernodal/t_cholmod_super_solve.c:241:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
nsrow2, n, ps2, j, i, d, nrhs ;
^
make[5]: Leaving directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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]
double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
^~
../Supernodal/t_cholmod_super_numeric.c:111:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
^~
In file included from ../Supernodal/cholmod_super_numeric.c:80:
../Supernodal/t_cholmod_super_numeric.c: In function 'c_cholmod_super_numeric':
../Supernodal/t_cholmod_super_numeric.c:111:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
^~
../Supernodal/t_cholmod_super_numeric.c:111:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
^~
make[5]: Leaving directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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]
Int nrow, ncol, up, lo, values, diag, astype ;
^~
../Core/cholmod_copy.c:278:21: warning: variable 'up' set but not used [-Wunused-but-set-variable]
Int nrow, ncol, up, lo, values, diag, astype ;
^~
make[5]: Leaving directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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]
double *Ax, *Xx, *Az, *Xz ;
^~
../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Xx, *Az, *Xz ;
^~
../Core/t_cholmod_dense.c:30:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
double *Ax, *Xx, *Az, *Xz ;
^~
In file included from ../Core/cholmod_dense.c:50:
../Core/t_cholmod_dense.c: In function 'r_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
double *Ax, *Xx, *Az, *Xz ;
^~
../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Xx, *Az, *Xz ;
^~
../Core/t_cholmod_dense.c: In function 'r_cholmod_dense_to_sparse':
../Core/t_cholmod_dense.c:136:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable]
double *Xx, *Cx, *Xz, *Cz ;
^~
../Core/t_cholmod_dense.c:136:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
double *Xx, *Cx, *Xz, *Cz ;
^~
../Core/t_cholmod_dense.c: In function 'r_cholmod_copy_dense2':
../Core/t_cholmod_dense.c:229:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
double *Xx, *Xz, *Yx, *Yz ;
^~
../Core/t_cholmod_dense.c:229:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
double *Xx, *Xz, *Yx, *Yz ;
^~
In file included from ../Core/cholmod_dense.c:52:
../Core/t_cholmod_dense.c: In function 'c_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
double *Ax, *Xx, *Az, *Xz ;
^~
../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Xx, *Az, *Xz ;
^~
../Core/t_cholmod_dense.c: In function 'c_cholmod_dense_to_sparse':
../Core/t_cholmod_dense.c:136:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable]
double *Xx, *Cx, *Xz, *Cz ;
^~
../Core/t_cholmod_dense.c:136:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
double *Xx, *Cx, *Xz, *Cz ;
^~
../Core/t_cholmod_dense.c: In function 'c_cholmod_copy_dense2':
../Core/t_cholmod_dense.c:229:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
double *Xx, *Xz, *Yx, *Yz ;
^~
../Core/t_cholmod_dense.c:229:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
double *Xx, *Xz, *Yx, *Yz ;
^~
../Core/cholmod_dense.c: In function 'cholmod_l_eye':
../Core/cholmod_dense.c:303:15: warning: variable 'nz' set but not used [-Wunused-but-set-variable]
Int i, n, nz ;
^~
../Core/cholmod_dense.c:302:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
double *Xx, *Xz ;
^~
make[5]: Leaving directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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]
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]
double *Lx, *Lz ;
^~
../Core/cholmod_change_factor.c: In function 'simplicial_symbolic_to_super_symbolic':
../Core/cholmod_change_factor.c:265:17: warning: variable 'xsize' set but not used [-Wunused-but-set-variable]
Int nsuper, xsize, ssize ;
^~~~~
../Core/cholmod_change_factor.c: In function 'change_simplicial_numeric':
../Core/cholmod_change_factor.c:680:15: warning: variable 'Li' set but not used [-Wunused-but-set-variable]
Int *Lp, *Li, *Lnz ;
^~
../Core/cholmod_change_factor.c:680:10: warning: variable 'Lp' set but not used [-Wunused-but-set-variable]
Int *Lp, *Li, *Lnz ;
^~
../Core/cholmod_change_factor.c:679:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
double *Lx, *Lz ;
^~
../Core/cholmod_change_factor.c:679:13: warning: variable 'Lx' set but not used [-Wunused-but-set-variable]
double *Lx, *Lz ;
^~
../Core/cholmod_change_factor.c: In function 'll_super_to_simplicial_numeric':
../Core/cholmod_change_factor.c:827:9: warning: variable 'n' set but not used [-Wunused-but-set-variable]
Int n, lnz, s, nsuper, psi, psend, nsrow, nscol, k1, k2, erows ;
^
../Core/cholmod_change_factor.c:826:21: warning: variable 'Lpx' set but not used [-Wunused-but-set-variable]
Int *Ls, *Lpi, *Lpx, *Super, *Li ;
^~~
../Core/cholmod_change_factor.c:826:10: warning: variable 'Ls' set but not used [-Wunused-but-set-variable]
Int *Ls, *Lpi, *Lpx, *Super, *Li ;
^~
make[5]: Leaving directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^~~~~~~
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^~~~~~~
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^~~~
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
^~~
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
^~
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^~
../Core/t_cholmod_transpose.c:45:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^~
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^~
../Core/t_cholmod_transpose.c:45:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^~
../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
^~
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^~
../Core/t_cholmod_transpose.c:142:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^~
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^~
../Core/t_cholmod_transpose.c:142:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^~
In file included from ../Core/cholmod_transpose.c:126:
../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^~~~~~~
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^~~~~~~
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^~~~
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
^~~
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
^~
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^~
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^~
../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
^~
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^~
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^~
In file included from ../Core/cholmod_transpose.c:128:
../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^~~~~~~
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^~~~~~~
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^~~~
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
^~~
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
^~
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^~
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^~
../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
^~
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^~
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^~
In file included from ../Core/cholmod_transpose.c:131:
../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^~~~~~~
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^~~~~~~
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^~~~
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
^~~
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
^~
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^~
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^~
../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
^~
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^~
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^~
In file included from ../Core/cholmod_transpose.c:133:
../Core/t_cholmod_transpose.c: In function 'z_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^~~~~~~
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^~~~~~~
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^~~~
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
^~~
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
^~
../Core/t_cholmod_transpose.c: In function 'z_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
^~
In file included from ../Core/cholmod_transpose.c:136:
../Core/t_cholmod_transpose.c: In function 'zt_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^~~~~~~
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^~~~~~~
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^~~~
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
^~~
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
^~
../Core/t_cholmod_transpose.c: In function 'zt_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
^~
make[5]: Leaving directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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]
Int nrow, ncol, is_complex, symmetry, i, j, q, iz, p, nz, is_binary, stype,
^~~~~~~~
make[5]: Leaving directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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]
Int p, pend, j, ncol, packed, nzmax, nz, xtype ;
^~~~~
make[5]: Leaving directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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]
double *Rx, *Rz, *Tx, *Tz ;
^~
../Core/t_cholmod_triplet.c:31:23: warning: variable 'Tx' set but not used [-Wunused-but-set-variable]
double *Rx, *Rz, *Tx, *Tz ;
^~
../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
double *Rx, *Rz, *Tx, *Tz ;
^~
../Core/t_cholmod_triplet.c:31:13: warning: variable 'Rx' set but not used [-Wunused-but-set-variable]
double *Rx, *Rz, *Tx, *Tz ;
^~
In file included from ../Core/cholmod_triplet.c:110:
../Core/t_cholmod_triplet.c: In function 'r_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
double *Rx, *Rz, *Tx, *Tz ;
^~
../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
double *Rx, *Rz, *Tx, *Tz ;
^~
In file included from ../Core/cholmod_triplet.c:112:
../Core/t_cholmod_triplet.c: In function 'c_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
double *Rx, *Rz, *Tx, *Tz ;
^~
../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
double *Rx, *Rz, *Tx, *Tz ;
^~
../Core/cholmod_triplet.c: In function 'cholmod_l_triplet_to_sparse':
../Core/cholmod_triplet.c:345:44: warning: variable 'ok' set but not used [-Wunused-but-set-variable]
Int i, j, p, k, stype, nrow, ncol, nz, ok ;
^~
../Core/cholmod_triplet.c:344:20: warning: variable 'Ri' set but not used [-Wunused-but-set-variable]
Int *Wj, *Rp, *Ri, *Rnz, *Ti, *Tj ;
^~
make[5]: Leaving directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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]
Int k, n, ordering, method, nmethods, status, default_strategy, ncol, uncol,
^~~~
../Cholesky/cholmod_analyze.c:419:45: warning: variable 'CParent' set but not used [-Wunused-but-set-variable]
Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent,
^~~~~~~
../Cholesky/cholmod_analyze.c:419:35: warning: variable 'Cmember' set but not used [-Wunused-but-set-variable]
Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent,
^~~~~~~
make[5]: Leaving directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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]
Int nrow, ncol, stype, convert, n, nsuper, grow2, status ;
^
make[5]: Leaving directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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]
Int i, nrow, nmethods, ordering, xworksize, amd_backup, init_print ;
^~~~~~~~~~
../Check/cholmod_check.c: In function 'check_dense':
../Check/cholmod_check.c:961:37: warning: variable 'nz' set but not used [-Wunused-but-set-variable]
Int i, j, d, nrow, ncol, nzmax, nz, init_print, count, xtype ;
^~
../Check/cholmod_check.c: In function 'check_factor':
../Check/cholmod_check.c:1508:2: warning: variable 'ps2' set but not used [-Wunused-but-set-variable]
ps2, psxend, ssize, xsize, maxcsize, maxesize, nsrow2, jj, ii, xtype ;
^~~
../Check/cholmod_check.c:1506:9: warning: variable 'precise' set but not used [-Wunused-but-set-variable]
count, precise, init_print, ilast, lnz, head, tail, jprev, plast,
^~~~~~~
../Check/cholmod_check.c:1505:38: warning: variable 'ordering' set but not used [-Wunused-but-set-variable]
Int n, nzmax, j, p, pend, i, nz, ordering, space, is_monotonic, minor,
^~~~~~~~
../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]
jnext, examine_super, nsuper, s, k1, k2, psi, psend, psx, nsrow, nscol,
^~~
make[5]: Leaving directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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]
Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
^~~~
../MatrixOps/t_cholmod_sdmult.c:52:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
^~
../MatrixOps/t_cholmod_sdmult.c:52:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
^~
../MatrixOps/t_cholmod_sdmult.c:52:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
^~
../MatrixOps/t_cholmod_sdmult.c:52:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
^~
In file included from ../MatrixOps/cholmod_sdmult.c:48:
../MatrixOps/t_cholmod_sdmult.c: In function 'c_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
^~~~
../MatrixOps/t_cholmod_sdmult.c:52:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
^~
../MatrixOps/t_cholmod_sdmult.c:52:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
^~
../MatrixOps/t_cholmod_sdmult.c:52:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
^~
../MatrixOps/t_cholmod_sdmult.c:52:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
^~
In file included from ../MatrixOps/cholmod_sdmult.c:50:
../MatrixOps/t_cholmod_sdmult.c: In function 'z_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
^~~~
make[5]: Leaving directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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]
use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
^~~~~
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^~
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^~
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^~
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^~
In file included from ../Cholesky/cholmod_rowfac.c:166:
../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
^~~~~
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^~
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^~
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^~
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^~
In file included from ../Cholesky/cholmod_rowfac.c:168:
../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
^~~~~
In file included from ../Cholesky/cholmod_rowfac.c:172:
../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
^~~~~
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^~
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^~
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^~
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^~
In file included from ../Cholesky/cholmod_rowfac.c:174:
../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
^~~~~
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^~
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^~
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^~
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^~
In file included from ../Cholesky/cholmod_rowfac.c:176:
../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
^~~~~
make[5]: Leaving directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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]
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]
double *Lx, *Yx, *Yz ;
^~
../Cholesky/cholmod_solve.c: In function 'iperm':
../Cholesky/cholmod_solve.c:337:13: warning: variable 'nk' set but not used [-Wunused-but-set-variable]
Int k2, nk, p, k, j, nrow, ncol, d, dj, j2 ;
^~
make[5]: Leaving directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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]
Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
^~~~
../MatrixOps/t_cholmod_sdmult.c:52:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
^~
../MatrixOps/t_cholmod_sdmult.c:52:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
^~
../MatrixOps/t_cholmod_sdmult.c:52:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
^~
../MatrixOps/t_cholmod_sdmult.c:52:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
^~
In file included from ../MatrixOps/cholmod_sdmult.c:48:
../MatrixOps/t_cholmod_sdmult.c: In function 'c_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
^~~~
../MatrixOps/t_cholmod_sdmult.c:52:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
^~
../MatrixOps/t_cholmod_sdmult.c:52:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
^~
../MatrixOps/t_cholmod_sdmult.c:52:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
^~
../MatrixOps/t_cholmod_sdmult.c:52:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
^~
In file included from ../MatrixOps/cholmod_sdmult.c:50:
../MatrixOps/t_cholmod_sdmult.c: In function 'z_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
^~~~
make[5]: Leaving directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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]
nsrow2, n, ps2, j, i, d, nrhs ;
^
../Supernodal/t_cholmod_super_solve.c: In function 'r_cholmod_super_ltsolve':
../Supernodal/t_cholmod_super_solve.c:241:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
nsrow2, n, ps2, j, i, d, nrhs ;
^
In file included from ../Supernodal/cholmod_super_solve.c:30:
../Supernodal/t_cholmod_super_solve.c: In function 'c_cholmod_super_lsolve':
../Supernodal/t_cholmod_super_solve.c:33:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
nsrow2, n, ps2, j, i, d, nrhs ;
^
../Supernodal/t_cholmod_super_solve.c: In function 'c_cholmod_super_ltsolve':
../Supernodal/t_cholmod_super_solve.c:241:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
nsrow2, n, ps2, j, i, d, nrhs ;
^
make[5]: Leaving directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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]
double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
^~
../Supernodal/t_cholmod_super_numeric.c:111:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
^~
In file included from ../Supernodal/cholmod_super_numeric.c:80:
../Supernodal/t_cholmod_super_numeric.c: In function 'c_cholmod_super_numeric':
../Supernodal/t_cholmod_super_numeric.c:111:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
^~
../Supernodal/t_cholmod_super_numeric.c:111:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
^~
make[5]: Leaving directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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]
Int totsize ;
^~~~~~~
make[5]: Leaving directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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]
*Set_ps1 [32], *Set_ps2 [32], *ps1, *ps2 ;
^~~
make[5]: Leaving directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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]
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]
double *Lx, *Yx, *Yz ;
^~
../Cholesky/cholmod_solve.c: In function 'iperm':
../Cholesky/cholmod_solve.c:337:13: warning: variable 'nk' set but not used [-Wunused-but-set-variable]
Int k2, nk, p, k, j, nrow, ncol, d, dj, j2 ;
^~
make[5]: Leaving directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -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]
*Set_ps1 [32], *Set_ps2 [32], *ps1, *ps2 ;
^~~
make[5]: Leaving directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/CHOLMOD/Lib'
( cd Source ; make -f "/usr/src/RPM/BUILD/R-3.5.3/etc/Makeconf" -f Makefile lib )
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/COLAMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/COLAMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/COLAMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/COLAMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/COLAMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/COLAMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/COLAMD/Source'
ar -rucs ../../COLAMD.a colamd_global.o colamd.o colamd_l.o
make[5]: Leaving directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/COLAMD/Source'
( cd Source ; make -f "/usr/src/RPM/BUILD/R-3.5.3/etc/Makeconf" -f Makefile lib )
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/AMD/Source'
make[4]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/SuiteSparse_config'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/SuiteSparse_config'
make[4]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/SuiteSparse_config'
ar -rucs ../SuiteSparse_config.a SuiteSparse_config.o
make[4]: Leaving directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src/SuiteSparse_config'
make[3]: Entering directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src'
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.5.3/lib -L/usr/local/lib64 -o Matrix.so CHMfactor.o Csparse.o TMatrix_as.o Tsparse.o init.o Mutils.o chm_common.o cs.o cs_utils.o dense.o dgCMatrix.o dgTMatrix.o dgeMatrix.o dpoMatrix.o dppMatrix.o dsCMatrix.o dsyMatrix.o dspMatrix.o dtCMatrix.o dtTMatrix.o dtrMatrix.o dtpMatrix.o factorizations.o ldense.o lgCMatrix.o sparseQR.o abIndex.o CHOLMOD.a COLAMD.a AMD.a SuiteSparse_config.a -llapack -lopenblas -lgfortran -lm -lquadmath -L/usr/src/RPM/BUILD/R-3.5.3/lib -lR
make[3]: Leaving directory '/usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/Matrix/src'
installing to /usr/src/RPM/BUILD/R-3.5.3/library/Matrix/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for 'chol2inv' from 'base' in package 'Matrix'
(from the saved implicit definition)
Creating a generic function for 'chol2inv' from package 'base' in package 'Matrix'
Creating a generic function for 'diag' from package 'base' in package 'Matrix'
Creating a generic function for 'drop' from package 'base' in package 'Matrix'
Creating a generic function for 'cov2cor' from package 'stats' in package 'Matrix'
Creating a generic function for 'unname' from package 'base' in package 'Matrix'
Creating a generic function for 'norm' from package 'base' in package 'Matrix'
Creating a generic function for 'rcond' from 'base' in package 'Matrix'
(from the saved implicit definition)
Creating a generic function for 'rcond' from package 'base' in package 'Matrix'
in method for 'coerce' with signature '"matrix.csr","dgRMatrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"dgRMatrix","matrix.csr"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.csc","dgCMatrix"': no definition for class "matrix.csc"
in method for 'coerce' with signature '"dgCMatrix","matrix.csc"': no definition for class "matrix.csc"
in method for 'coerce' with signature '"matrix.coo","dgTMatrix"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"dgTMatrix","matrix.coo"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"dsparseMatrix","matrix.csr"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.csr","dgCMatrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.coo","dgCMatrix"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"matrix.csr","RsparseMatrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.csc","CsparseMatrix"': no definition for class "matrix.csc"
in method for 'coerce' with signature '"matrix.coo","TsparseMatrix"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"matrix.csr","CsparseMatrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.coo","CsparseMatrix"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"matrix.csc","TsparseMatrix"': no definition for class "matrix.csc"
in method for 'coerce' with signature '"matrix.csr","TsparseMatrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"CsparseMatrix","matrix.csr"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"CsparseMatrix","matrix.coo"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"CsparseMatrix","matrix.csc"': no definition for class "matrix.csc"
in method for 'coerce' with signature '"matrix.csr","Matrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.coo","Matrix"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"matrix.csc","Matrix"': no definition for class "matrix.csc"
Creating a generic function for 'colSums' from package 'base' in package 'Matrix'
Creating a generic function for 'colMeans' from package 'base' in package 'Matrix'
Creating a generic function for 'rowSums' from package 'base' in package 'Matrix'
Creating a generic function for 'rowMeans' from package 'base' in package 'Matrix'
in method for 'colSums' with signature 'x="igCMatrix"': no definition for class "igCMatrix"
in method for 'rowSums' with signature 'x="igCMatrix"': no definition for class "igCMatrix"
in method for 'colMeans' with signature 'x="igCMatrix"': no definition for class "igCMatrix"
in method for 'rowMeans' with signature 'x="igCMatrix"': no definition for class "igCMatrix"
Creating a generic function for 'zapsmall' from package 'base' in package 'Matrix'
Creating a generic function for 'diag<-' from package 'base' in package 'Matrix'
Creating a generic function for 'crossprod' from package 'base' in package 'Matrix'
Creating a generic function for 'tcrossprod' from package 'base' in package 'Matrix'
Creating a generic function for 'which' from package 'base' in package 'Matrix'
in method for 'coerce' with signature '"graphAM","sparseMatrix"': no definition for class "graphAM"
in method for 'coerce' with signature '"graph","CsparseMatrix"': no definition for class "graph"
in method for 'coerce' with signature '"graph","Matrix"': no definition for class "graph"
in method for 'coerce' with signature '"graphNEL","CsparseMatrix"': no definition for class "graphNEL"
in method for 'coerce' with signature '"graphNEL","TsparseMatrix"': no definition for class "graphNEL"
in method for 'coerce' with signature '"sparseMatrix","graph"': no definition for class "graph"
in method for 'coerce' with signature '"sparseMatrix","graphNEL"': no definition for class "graphNEL"
in method for 'coerce' with signature '"TsparseMatrix","graphNEL"': no definition for class "graphNEL"
Creating a generic function for 'qr.R' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.Q' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.qy' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.qty' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.coef' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.resid' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.fitted' from package 'base' in package 'Matrix'
Creating a generic function for 'toeplitz' from package 'stats' in package 'Matrix'
** help
*** installing help indices
converting help for package 'Matrix'
finding HTML links ... done
BunchKaufman-methods html
CAex html
CHMfactor-class html
Cholesky-class html
Cholesky html
CsparseMatrix-class html
Diagonal html
Hilbert html
KNex html
KhatriRao html
LU-class html
Matrix-class html
Matrix html
MatrixClass html
MatrixFactorization-class html
RsparseMatrix-class html
Schur-class html
Schur html
SparseM-conv html
Subassign-methods html
TsparseMatrix-class html
USCounties html
Xtrct-methods html
abIndex-class html
Rd warning: /usr/src/tmp/RtmpNiywGm/R.INSTALL14752a93d20d/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/RtmpNiywGm/R.INSTALL14752a93d20d/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/RtmpNiywGm/R.INSTALL14752a93d20d/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/RtmpNiywGm/R.INSTALL14752a93d20d/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
Loading required package: Matrix
** installing vignettes
** testing if installed package can be loaded
* DONE (Matrix)
Making 'packages.html' ... done
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended'
begin installing recommended package mgcv
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended'
begin installing recommended package survival
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended'
* installing *source* package 'survival' ...
** package 'survival' successfully unpacked and MD5 sums checked
** libs
make[3]: Entering directory '/usr/src/tmp/RtmpeoMKqd/R.INSTALL9807eddb302/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpeoMKqd/R.INSTALL9807eddb302/survival/src'
make[3]: Entering directory '/usr/src/tmp/RtmpeoMKqd/R.INSTALL9807eddb302/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c agfit4.c -o agfit4.o
agfit4.c: In function 'agfit4':
agfit4.c:531:24: warning: 'dtime' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (start[p1] < dtime) break;
^
make[3]: Leaving directory '/usr/src/tmp/RtmpeoMKqd/R.INSTALL9807eddb302/survival/src'
make[3]: Entering directory '/usr/src/tmp/RtmpeoMKqd/R.INSTALL9807eddb302/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpeoMKqd/R.INSTALL9807eddb302/survival/src'
make[3]: Entering directory '/usr/src/tmp/RtmpeoMKqd/R.INSTALL9807eddb302/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpeoMKqd/R.INSTALL9807eddb302/survival/src'
make[3]: Entering directory '/usr/src/tmp/RtmpeoMKqd/R.INSTALL9807eddb302/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c agmart2.c -o agmart2.o
make[3]: Leaving directory '/usr/src/tmp/RtmpeoMKqd/R.INSTALL9807eddb302/survival/src'
make[3]: Entering directory '/usr/src/tmp/RtmpeoMKqd/R.INSTALL9807eddb302/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpeoMKqd/R.INSTALL9807eddb302/survival/src'
make[3]: Entering directory '/usr/src/tmp/RtmpeoMKqd/R.INSTALL9807eddb302/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c agscore.c -o agscore.o
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norisk.c: In function 'norisk':
norisk.c:12:23: warning: 'p1' may be used uninitialized in this function [-Wmaybe-uninitialized]
int i, j, istrat, p1, p2;
^~
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c survregc1.c -o survregc1.o
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c survfitci.c -o survfitci.o
survfitci.c: In function 'survfitci':
survfitci.c:216:37: warning: 'umat' may be used uninitialized in this function [-Wmaybe-uninitialized]
umat[j][k] -= hmat[oldstate][k]* p[oldstate]/ ws[oldstate];
~~~~^~~
survfitci.c:46:38: warning: 'usave' may be used uninitialized in this function [-Wmaybe-uninitialized]
double **pmat, **vmat, *cumhaz, *usave;
^~~~~
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x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.5.3/lib -L/usr/local/lib64 -o survival.so agexact.o agfit4.o agfit5.o agmart.o agmart2.o agmart3.o agscore.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 coxscore.o dmatrix.o doloop.o finegray.o gchol.o init.o norisk.o pyears1.o pyears2.o pyears3b.o pystep.o survConcordance.o survdiff2.o survfit4.o survfitci.o survpenal.o survreg6.o survreg7.o survregc1.o survregc2.o survsplit.o tmerge.o -L/usr/src/RPM/BUILD/R-3.5.3/lib -lR
make[3]: Leaving directory '/usr/src/tmp/RtmpeoMKqd/R.INSTALL9807eddb302/survival/src'
installing to /usr/src/RPM/BUILD/R-3.5.3/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/RtmpeoMKqd/R.INSTALL9807eddb302/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/RtmpeoMKqd/R.INSTALL9807eddb302/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
cox.zph html
coxph html
coxph.control html
coxph.detail html
coxph.object html
coxph.wtest html
diabetic html
dsurvreg html
finegray html
flchain html
frailty html
genfan 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
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
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 html
survSplit 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
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
** 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-3.5.3/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended'
begin installing recommended package boot
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended'
* installing *source* package 'boot' ...
** package 'boot' successfully unpacked and MD5 sums checked
** 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
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motor html
neuro html
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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-3.5.3/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended'
* installing *source* package 'mgcv' ...
** package 'mgcv' successfully unpacked and MD5 sums checked
** libs
make[3]: Entering directory '/usr/src/tmp/Rtmp6ZwqEe/R.INSTALL98132cd0f7c/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp6ZwqEe/R.INSTALL98132cd0f7c/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp6ZwqEe/R.INSTALL98132cd0f7c/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp6ZwqEe/R.INSTALL98132cd0f7c/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp6ZwqEe/R.INSTALL98132cd0f7c/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp6ZwqEe/R.INSTALL98132cd0f7c/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp6ZwqEe/R.INSTALL98132cd0f7c/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp6ZwqEe/R.INSTALL98132cd0f7c/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp6ZwqEe/R.INSTALL98132cd0f7c/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp6ZwqEe/R.INSTALL98132cd0f7c/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp6ZwqEe/R.INSTALL98132cd0f7c/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c misc.c -o misc.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp6ZwqEe/R.INSTALL98132cd0f7c/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp6ZwqEe/R.INSTALL98132cd0f7c/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp6ZwqEe/R.INSTALL98132cd0f7c/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp6ZwqEe/R.INSTALL98132cd0f7c/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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 'Xbd':
discrete.c:368: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
#pragma omp critical (xbdcalloc)
discrete.c:391: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
#pragma omp critical (xbdcalloc)
discrete.c:413: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
#pragma omp critical (xbdcalloc)
discrete.c: In function 'indReduce':
discrete.c:101:24: warning: 'wl' may be used uninitialized in this function [-Wmaybe-uninitialized]
i=ka[l+1];j=kb[l];Wij = wl[l];
~~~~^~~~~~~
discrete.c:99:31: warning: 'ws' may be used uninitialized in this function [-Wmaybe-uninitialized]
i=ka[l];j=kb[l+1];Wij = ws[l];
~~~~^~~~~~~
discrete.c: In function 'XWXijs':
discrete.c:834:9: warning: 'D' may be used uninitialized in this function [-Wmaybe-uninitialized]
*C,*D,*W,*wb,*p0,*p1,*p2,*p3,*pw,*pw1,*pl,*ps,*wi,*wsi,*wli,*wo,*psi,*pwi,*pli;
^
discrete.c:834:6: warning: 'C' may be used uninitialized in this function [-Wmaybe-uninitialized]
*C,*D,*W,*wb,*p0,*p1,*p2,*p3,*pw,*pw1,*pl,*ps,*wi,*wsi,*wli,*wo,*psi,*pwi,*pli;
^
discrete.c:1019:27: warning: 'W' may be used uninitialized in this function [-Wmaybe-uninitialized]
W[*Kik + mim * *Kjk1] += *ps * *p3;
^~
discrete.c:1050:51: warning: 'wl' may be used uninitialized in this function [-Wmaybe-uninitialized]
*pwi = *pw * *p0;*psi = *ps * *p0;*pli = *pl * *p2;
^~~
discrete.c: In function 'XWXd0':
discrete.c:1308:5: warning: 'ws' may be used uninitialized in this function [-Wmaybe-uninitialized]
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,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tri,off,work + tid * q,worki + tid * (ptrdiff_t) qi,nxwx,ht,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sm + tid * (ptrdiff_t) *n,SMstack + 3 * tid * (ptrdiff_t) *n ); /* compute r,c block */
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/usr/src/tmp/Rtmp6ZwqEe/R.INSTALL98132cd0f7c/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp6ZwqEe/R.INSTALL98132cd0f7c/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp6ZwqEe/R.INSTALL98132cd0f7c/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp6ZwqEe/R.INSTALL98132cd0f7c/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp6ZwqEe/R.INSTALL98132cd0f7c/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp6ZwqEe/R.INSTALL98132cd0f7c/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp6ZwqEe/R.INSTALL98132cd0f7c/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp6ZwqEe/R.INSTALL98132cd0f7c/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp6ZwqEe/R.INSTALL98132cd0f7c/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp6ZwqEe/R.INSTALL98132cd0f7c/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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_down':
mat.c:1744:9: warning: unused variable 'j' [-Wunused-variable]
int i,j,n1;
^
mat.c: In function 'chol_up':
mat.c:1869:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (*n>1) R[1] = -2.0;return; /* signals error */
^~
mat.c:1869:29: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (*n>1) R[1] = -2.0;return; /* signals error */
^~~~~~
make[3]: Leaving directory '/usr/src/tmp/Rtmp6ZwqEe/R.INSTALL98132cd0f7c/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp6ZwqEe/R.INSTALL98132cd0f7c/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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]
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'
if (!dim_sym) dim_sym = install("dim");if (!dist_sym) dist_sym = install("dist");
^~
make[3]: Leaving directory '/usr/src/tmp/Rtmp6ZwqEe/R.INSTALL98132cd0f7c/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp6ZwqEe/R.INSTALL98132cd0f7c/mgcv/src'
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.5.3/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-3.5.3/lib -lR
make[3]: Leaving directory '/usr/src/tmp/Rtmp6ZwqEe/R.INSTALL98132cd0f7c/mgcv/src'
installing to /usr/src/RPM/BUILD/R-3.5.3/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
anova.gam html
bam html
Rd warning: /usr/src/tmp/Rtmp6ZwqEe/R.INSTALL98132cd0f7c/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/Rtmp6ZwqEe/R.INSTALL98132cd0f7c/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/Rtmp6ZwqEe/R.INSTALL98132cd0f7c/mgcv/man/bam.Rd:188: file link 'makeForkCluster' in package 'parallel' does not exist and so has been treated as a topic
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cSplineDes html
chol.down html
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columb html
concurvity html
coxph html
coxpht html
dDeta html
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extract.lme.cov html
family.mgcv html
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fixDependence html
formXtViX html
formula.gam html
fs.test html
full.score html
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gam.check html
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gam.convergence html
gam.fit html
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influence.gam html
initial.sp html
interpret.gam html
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k.check html
ldTweedie html
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ls.size html
magic html
magic.post.proc html
mgcv-FAQ html
mgcv-package html
mgcv-parallel html
Rd warning: /usr/src/tmp/Rtmp6ZwqEe/R.INSTALL98132cd0f7c/mgcv/man/mgcv-parallel.Rd:11: file link 'parallel' in package 'parallel' does not exist and so has been treated as a topic
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polys.plot html
predict.bam html
Rd warning: /usr/src/tmp/Rtmp6ZwqEe/R.INSTALL98132cd0f7c/mgcv/man/predict.bam.Rd:76: file link 'parLapply' in package 'parallel' does not exist and so has been treated as a topic
predict.gam html
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qq.gam html
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rig html
rmvn html
s html
scat html
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sp.vcov html
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summary.gam html
t2 html
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totalPenaltySpace html
trichol html
trind.generator html
twlss html
uniquecombs html
vcov.gam html
vis.gam html
ziP html
ziplss html
** building package indices
** testing if installed package can be loaded
* DONE (mgcv)
Making 'packages.html' ... done
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended'
make[1]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library'
building/updating vignettes for package 'grid' ...
building/updating vignettes for package 'parallel' ...
building/updating vignettes for package 'utils' ...
make[1]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library'
+ make -j8 pdf info
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[1] [2] Chapter 1 [3]
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[7] [8] [9] [10] [11] [12] Chapter 3 [13] [14] Chapter 4 [15] [16] [17]
[18] [19] [20] Chapter 5 [21] Chapter 6 [22] Chapter 7 [23] [24] [25] [26]
Chapter 8 [27] Chapter 9 [28] Appendix A [29] (Function and variable index)
[30]
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(Concept index) [31]
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[32] )
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[][]@textbf RNetCDF
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[1] [2] Chapter 1 [3]
Writing index file R-data.cp
[4] [5] [6] Chapter 2 [7] [8] [9] [10] [11] [12] Chapter 3 [13] [14] Chapter 4
[15] [16] [17] [18] [19] [20] Chapter 5 [21] Chapter 6 [22] Chapter 7 [23]
[24] [25] [26] Chapter 8 [27] Chapter 9 [28] Appendix A [29]
(Function and variable index) [30] [31] (Concept index) [32] [33] )
(see the transcript file for additional information)</usr/share/texmf-dist/font
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[1] [2] Chapter 1 [3]
Writing index file R-data.cp
[4] [5] [6] Chapter 2 [7] [8] [9] [10] [11] [12] Chapter 3 [13] [14] Chapter 4
[15] [16] [17] [18] [19] [20] Chapter 5 [21] Chapter 6 [22] Chapter 7 [23]
[24] [25] [26] Chapter 8 [27] Chapter 9 [28] Appendix A [29]
(Function and variable index) [30] [31] (Concept index) [32] [33] )
(see the transcript file for additional information)</usr/share/texmf-dist/font
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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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[] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX
11PICFLAGS)")[]
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[46] [47] [48] [49] [50] [51] [52]
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[]@texttt 'register' storage class specifier is deprecated and incompatible wi
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[61] [62] [63] [64] [65] Chapter 2 [66] [67] [68] [69] [70] [71] [72] [73]
[74] [75] [76] [77]
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-ally be used within the @textsl text[] @textrm part of
[80] [81] [82] [83] Chapter 3 [84] [85] [86] [87] [88] [89] [90] [91]
Chapter 4 [92] [93] [94] [95] [96]
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[97] [98] [99]
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[][][]@smallrm see [][]@smalltt http: / / llvm . org / devmtg / 2014-04 / PDFs
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[]@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de
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" -lpackB[]
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[]@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated
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NilValue);[]
[145] [146] Chapter 6 [147] [148] [149] [150] [151] [152] [153] [154] [155]
[156] [157] [158] [159] Warning: unbalanced parentheses in @def... [160]
[161] [162] [163] [164] [165]
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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 [166] [167] Chapter 8 [168] [169] [170]
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nst char *);[]
[172] [173] [174] [175] [176] [177]
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tive in-stall and
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[2] [3] [4] [5]
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[]@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t
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[]@textrm '[] and
[6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21]
[22] [23] [24] [25]
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[26] [27] [28]
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[][][]@smallrm The changes are linked from [][]@smalltt https: / / isocpp . org
/ std / standing-documents /
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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] [50] [51] [52]
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[]@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v
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[] @texttt if(jvn < 1.8) stop("Java >= 8 is needed for this package but not a
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[53] [54] [55] [56] [57] [58] [59]
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[]@texttt 'register' storage class specifier is deprecated and incompatible wi
th C++17[]
[60] [61] [62] [63] [64] [65] Chapter 2 [66] [67] [68] [69] [70] [71] [72]
[73] [74] [75] [76] [77]
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[]@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi
lename@texttt }[] @textrm and
[78] [79]
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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
[80] [81] [82] [83] Chapter 3 [84] [85] [86] [87] [88] [89] [90] [91]
Chapter 4 [92] [93] [94] [95] [96]
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[97] [98] [99]
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[][][]@smallrm see [][]@smalltt http: / / llvm . org / devmtg / 2014-04 / PDFs
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[100] [101]
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[103] [104] [105] [106] Chapter 5 [107] [108] [109] [110] [111] [112] [113]
[114] [115] [116]
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[]@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de
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[117] [118] [119] [120] [121] [122]
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[]@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated
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[133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144]
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[] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_
NilValue);[]
[145] [146] Chapter 6 [147] [148] [149] [150] [151] [152] [153] [154] [155]
[156] [157] [158] [159] Warning: unbalanced parentheses in @def... [160]
[161] [162] [163] [164] [165]
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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 [166] [167] Chapter 8 [168] [169] [170]
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[]@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s
tatic libR[]
[171]
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[]@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co
nst char *);[]
[172] [173] [174] [175] [176] [177]
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@texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra-
tive in-stall and
[178] [179]
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-core\R32[] @textrm or
(Function and variable index) [180] [181] [182]
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[2] [3] [4] [5]
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[]@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t
exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo
[]@textrm '[] and
[6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21]
[22] [23] [24] [25]
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[26] [27] [28]
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[][][]@smallrm The changes are linked from [][]@smalltt https: / / isocpp . org
/ std / standing-documents /
[29] [30]
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[] @texttt CXX="$(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] [50] [51] [52]
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[]@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v
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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
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version 52.0[]
[53] [54] [55] [56] [57] [58] [59]
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[]@texttt 'register' storage class specifier is deprecated and incompatible wi
th C++17[]
[60] [61] [62] [63] [64] [65] Chapter 2 [66] [67] [68] [69] [70] [71] [72]
[73] [74] [75] [76] [77]
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lename@texttt }[] @textrm and
[78] [79]
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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
[80] [81] [82] [83] Chapter 3 [84] [85] [86] [87] [88] [89] [90] [91]
Chapter 4 [92] [93] [94] [95] [96]
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[97] [98] [99]
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[][][]@smallrm see [][]@smalltt http: / / llvm . org / devmtg / 2014-04 / PDFs
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[100] [101]
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[]@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated
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[145] [146] Chapter 6 [147] [148] [149] [150] [151] [152] [153] [154] [155]
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[16] [17] [18] [19] [20] [21] Chapter 2 [22] [23] [24] [25] [26] Chapter 3
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[44] Chapter 8 [45] [46]
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hoice of
[47] [48] [49] [50] [51] [52] Chapter 9 [53] [54] Chapter 10 [55] Chapter 11
[56] Chapter 12 [57] [58] (Function and variable index) [59]
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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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[44] Chapter 8 [45] [46]
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hoice of
[47] [48] [49] [50] [51] [52] Chapter 9 [53] [54] Chapter 10 [55] Chapter 11
[56] Chapter 12 [57] [58] (Function and variable index) [59] [60]
(Concept index) [61] [62] )
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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 frame-works can con-tain mul-ti-ple ver-sions of R. It even-tu-ally re-
solves to
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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] Chapter 9 [53] [54] Chapter 10 [55] Chapter 11
[56] Chapter 12 [57] [58] (Function and variable index) [59] [60]
(Concept index) [61] [62] )
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[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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[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]
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[65] [66] [67] [68] Appendix D [69] [70] [71] (Function and variable index)
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[65] [66] [67] [68] Appendix D [69] [70] [71] (Function and variable index)
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[8]
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[]\T1/ptm/m/n/10 logical: should \T1/pcr/m/n/10 minlength \T1/ptm/m/n/10 be ob-
served strictly? Note that set-ting
[9] [10]
Underfull \hbox (badness 1072) in paragraph at lines 534--540
[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T
1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ',
[11] [12] (/usr/share/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [13] [14] [15]
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[]\T1/pcr/m/n/10 all.names(expr, functions = TRUE, max.names = -1L, unique = F
ALSE)
[16] [17] [18] [19]
Underfull \hbox (badness 1838) in paragraph at lines 1147--1150
[]\T1/ptm/m/n/10 If the calls to \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec-
tors of dif-fer-ent lengths, \T1/pcr/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis
t of length
[20] [21] [22] [23]
Underfull \hbox (badness 5862) in paragraph at lines 1381--1387
[]\T1/pcr/m/n/10 %% \T1/ptm/m/n/10 in-di-cates \T1/pcr/m/n/10 x mod y \T1/ptm/m
/n/10 and \T1/pcr/m/n/10 %/% \T1/ptm/m/n/10 in-di-cates in-te-ger di-vi-sion. I
t is guar-an-teed that
[24] [25] [26]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 1639--1639
[] \T1/pcr/m/n/10 cut.names = FALSE, col.names = names(x), fix.em
pty.names = TRUE,[]
Underfull \hbox (badness 3168) in paragraph at lines 1656--1663
[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , set-ting row n
ames and con-vert-ing col-umn names
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\T1/ptm/m/n/10 (to syn-tac-tic names: see [][]\T1/pcr/m/n/10 make.names[][][]\T
1/ptm/m/n/10 ) is op-tional. Note that all
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\T1/ptm/m/n/10 of \T1/phv/m/n/10 R\T1/ptm/m/n/10 's \T1/ptm/b/n/10 base \T1/ptm
/m/n/10 pack-age \T1/pcr/m/n/10 as.data.frame() \T1/ptm/m/n/10 meth-ods use \T1
/pcr/m/n/10 optional
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\T1/ptm/m/n/10 only for col-umn names treat-ment, ba-si-cally with the mean-ing
of
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[][]\T1/pcr/m/n/10 data.frame[][][](*, check.names = !optional)\T1/ptm/m/n/10 .
See also the
[27]
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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
[28]
Underfull \hbox (badness 10000) in paragraph at lines 1785--1787
[]\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
[29] [30]
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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)[]
[31]
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[]\T1/ptm/m/n/10 If it is a list, the equiv-a-lent of [][]\T1/pcr/m/n/10 list2e
nv[][][](x, parent = emptyenv())
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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]
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[]\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by
[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]
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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
[38] [39]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 2533--2533
[]\T1/pcr/m/n/10 attach(what, pos = 2L, name = deparse(substitute(what), backt
ick=FALSE),
[40] [41] [42]
Underfull \hbox (badness 5878) in paragraph at lines 2698--2703
[]\T1/ptm/m/n/10 The ex-trac-tion func-tion first looks for an ex-act match to
\T1/pcr/m/n/10 which \T1/ptm/m/n/10 amongst the at-
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\T1/ptm/m/n/10 tributes of \T1/pcr/m/n/10 x\T1/ptm/m/n/10 , then (un-less \T1/p
cr/m/n/10 exact = TRUE\T1/ptm/m/n/10 ) a unique par-tial match. (Set-ting
[43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56]
Underfull \hbox (badness 10000) in paragraph at lines 3656--3658
[]\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim
-ited by set-ting
[57] [58] [59]
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[] \T1/pcr/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...)
, recursive=recursive)
[60] [61] [62] [63]
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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
[64] [65]
Underfull \hbox (badness 4595) in paragraph at lines 4280--4283
[]\T1/ptm/m/n/10 is ICU avail-able for col-la-tion? See the help on [][]Com-par
-i-son[][][] and
[66] [67]
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[]\T1/pcr/m/n/9 cat(paste(letters, 100* 1:26), fill = TRUE, labels = paste0("{
", 1:10, "}:"))[]
[68]
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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
[69]
Underfull \hbox (badness 10000) in paragraph at lines 4556--4561
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 cbind \T1/ptm/m/n/10 data frame method is j
ust a wrap-per for
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[][]\T1/pcr/m/n/10 data.frame[][][](..., check.names = FALSE)\T1/ptm/m/n/10 . T
his means that it will split ma-
Underfull \hbox (badness 2181) in paragraph at lines 4556--4561
\T1/ptm/m/n/10 trix columns in data frame ar-gu-ments, and con-vert char-ac-ter
columns to fac-tors un-less
[70]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 4635--4635
[]\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna
mes (default)[]
[71] [72] [73] [74]
Underfull \hbox (badness 2521) in paragraph at lines 4888--4890
[]\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
[75] [76] [77] [78] [79] [80]
Underfull \hbox (badness 10000) in paragraph at lines 5285--5293
[]\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
[81] [82] [83] [84] [85] [86] [87] [88]
Underfull \hbox (badness 1796) in paragraph at lines 5845--5853
[]\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 : / /
[89] [90]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 6039--6039
[]\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 6042--6042
[]\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}[]
[91] [92] [93]
Underfull \hbox (badness 1635) in paragraph at lines 6208--6211
[]\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 6212--6215
[]\T1/ptm/m/n/10 Restarts are used for es-tab-lish-ing re-cov-ery pro-to-cols.
They can be es-tab-lished us-ing
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[]\T1/ptm/m/n/10 New restarts for \T1/pcr/m/n/10 withRestarts \T1/ptm/m/n/10 ca
n be spec-i-fied in sev-eral ways. The sim-plest is in
Underfull \hbox (badness 1308) in paragraph at lines 6243--6251
[]\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
[94] [95]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 6396--6396
[]\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e
ncoding"))[]
[96]
Overfull \hbox (107.35893pt too wide) in paragraph at lines 6438--6440
[]\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 :
[97] [98]
Underfull \hbox (badness 10000) in paragraph at lines 6580--6583
[]\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 6580--6583
\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
[99] [100]
Underfull \hbox (badness 1248) in paragraph at lines 6762--6768
\T1/ptm/m/n/10 Byte Or-der Mark if present (which it of-ten is for files and we
b-pages gen-er-ated by Mi-
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\T1/ptm/m/n/10 crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not rec-o
m-mended) when writ-ing it
Underfull \hbox (badness 10000) in paragraph at lines 6782--6784
[]\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in
g from
[101]
Underfull \hbox (badness 1067) in paragraph at lines 6824--6831
\T1/ptm/m/n/10 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http : / / standar
ds . freedesktop . org / clipboards-[]spec /
[102] [103]
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Overfull \hbox (4.38043pt too wide) in paragraph at lines 7016--7016
[]\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE"))
; close(con)[]
[105]
Underfull \hbox (badness 1231) in paragraph at lines 7141--7147
\T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the
first el-e-
[106] [107] [108] [109]
Underfull \hbox (badness 10000) in paragraph at lines 7352--7354
[]\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th
e call to
[110] [111]
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[]\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org") ## this redirect
s to https://[]
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[]\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h
igh-est, for
[112] [113] [114]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7735--7735
[]\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng
th.out = 24)[]
[115] [116]
Underfull \hbox (badness 8132) in paragraph at lines 7836--7840
[]\T1/ptm/m/n/10 logical: should char-ac-ter vec-tors be con-verted to fac-tors
? The
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\T1/ptm/m/n/10 `factory-fresh' de-fault is \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ,
but this can be changed by set-ting
Underfull \hbox (badness 10000) in paragraph at lines 7855--7865
[]\T1/pcr/m/n/10 data.frame \T1/ptm/m/n/10 con-verts each of its ar-gu-ments to
a data frame by call-ing
Underfull \hbox (badness 1062) in paragraph at lines 7855--7865
[][]\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
[117]
Overfull \hbox (4.63962pt too wide) in paragraph at lines 7887--7891
[]\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")
Underfull \hbox (badness 7451) in paragraph at lines 7926--7936
[][][]\T1/pcr/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.data.frame
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10
, [][]\T1/pcr/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 names[]
[][] \T1/ptm/m/n/10 (for the col-
Underfull \hbox (badness 3449) in paragraph at lines 7926--7936
\T1/ptm/m/n/10 umn names), [][]\T1/pcr/m/n/10 [.data.frame[][][] \T1/ptm/m/n/10
for sub-set-ting meth-ods and \T1/pcr/m/n/10 I(matrix(..)) \T1/ptm/m/n/10 ex-a
m-
[118] [119] [120] [121] [122] [123]
Underfull \hbox (badness 10000) in paragraph at lines 8358--8370
\T1/pcr/m/n/10 23:59:59", format = "%Y-%m-%d %H:%M:%S", tz = "UTC") \T1/ptm/m/n
/10 may give \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 8358--8370
\T1/ptm/m/n/10 and hence \T1/pcr/m/n/10 as.POSIXct("1969-12-31 23:59:59", tz =
"UTC") \T1/ptm/m/n/10 will give
[124] [125] [126]
Underfull \hbox (badness 5802) in paragraph at lines 8585--8589
[]\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 read.dcf(all = FALSE) \T1/ptm/m/n/10
reads the file byte-by-byte. This al-lows a
Underfull \hbox (badness 10000) in paragraph at lines 8620--8621
[][][]$\T1/pcr/m/n/10 https : / / www . debian . org / doc / debian-[]policy /
index . html #
[127] [128] [129]
Underfull \hbox (badness 10000) in paragraph at lines 8805--8809
[]\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
[130]
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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})[]
[131]
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[] \T1/pcr/m/n/10 backtick = mode(expr) %in% c("call", "expression", "(
", "function"),[]
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[] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "sh
owAttributes"),[]
[132] [133]
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[]\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
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[]\T1/ptm/m/n/10 Surround un-eval-u-ated ex-pres-sions, but not [][]\T1/pcr/m/n
/10 formula[][][]\T1/ptm/m/n/10 s, with
[134]
Underfull \hbox (badness 1132) in paragraph at lines 9130--9137
\T1/ptm/m/n/10 at-tributes as well, but not to use any of the other op-tions to
make the re-sult parseable.
[135]
Underfull \hbox (badness 1603) in paragraph at lines 9266--9269
[]\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
[136] [137] [138] [139] [140] [141] [142] [143] [144]
Underfull \hbox (badness 1917) in paragraph at lines 9872--9877
[]\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
[145]
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[]\T1/pcr/m/n/9 strd(provideDimnames(N, base= list(letters[-(1:9)], tail(LETTE
RS)))) # recycling[]
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[]\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling
on both levels[]
[146] [147]
Underfull \hbox (badness 1168) in paragraph at lines 10030--10035
\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 10069--10075
[]\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
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[]\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
[148] [149]
Underfull \hbox (badness 2828) in paragraph at lines 10235--10239
[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / IEEE _ 754-[]19
85$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / en . wikipedia .
Underfull \hbox (badness 10000) in paragraph at lines 10235--10239
\T1/pcr/m/n/10 org / wiki / IEEE _ 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr
/m/n/10 https : / / en . wikipedia . org / wiki / Double _
[150]
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[] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "showA
ttributes"))[]
[151] [152] [153]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10483--10483
[]\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon
th.abb[5:9]))
[154]
Underfull \hbox (badness 1629) in paragraph at lines 10557--10561
[]\T1/ptm/m/n/10 Promises will nor-mally only be en-coun-tered by users as a re
-sult of lazy-loading (when
[155] [156]
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered
from the re-verse
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\T1/ptm/m/n/10 and \T1/pcr/m/n/10 anyDuplicated\T1/ptm/m/n/10 , \T1/pcr/m/n/10
anyDuplicated(x, ...) \T1/ptm/m/n/10 is a ``gen-er-al-ized'' short-cut for
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[]\T1/pcr/m/n/10 duplicated(x, fromLast = TRUE) \T1/ptm/m/n/10 is equiv-a-lent
to but faster than
[157]
Underfull \hbox (badness 3735) in paragraph at lines 10701--10708
[]\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \
T1/pcr/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to
[158] [159]
Underfull \hbox (badness 10000) in paragraph at lines 10897--10900
[]\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
[160] [161] [162] [163] [164] [165] [166] [167] [168] [169]
Underfull \hbox (badness 5288) in paragraph at lines 11594--11596
[]\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val
ue of
Underfull \hbox (badness 3039) in paragraph at lines 11604--11609
[]\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
[170]
Underfull \hbox (badness 10000) in paragraph at lines 11664--11666
[]\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for
[171]
Underfull \hbox (badness 4569) in paragraph at lines 11781--11785
[]\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 11781--11785
\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
[172] [173]
Underfull \hbox (badness 10000) in paragraph at lines 11896--11898
[]\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
[174]
Underfull \hbox (badness 2790) in paragraph at lines 11939--11941
[]\T1/pcr/m/n/10 get0(): \T1/ptm/m/n/10 The object---as from [][]\T1/pcr/m/n/10
get[][][](x, *)\T1/ptm/m/n/10 --- if \T1/pcr/m/n/10 exists(x, *) \T1/ptm/m/n/1
0 is true, oth-er-wise
[175] [176]
Underfull \hbox (badness 4048) in paragraph at lines 12110--12120
[]\T1/pcr/m/n/10 as.expression \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-me
nt into an ex-pres-sion ob-ject. It is
Underfull \hbox (badness 3657) in paragraph at lines 12110--12120
\T1/ptm/m/n/10 generic, and only the de-fault method is de-scribed here. (The d
e-fault method calls
[177] [178] [179]
Underfull \hbox (badness 5460) in paragraph at lines 12358--12367
[]\T1/ptm/m/n/10 Both \T1/pcr/m/n/10 $ \T1/ptm/m/n/10 and \T1/pcr/m/n/10 [[ \T1
/ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a
l-
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\T1/ptm/m/n/10 lowed and no par-tial match-ing is done. The se-man-tics of thes
e op-er-a-tions are those
Underfull \hbox (badness 2707) in paragraph at lines 12358--12367
\T1/ptm/m/n/10 of \T1/pcr/m/n/10 get(i, env = x, inherits = FALSE)\T1/ptm/m/
n/10 . If no match is found then \T1/pcr/m/n/10 NULL
Underfull \hbox (badness 2818) in paragraph at lines 12358--12367
\T1/ptm/m/n/10 is re-turned. The re-place-ment ver-sions, \T1/pcr/m/n/10 $<- \T
1/ptm/m/n/10 and \T1/pcr/m/n/10 [[<-\T1/ptm/m/n/10 , can also be used. Again,
Underfull \hbox (badness 6978) in paragraph at lines 12358--12367
\T1/ptm/m/n/10 only char-ac-ter ar-gu-ments are al-lowed. The se-man-tics in th
is case are those of
[180] [181] [182] [183] [184] [185]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12732--12732
[]\T1/pcr/m/n/9 ## "avector" := vector that keeps attributes. Could provide
a constructor[]
[186] [187] [188] [189]
Underfull \hbox (badness 5119) in paragraph at lines 13017--13020
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 iconv \T1/ptm/m/n/10 this will give the im-
ple-men-ta-tion as well as the ver-sion, for ex-am-ple
[190] [191]
Underfull \hbox (badness 2221) in paragraph at lines 13178--13187
\T1/ptm/m/n/10 en-tries. If ar-gu-ment \T1/pcr/m/n/10 ordered \T1/ptm/m/n/10 is
true (or \T1/pcr/m/n/10 ordered() \T1/ptm/m/n/10 is used) the re-sult has clas
s
[192] [193] [194] [195]
Underfull \hbox (badness 2253) in paragraph at lines 13439--13441
[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
done: see
[196] [197]
Underfull \hbox (badness 10000) in paragraph at lines 13554--13556
[]\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/pcr/m
/n/10 PATH \T1/ptm/m/n/10 and \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 with
[198] [199]
Underfull \hbox (badness 10000) in paragraph at lines 13704--13706
[]\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See
[200]
Underfull \hbox (badness 10000) in paragraph at lines 13813--13817
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac
cess[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][][]\T1/ptm/m/n/10 ,
[201]
Underfull \hbox (badness 10000) in paragraph at lines 13824--13827
[][][]$\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[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 13868--13868
[]\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode
= "0777")[]
[202]
Underfull \hbox (badness 10000) in paragraph at lines 13960--13963
[][][]\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 ,
[203]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13970--13970
[]\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu
rsive = TRUE)[]
[204]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 14045--14045
[]\T1/pcr/m/n/9 ## will not give an error, maybe a warning about *all* locatio
ns it is found:[]
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[]\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F
ALSE,
Underfull \hbox (badness 7238) in paragraph at lines 14098--14105
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 findInterval \T1/ptm/m/n/10 finds
the in-dex of one vec-tor \T1/pcr/m/n/10 x \T1/ptm/m/n/10 in an-other, \T1/pcr
/m/n/10 vec\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 14098--14105
\T1/ptm/m/n/10 where the lat-ter must be non-decreasing. Where this is triv-ial
, equiv-a-lent to
Underfull \hbox (badness 2126) in paragraph at lines 14098--14105
\T1/pcr/m/n/10 apply( outer(x, vec, ">="), 1, sum)\T1/ptm/m/n/10 , as a mat-ter
of fact, the in-ter-nal al-go-
[205]
Underfull \hbox (badness 3965) in paragraph at lines 14106--14110
[]\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,
[206] [207]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 14269--14269
[] \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING)
Overfull \hbox (0.78088pt too wide) in paragraph at lines 14270--14270
[] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING)[]
[208] [209]
Underfull \hbox (badness 10000) in paragraph at lines 14349--14353
[]\T1/ptm/m/n/10 The C type \T1/pcr/m/n/10 Rcomplex \T1/ptm/m/n/10 is de-fined
in `\T1/pcr/m/n/10 Complex.h\T1/ptm/m/n/10 ' as a
Underfull \hbox (badness 1389) in paragraph at lines 14349--14353
\T1/pcr/m/n/10 typedef struct {double r; double i;}\T1/ptm/m/n/10 . It may or m
ay not be equiv-a-lent to
[210] [211]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 14497--14497
[]\T1/pcr/m/n/9 ## formals returns a pairlist. Arguments with no default have
type symbol (aka name).[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 14500--14500
[]\T1/pcr/m/n/9 ## formals returns NULL for primitive functions. Use it in co
mbination with[]
[212]
Underfull \hbox (badness 1168) in paragraph at lines 14584--14588
[]\T1/ptm/m/n/10 Either a log-i-cal spec-i-fy-ing whether el-e-ments of a real
or com-plex vec-
Underfull \hbox (badness 2012) in paragraph at lines 14584--14588
\T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger
penalty (see
[213]
Underfull \hbox (badness 6944) in paragraph at lines 14679--14682
[][][]\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 ,
[214]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 14704--14704
[]\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1
0,100,1000),[]
[215] [216]
Underfull \hbox (badness 10000) in paragraph at lines 14838--14840
[]\T1/pcr/m/n/10 prettyNum() \T1/ptm/m/n/10 is used for ``pret-ti-fy-ing'' (pos
-si-bly for-mat-ted) num-bers, also in
Overfull \hbox (48.78088pt too wide) in paragraph at lines 14857--14857
[] \T1/pcr/m/n/10 decimal.mark = getOption("OutDec"), input.d.mark =
decimal.mark,[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 14859--14859
[] \T1/pcr/m/n/10 zero.print = NULL, drop0trailing = FALSE, is.cmplx
= NA,[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 14862--14862
[]\T1/pcr/m/n/10 .format.zeros(x, zero.print, nx = suppressWarnings(as.numeric
(x)))[]
Underfull \hbox (badness 2790) in paragraph at lines 14868--14871
[]\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/ptm/m/n/10 the to-tal field width; if both \T1/pcr/m/n/10 digits \T1/ptm/
m/n/10 and \T1/pcr/m/n/10 width \T1/ptm/m/n/10 are un-spec-i-fied,
Underfull \hbox (badness 1024) in paragraph at lines 14899--14903
[]\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
[217]
Underfull \hbox (badness 10000) in paragraph at lines 14968--14970
[]\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
[218]
Underfull \hbox (badness 10000) in paragraph at lines 14974--14978
[]\T1/pcr/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b
ers on the dec-i-mal point,
Underfull \hbox (badness 10000) in paragraph at lines 14974--14978
\T1/ptm/m/n/10 so \T1/pcr/m/n/10 formatC(c(6.11, 13.1), digits = 2, format = "f
g") \T1/ptm/m/n/10 gives
Underfull \hbox (badness 10000) in paragraph at lines 14979--14987
[]\T1/pcr/m/n/10 prettyNum \T1/ptm/m/n/10 is the util-ity func-tion for pret-ti
-fy-ing \T1/pcr/m/n/10 x\T1/ptm/m/n/10 . \T1/pcr/m/n/10 x \T1/ptm/m/n/10 can be
com-plex (or
Underfull \hbox (badness 3601) in paragraph at lines 15013--15017
[]\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 decimal.mark \T1/ptm/m/n/10 in
\T1/pcr/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt
m/m/n/10 3.2.0: for use
Underfull \hbox (badness 3302) in paragraph at lines 15013--15017
\T1/ptm/m/n/10 within [][]\T1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in
pack-ages which might be used with ear-lier ver-sions: use
[219]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 15080--15080
[]\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 [220]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 15102--15102
[]\T1/pcr/m/n/9 doLC <- FALSE # R warns, so change to TRUE manually if you wan
t see the effect[]
[221] [222] [223] [224] [225] [226] [227] [228] [229] [230] [231]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 15920--15920
[]\T1/pcr/m/n/9 utils::tail(getLoadedDLLs(), 2) # the last 2 loaded ones, stil
l a DLLInfoList[]
[232] [233]
Underfull \hbox (badness 2418) in paragraph at lines 16029--16033
\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 16036--16039
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 name \T1/ptm/m/n/10 con-tains only one sym-b
ol name and \T1/pcr/m/n/10 unlist \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\T1/ptm/
m/n/10 , then the sin-gle
Underfull \hbox (badness 2326) in paragraph at lines 16064--16071
[][][]\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 ,
[234] [235] [236] [237]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 16310--16310
[]\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F
ALSE,
Underfull \hbox (badness 1867) in paragraph at lines 16335--16342
[]\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][]
[] (or char-ac-ter string for
[238] [239] [240] [241]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 16603--16603
[] \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around
"checking hack"[]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 16632--16632
[]\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 16683--16683
[] \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F
ALSE)[]
Underfull \hbox (badness 10000) in paragraph at lines 16689--16693
[]\T1/ptm/m/n/10 raw vec-tor con-tain-ing a [][]reg-u-lar ex-pres-sion[][][] (o
r fixed pat-tern for
Underfull \hbox (badness 1028) in paragraph at lines 16689--16693
\T1/pcr/m/n/10 fixed = TRUE\T1/ptm/m/n/10 ) to be matched in the given raw vec-
tor. Co-erced by
[243] [244] [245] [246] [247]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17048--17048
[]\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)))
[248] [249] [250] [251]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 17302--17302
[]\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F
ALSE)
[252] [253] [254]
Underfull \hbox (badness 2435) in paragraph at lines 17563--17565
[]\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/pcr/m/n/10 http : / / www
. unicode . org / reports / tr35 /
[255]
Underfull \hbox (badness 1867) in paragraph at lines 17605--17612
[]\T1/ptm/m/n/10 It is op-tional on Win-dows: if \T1/phv/m/n/10 R \T1/ptm/m/n/1
0 has been built against ICU, it will only be used if
Underfull \hbox (badness 1490) in paragraph at lines 17605--17612
\T1/ptm/m/n/10 en-vi-ron-ment vari-able \T1/pcr/m/n/10 R_ICU_LOCALE \T1/ptm/m/n
/10 is set or once \T1/pcr/m/n/10 icuSetCollate \T1/ptm/m/n/10 is called to se-
Underfull \hbox (badness 1490) in paragraph at lines 17605--17612
\T1/ptm/m/n/10 lect the lo-cale (as ICU and Win-dows dif-fer in their idea of l
o-cale names). Note that
Underfull \hbox (badness 2285) in paragraph at lines 17620--17622
[]\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1
0 http : / / userguide . icu-[]project . org /
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17628--17628
[]\T1/pcr/m/n/9 ## As we don\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 t know the current s
ettings, we can only reset to the default.[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17638--17638
[] \T1/pcr/m/n/9 icuSetCollate(locale = "da_DK", case_first = "default"); p
rint(sort(x))[]
[256]
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[]\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se
t = TRUE,
[257] [258]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 17792--17792
[]\T1/pcr/m/n/9 ### For functions ("closure"s): ------------------------------
----------------[]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 17798--17798
[]\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:[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17807--17807
[]\T1/pcr/m/n/9 op <- options(keep.source = TRUE) # and so, these have differi
ng "srcref" :[]
[259] [260]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 17934--17934
[]\T1/pcr/m/n/9 ## This is a (not atypical) case where it is better *not* to u
se ifelse(),[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17942--17942
[]\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):[]
[261] [262] [263]
Underfull \hbox (badness 10000) in paragraph at lines 18147--18149
[]\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
[264]
Underfull \hbox (badness 4217) in paragraph at lines 18231--18240
[][][]\T1/pcr/m/n/10 length[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 length<-[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 dimnames<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dim[][][]\T1/ptm
/m/n/10 , [][]\T1/pcr/m/n/10 dim<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 nam
es[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 names<-[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 2057) in paragraph at lines 18246--18262
[][][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.c
omplex[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.double[][][]\T1/ptm/m/n/10 ,
[][]\T1/pcr/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.logi
cal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.raw[][][]\T1/ptm/m/n/10 ,
[265] [266] [267] [268] [269] [270]
Underfull \hbox (badness 4699) in paragraph at lines 18660--18663
[]\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 ,
[271] [272]
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[]\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = "
GMT")[]
[273] [274]
Underfull \hbox (badness 4739) in paragraph at lines 18918--18920
[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
[275] [276] [277] [278] [279] [280] [281]
Underfull \hbox (badness 1430) in paragraph at lines 19331--19336
\T1/ptm/m/n/10 if \T1/pcr/m/n/10 simplify = "array"\T1/ptm/m/n/10 , an ar-ray i
f ap-pro-pri-ate, by ap-ply-ing \T1/pcr/m/n/10 simplify2array()\T1/ptm/m/n/10 .
Underfull \hbox (badness 10000) in paragraph at lines 19331--19336
\T1/pcr/m/n/10 sapply(x, f, simplify = FALSE, USE.NAMES = FALSE) \T1/ptm/m/n/10
is the same as
[282]
Underfull \hbox (badness 10000) in paragraph at lines 19392--19397
[]\T1/ptm/m/n/10 logical; if true, \T1/pcr/m/n/10 simplify2array() \T1/ptm/m/n/
10 will pro-duce a (``higher
Underfull \hbox (badness 10000) in paragraph at lines 19392--19397
\T1/ptm/m/n/10 rank'') ar-ray when ap-pro-pri-ate, whereas \T1/pcr/m/n/10 highe
r = FALSE \T1/ptm/m/n/10 would
Underfull \hbox (badness 5008) in paragraph at lines 19392--19397
\T1/ptm/m/n/10 re-turn a ma-trix (or vec-tor) only. These two cases cor-re-spon
d to
Underfull \hbox (badness 10000) in paragraph at lines 19392--19397
\T1/pcr/m/n/10 sapply(*, simplify = "array") \T1/ptm/m/n/10 or \T1/pcr/m/n/10 s
implify = TRUE\T1/ptm/m/n/10 , re-
[283]
Underfull \hbox (badness 10000) in paragraph at lines 19452--19459
[]\T1/pcr/m/n/10 vapply \T1/ptm/m/n/10 re-turns a vec-tor or ar-ray of type mat
ch-ing the \T1/pcr/m/n/10 FUN.VALUE\T1/ptm/m/n/10 . If
Underfull \hbox (badness 6364) in paragraph at lines 19452--19459
\T1/pcr/m/n/10 length(FUN.VALUE) == 1 \T1/ptm/m/n/10 a vec-tor of the same leng
th as \T1/pcr/m/n/10 X \T1/ptm/m/n/10 is re-turned, oth-
Underfull \hbox (badness 5064) in paragraph at lines 19452--19459
\T1/ptm/m/n/10 er-wise an ar-ray. If \T1/pcr/m/n/10 FUN.VALUE \T1/ptm/m/n/10 is
not an [][]\T1/pcr/m/n/10 array[][][]\T1/ptm/m/n/10 , the re-sult is a ma-trix
with
Underfull \hbox (badness 5908) in paragraph at lines 19452--19459
\T1/pcr/m/n/10 length(FUN.VALUE) \T1/ptm/m/n/10 rows and \T1/pcr/m/n/10 length(
X) \T1/ptm/m/n/10 columns, oth-er-wise an ar-ray \T1/pcr/m/n/10 a \T1/ptm/m/n/1
0 with
Underfull \hbox (badness 10000) in paragraph at lines 19468--19470
[]\T1/pcr/m/n/10 sapply(*, simplify = FALSE, USE.NAMES = FALSE) \T1/ptm/m/n/10
is equiv-a-lent to
[284]
Underfull \hbox (badness 1975) in paragraph at lines 19540--19543
[]\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
[285] [286] [287] [288] [289] [290]
Underfull \hbox (badness 1077) in paragraph at lines 19935--19940
[]\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
[291]
Underfull \hbox (badness 10000) in paragraph at lines 19949--19956
[][][]$\T1/pcr/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][]
\T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 http : / / curl . haxx . se /
[292]
Underfull \hbox (badness 10000) in paragraph at lines 20023--20027
[]\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
[293]
Underfull \hbox (badness 10000) in paragraph at lines 20153--20157
[]\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 20153--20157
[][]\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
[294] [295]
Underfull \hbox (badness 10000) in paragraph at lines 20251--20258
[][][]\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 ,
[296] [297]
Underfull \hbox (badness 10000) in paragraph at lines 20372--20376
[]\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
[298]
Underfull \hbox (badness 5161) in paragraph at lines 20442--20447
[]\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 20442--20447
\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 20442--20447
\T1/ptm/m/n/10 this li-cense is in file `\T1/pcr/m/n/10 $R_SHARE_DIR/licenses/L
GPL-2.1\T1/ptm/m/n/10 ' and can be viewed
Underfull \hbox (badness 10000) in paragraph at lines 20442--20447
\T1/ptm/m/n/10 by \T1/pcr/m/n/10 RShowDoc("LGPL-2.1")\T1/ptm/m/n/10 . Ver-sion
3 of the li-cense can be dis-played by
[299] [300]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 20609--20609
[] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. =
FALSE)[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 20613--20613
[] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. =
FALSE)[]
[301]
Underfull \hbox (badness 3343) in paragraph at lines 20669--20673
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac
cess[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 files[][][] \T1/ptm/m/n/10 for
many more file han-dling func-tions and
[302]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20755--20755
[] \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments
as for lists[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 20766--20766
[] \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1,
pr = 0.2))),[]
[303] [304]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 20877--20877
[]\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 20880--20880
[]\T1/pcr/m/n/9 attach("all.rda") # safer and will warn about masked objects w
/ same name in .GlobalEnv[]
[305]
Underfull \hbox (badness 6380) in paragraph at lines 20925--20930
[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways
be sup-
Underfull \hbox (badness 1337) in paragraph at lines 20983--20990
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 category = "LC_ALL" \T1/ptm/m/n/10 the de-t
ails of the string are system-specific: it might be
Underfull \hbox (badness 1960) in paragraph at lines 20983--20990
\T1/ptm/m/n/10 a sin-gle lo-cale name or a set of lo-cale names sep-a-rated by
\T1/pcr/m/n/10 "/" \T1/ptm/m/n/10 (So-laris, ma-cOS) or
Underfull \hbox (badness 1043) in paragraph at lines 20983--20990
\T1/ptm/m/n/10 not nec-es-sar-ily the case that the re-sult of \T1/pcr/m/n/10 f
oo <- Sys.getlocale() \T1/ptm/m/n/10 can be used in
[306]
Underfull \hbox (badness 2564) in paragraph at lines 21016--21019
[]\T1/ptm/m/n/10 Almost all the out-put rou-tines used by \T1/phv/m/n/10 R \T1/
ptm/m/n/10 it-self un-der Win-dows ig-nore the set-ting of
Overfull \hbox (4.38043pt too wide) in paragraph at lines 21046--21046
[]\T1/pcr/m/n/9 Sys.setlocale("LC_TIME", "de_DE.UTF-8") # Linux, macOS, other
Unix-alikes[]
[307]
Underfull \hbox (badness 1205) in paragraph at lines 21069--21074
\T1/ptm/m/n/10 10) log-a-rithms, and \T1/pcr/m/n/10 log2 \T1/ptm/m/n/10 com-put
es bi-nary (i.e., base 2) log-a-rithms. The gen-eral form
[308] [309]
Underfull \hbox (badness 1400) in paragraph at lines 21214--21218
[][][]\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
Overfull \hbox (36.83002pt too wide) in paragraph at lines 21234--21241
[]\T1/pcr/m/n/10 isTRUE(x) \T1/ptm/m/n/10 is the same as \T1/pcr/m/n/10 { is.lo
gical(x) && length(x) == 1 && !is.na(x) && x }\T1/ptm/m/n/10 ;
Underfull \hbox (badness 4886) in paragraph at lines 21234--21241
\T1/ptm/m/n/10 In ear-lier \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions, \T1/pcr/m
/n/10 isTRUE <- function(x) identical(x, TRUE)\T1/ptm/m/n/10 , had the
[310] [311]
Underfull \hbox (badness 2469) in paragraph at lines 21384--21390
[]\T1/pcr/m/n/10 as.logical \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-ment
to be of log-i-cal type. For [][]\T1/pcr/m/n/10 factor[][][]\T1/ptm/m/n/10 s,
Underfull \hbox (badness 1939) in paragraph at lines 21384--21390
\T1/ptm/m/n/10 this uses the [][]\T1/pcr/m/n/10 levels[][][] \T1/ptm/m/n/10 (la
-bels). Like [][]\T1/pcr/m/n/10 as.vector[][][] \T1/ptm/m/n/10 it strips at-tri
butes in-clud-ing names.
Underfull \hbox (badness 10000) in paragraph at lines 21384--21390
\T1/ptm/m/n/10 Char-ac-ter strings \T1/pcr/m/n/10 c("T", "TRUE", "True", "true"
) \T1/ptm/m/n/10 are re-garded as true,
[312] [313] [314] [315] [316]
Underfull \hbox (badness 10000) in paragraph at lines 21701--21703
[]\T1/ptm/m/n/10 The al-go-rithm used by \T1/pcr/m/n/10 make.unique \T1/ptm/m/n
/10 has the prop-erty that
[317] [318] [319] [320] [321]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 22005--22005
[]\T1/pcr/m/n/9 zN <- c(complex(real = NA , imaginary = r ), complex(real =
r , imaginary = NA ),[]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 22006--22006
[] \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 22009--22009
[]\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)[]
[322] [323]
Underfull \hbox (badness 1655) in paragraph at lines 22133--22137
[]\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion
(also known as a `clo-sure'):
[324] [325] [326]
Underfull \hbox (badness 2277) in paragraph at lines 22382--22385
[]\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.
[327] [328] [329] [330] [331] [332] [333] [334]
Underfull \hbox (badness 10000) in paragraph at lines 22867--22873
[]\T1/ptm/m/n/10 There are also lim-its on in-di-vid-ual ob-jects. The stor-age
space can-not ex-ceed
Underfull \hbox (badness 6316) in paragraph at lines 22867--22873
\T1/ptm/m/n/10 the ad-dress limit, and if you try to ex-ceed that limit, the er
-ror mes-sage be-gins
Underfull \hbox (badness 1484) in paragraph at lines 22899--22907
[]\T1/ptm/m/n/10 The address-space limit is 2Gb un-der 32-bit Win-dows un-less
the OS's de-fault has been
Underfull \hbox (badness 2951) in paragraph at lines 22899--22907
\T1/ptm/m/n/10 changed to al-low more (up to 3Gb). See [][]$\T1/pcr/m/n/10 http
s : / / www . microsoft . com / whdc /
Underfull \hbox (badness 3460) in paragraph at lines 22899--22907
\T1/pcr/m/n/10 system / platform / server / PAE / PAEmem . mspx$[][] \T1/ptm/m/
n/10 and [][]$\T1/pcr/m/n/10 https : / / msdn . microsoft .
[335]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 22976--22976
[] \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y =
all,[]
[336]
Underfull \hbox (badness 10000) in paragraph at lines 23030--23034
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 by \T1/ptm/m/n/10 or both \T1/pcr/m/n/10 by.
x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 by.y \T1/ptm/m/n/10 are of length 0 (a leng
th zero vec-
Underfull \hbox (badness 10000) in paragraph at lines 23030--23034
\T1/ptm/m/n/10 tor or \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 ), the re-sult, \T1/pcr
/m/n/10 r\T1/ptm/m/n/10 , is the \T1/ptm/m/it/10 Carte-sian prod-uct \T1/ptm/m/
n/10 of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , i.
e.,
[337] [338] [339] [340] [341] [342]
Underfull \hbox (badness 10000) in paragraph at lines 23481--23489
\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 ;
[343] [344]
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[]\T1/pcr/m/n/10 as.name \T1/ptm/m/n/10 first co-erces its ar-gu-ment in-ter-na
lly to a char-ac-ter vec-tor (so meth-ods for
[345]
Underfull \hbox (badness 7308) in paragraph at lines 23672--23678
[]\T1/ptm/m/n/10 For an [][]\T1/pcr/m/n/10 environment[][][] env\T1/ptm/m/n/10
, \T1/pcr/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond-
ing
Underfull \hbox (badness 5077) in paragraph at lines 23672--23678
\T1/ptm/m/n/10 list, i.e., \T1/pcr/m/n/10 names(as.list(env, all.names = TRUE))
\T1/ptm/m/n/10 which are also given by
Underfull \hbox (badness 10000) in paragraph at lines 23682--23685
[]\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute
via the gen-eral rules:
Underfull \hbox (badness 10000) in paragraph at lines 23682--23685
\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
[346] [347]
Underfull \hbox (badness 10000) in paragraph at lines 23834--23836
[]\T1/ptm/m/n/10 character string: par-tial match-ing to one of
[348] [349] [350] [351]
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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
[352] [353] [354] [355] [356] [357] [358]
Underfull \hbox (badness 2197) in paragraph at lines 24535--24539
[]\T1/ptm/m/n/10 Loading a names-pace should where pos-si-ble be silent, with s
tartup mes-sages given by
Underfull \hbox (badness 4048) in paragraph at lines 24535--24539
\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 24549--24553
[]\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
[359]
Underfull \hbox (badness 10000) in paragraph at lines 24642--24648
[]\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 24642--24648
\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
[360]
Underfull \hbox (badness 10000) in paragraph at lines 24655--24657
[]\T1/pcr/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m
ore ef-fi-cient than
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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:[]
[361] [362] [363]
Underfull \hbox (badness 10000) in paragraph at lines 24899--24905
[]\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
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[][]\T1/ptm/m/n/10 mode[][][] \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/10 ([][]type
[][][] \T1/pcr/m/n/10 "double" \T1/ptm/m/n/10 or type \T1/pcr/m/n/10 "integer"\
T1/ptm/m/n/10 ) and not a fac-tor,
Underfull \hbox (badness 10000) in paragraph at lines 24899--24905
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 oth-er-wise. That is, \T
1/pcr/m/n/10 is.integer(x) || is.double(x)\T1/ptm/m/n/10 , or
[364]
Underfull \hbox (badness 4120) in paragraph at lines 24985--24992
[]\T1/ptm/m/n/10 Hexadecimal con-stants start with \T1/pcr/m/n/10 0x \T1/ptm/m/
n/10 or \T1/pcr/m/n/10 0X \T1/ptm/m/n/10 fol-lowed by a nonempty se-quence from
[365] [366]
Underfull \hbox (badness 1694) in paragraph at lines 25121--25124
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor with suit-able nu-meric ver-sion strings
(see `De-tails');
[367] [368] [369] [370]
Underfull \hbox (badness 1603) in paragraph at lines 25368--25370
[]\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a
re con-verted by
[371]
Overfull \hbox (73.28088pt too wide) in paragraph at lines 25491--25499
\T1/pcr/m/n/10 c("datasets", "utils", "grDevices", "graphics", "stats",
"methods")\T1/ptm/m/n/10 .
[372] [373]
Underfull \hbox (badness 5475) in paragraph at lines 25628--25638
[]\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/pcr/m
/n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to
Underfull \hbox (badness 3271) in paragraph at lines 25670--25673
[]\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men
t vari-able
Underfull \hbox (badness 10000) in paragraph at lines 25685--25687
[]\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v
alue
[374] [375] [376]
Underfull \hbox (badness 3138) in paragraph at lines 25948--25954
[]\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 25948--25954
\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 25948--25954
\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
[377]
Underfull \hbox (badness 1194) in paragraph at lines 25961--25964
[]\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/pcr/m/n/10 create.post[][
][] \T1/ptm/m/n/10 (and hence[][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/n/10
and
Underfull \hbox (badness 1389) in paragraph at lines 25987--25989
[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
l HTTP server, see
Underfull \hbox (badness 10000) in paragraph at lines 25999--26003
[]\T1/ptm/m/n/10 string used as the user agent in HTTP(S) re-quests. If
Underfull \hbox (badness 6592) in paragraph at lines 25999--26003
\T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 , re-quests will be made with-out a user agen
t header. The de-fault is
Underfull \hbox (badness 10000) in paragraph at lines 26004--26010
[]\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by
Underfull \hbox (badness 3826) in paragraph at lines 26019--26024
[]\T1/ptm/m/n/10 Used by [][]\T1/pcr/m/n/10 install.packages[][][] \T1/ptm/m/n/
10 (and in-di-rectly
Overfull \hbox (49.4607pt too wide) in paragraph at lines 26025--26036
[]\T1/ptm/m/n/10 Used by [][]\T1/pcr/m/n/10 install.packages[][][](type = "both
")
Underfull \hbox (badness 1009) in paragraph at lines 26037--26040
[]\T1/ptm/m/n/10 default email-ing method used by [][]\T1/pcr/m/n/10 create.pos
t[][][] \T1/ptm/m/n/10 and hence [][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/
n/10 and
Underfull \hbox (badness 10000) in paragraph at lines 26047--26059
[]\T1/ptm/m/n/10 The de-fault type of pack-ages to be down-loaded and in-stalle
d -- see
Underfull \hbox (badness 1072) in paragraph at lines 26047--26059
[][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 . Pos-si-ble val-ues ar
e \T1/pcr/m/n/10 "source" \T1/ptm/m/n/10 (the de-fault ex-cept un-der a
[378]
Underfull \hbox (badness 10000) in paragraph at lines 26061--26068
[]\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/pcr/m/n/10 upda
te.packages[][][]\T1/ptm/m/n/10 . De-faults to
Underfull \hbox (badness 10000) in paragraph at lines 26061--26068
\T1/pcr/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i
-ties to prompt for a
Underfull \hbox (badness 6380) in paragraph at lines 26061--26068
\T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi
ng like
Overfull \hbox (34.78088pt too wide) in paragraph at lines 26061--26068
\T1/pcr/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr
an";
[379] [380] [381] [382]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26392--26392
[]\T1/pcr/m/n/9 system.time(o <- sort.list(xx, method = "radix")) # 0.007 sec,
300X faster[]
Underfull \hbox (badness 10000) in paragraph at lines 26405--26409
[]\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/pcr/m/n/10 X \T1/ptm/m/n
/10 and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/pcr/m/n/10 A \T1/ptm/
m/n/10 with di-men-sion
Underfull \hbox (badness 10000) in paragraph at lines 26405--26409
\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)]
[383] [384] [385] [386] [387]
Underfull \hbox (badness 4341) in paragraph at lines 26729--26731
[]\T1/pcr/m/n/10 paste0(..., collapse) \T1/ptm/m/n/10 is equiv-a-lent to \T1/pc
r/m/n/10 paste(..., sep = "", collapse)\T1/ptm/m/n/10 ,
Underfull \hbox (badness 4518) in paragraph at lines 26765--26771
[][][]\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
[388]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 26787--26787
[]\T1/pcr/m/n/9 ## Notice that the recycling rules make every input as long as
the longest input.[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26799--26799
[]\T1/pcr/m/n/9 paste("1st", "2nd", "3rd", collapse = ", ") # probably not wha
t you wanted[]
[389] [390] [391] [392] [393] [394] [395]
Underfull \hbox (badness 10000) in paragraph at lines 27233--27237
[]\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,
[396]
Underfull \hbox (badness 1796) in paragraph at lines 27299--27302
[]\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
[397] [398] [399]
Underfull \hbox (badness 10000) in paragraph at lines 27499--27502
[]\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
[400] [401] [402] [403] [404] [405] [406] [407] [408]
Underfull \hbox (badness 1226) in paragraph at lines 28131--28136
\T1/pcr/m/n/10 ncol(X) <= nrow(X)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 complete \T
1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 or the ar-gu-ment \T1/pcr/m/
n/10 ncol \T1/ptm/m/n/10 is greater than
[409]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 28176--28176
[] \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))[]
[410] [411] [412] [413]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 28442--28442
[]\T1/pcr/m/n/9 (nn <- "\u0126\u0119\u1114\u022d\u2001\u03e2\u0954\u0f3f\u13d3
\u147b\u203c")[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 28453--28453
[]\T1/pcr/m/n/9 n2 <- "\U0126\U0119\U1114\U022d\U2001\U03e2\U0954\U0f3f\U13d3\
U147b\U203c"[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 28459--28459
[]\T1/pcr/m/n/9 ## https://cran.r-project.org/doc/manuals/r-release/R-lang.htm
l#Literal-constants[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 28460--28460
[]\T1/pcr/m/n/9 ## and bug 16098 https://bugs.r-project.org/bugzilla3/show_bug
.cgi?id=16098[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 28463--28463
[]\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow
ed (parse errors)[]
[414]
Underfull \hbox (badness 7415) in paragraph at lines 28538--28542
[]\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
[415]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 28559--28559
[]\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu
l bottom-right note[]
[416]
Underfull \hbox (badness 2418) in paragraph at lines 28718--28729
[]\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
[417] [418]
Underfull \hbox (badness 1248) in paragraph at lines 28852--28859
\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 28852--28859
\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 /
[419] [420]
Underfull \hbox (badness 1533) in paragraph at lines 28968--28971
[]\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
[421]
Underfull \hbox (badness 1337) in paragraph at lines 29065--29068
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 finite \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE
\T1/ptm/m/n/10 , the min-i-mum and max-i-mum of all fi-nite val-ues is com-pute
d, i.e.,
[422]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 29113--29113
[] \T1/pcr/m/n/10 ties.method = c("average", "first", "last", "random", "m
ax", "min"))[]
Underfull \hbox (badness 1038) in paragraph at lines 29131--29142
[]\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/pcr/m/n/10 NA\
T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in
Underfull \hbox (badness 10000) in paragraph at lines 29143--29146
[]\T1/pcr/m/n/10 NA \T1/ptm/m/n/10 val-ues are never con-sid-ered to be equal:
for \T1/pcr/m/n/10 na.last = TRUE \T1/ptm/m/n/10 and
[423] [424]
Underfull \hbox (badness 1117) in paragraph at lines 29238--29244
\T1/ptm/m/n/10 e-ments which have a class in-cluded in \T1/pcr/m/n/10 classes \
T1/ptm/m/n/10 are re-placed by the re-sult of ap-ply-ing
[425] [426] [427] [428] [429] [430]
Underfull \hbox (badness 4048) in paragraph at lines 29616--29621
[]\T1/ptm/m/n/10 Either an ob-ject whose mode will give the mode of the vec-tor
to
Underfull \hbox (badness 4582) in paragraph at lines 29616--29621
\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 29616--29621
\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 ,
[431] [432] [433] [434] [435] [436] [437] [438]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 30162--30162
[]\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene
d as needed.[]
[439] [440] [441] [442]
Overfull \hbox (13.9408pt too wide) in paragraph at lines 30448--30450
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 ! " # $ % & \TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 ( )
* + , - . / : ; < = > ? @ [ \ ] ^ _ \TS1/pcr/m/n/10 ` \T1/pcr/m/n/10 { | } ~\T
1/ptm/m/n/10 '.
[443] [444] [445]
Underfull \hbox (badness 7558) in paragraph at lines 30664--30668
[]\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 30674--30676
[]\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 30679--30682
[][][]\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 30683--30685
[]\T1/ptm/m/n/10 The TRE doc-u-men-ta-tion at [][]$\T1/pcr/m/n/10 http : / / la
urikari . net / tre / documentation /
Underfull \hbox (badness 10000) in paragraph at lines 30686--30688
[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 http : / / p
ubs . opengroup . org / onlinepubs /
[446] [447] [448] [449] [450] [451]
Underfull \hbox (badness 10000) in paragraph at lines 31091--31095
[][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] []
[]NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple
x_[][][]
[452] [453] [454] [455] [456]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 31422--31422
[] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"))[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 31425--31425
[] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"),[]
[457] [458] [459]
Underfull \hbox (badness 3375) in paragraph at lines 31653--31660
\T1/ptm/m/n/10 pen if the spec-i-fied row names, i.e., \T1/pcr/m/n/10 value\T1/
ptm/m/n/10 , are in-valid, e.g., du-
Underfull \hbox (badness 2359) in paragraph at lines 31653--31660
\T1/ptm/m/n/10 pli-cated or \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 . The de-fault (is
back com-pat-i-ble), \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 , will sig-nal
Underfull \hbox (badness 2582) in paragraph at lines 31653--31660
\T1/ptm/m/n/10 an er-ror, where \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 will ``au-to-m
atic'' row names and \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 will call
[460] [461] [462]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 31806--31806
[] \T1/pcr/m/n/10 useHash = (!replace && is.null(prob) && size <= n/
2 && n > 1e7))[]
[463] [464]
Underfull \hbox (badness 10000) in paragraph at lines 31937--31941
[]\T1/pcr/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c
ur-rent
Underfull \hbox (badness 10000) in paragraph at lines 31937--31941
\T1/ptm/m/n/10 workspace', i.e., \T1/pcr/m/n/10 save(list = ls(all.names = TRUE
), file =
[465] [466] [467]
Underfull \hbox (badness 2302) in paragraph at lines 32188--32195
[]\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d
e-fined as $[]$,
Underfull \hbox (badness 2837) in paragraph at lines 32188--32195
\T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no
n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non
-missing
Underfull \hbox (badness 3815) in paragraph at lines 32188--32195
\T1/ptm/m/n/10 val-ues. In the case \T1/pcr/m/n/10 center = TRUE\T1/ptm/m/n/10
, this is the same as the stan-dard de-vi-a-tion,
Underfull \hbox (badness 2181) in paragraph at lines 32188--32195
\T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti
ons with-out cen-ter-ing, use
[468]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 32240--32240
[] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul =
FALSE)[]
[469]
Underfull \hbox (badness 1158) in paragraph at lines 32344--32349
[]\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
[470]
Underfull \hbox (badness 10000) in paragraph at lines 32371--32377
[]\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac-
ters
Underfull \hbox (badness 1953) in paragraph at lines 32371--32377
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 \a, \b, \f, \n, \r, \t, \v\T1/ptm/m/n/10 ' and o
c-tal and hex-adec-i-mal rep-re-
[471]
Underfull \hbox (badness 10000) in paragraph at lines 32447--32452
[]\T1/ptm/m/n/10 Note that since \T1/pcr/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r
a-tor and not a ter-mi-na-tor, read-ing a file by
Underfull \hbox (badness 6725) in paragraph at lines 32447--32452
\T1/pcr/m/n/10 scan("foo", sep = "\n", blank.lines.skip = FALSE) \T1/ptm/m/n/10
will give an empty
[472]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 32529--32529
[]\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data
", sep = "\n")
[473] [474] [475]
Underfull \hbox (badness 2809) in paragraph at lines 32793--32799
[]\T1/ptm/m/n/10 The fifth form gen-er-ates the se-quence \T1/pcr/m/n/10 1, 2,
..., length(from) \T1/ptm/m/n/10 (as if ar-gu-ment
Underfull \hbox (badness 7759) in paragraph at lines 32800--32803
[]\T1/ptm/m/n/10 The fi-nal form gen-er-ates the in-te-ger se-quence \T1/pcr/m/
n/10 1, 2, ..., length.out \T1/ptm/m/n/10 un-less
[476] [477] [478] [479] [480] [481] [482] [483] [484] [485] [486] [487]
Underfull \hbox (badness 1735) in paragraph at lines 33605--33611
\T1/ptm/m/n/10 Only prompts and (most) mes-sages con-tinue to ap-pear on the co
n-sole. Mes-sages sent
[488]
Underfull \hbox (badness 4303) in paragraph at lines 33621--33624
[]\T1/pcr/m/n/10 split = TRUE \T1/ptm/m/n/10 only splits \T1/phv/m/n/10 R \T1/p
tm/m/n/10 out-put (via \T1/pcr/m/n/10 Rvprintf\T1/ptm/m/n/10 ) and the de-fault
out-put from
[489] [490] [491] [492]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 33939--33939
[] \T1/pcr/m/n/10 method = c("auto", "shell", "quick", "radix"), index
.return = FALSE)[]
[493] [494] [495] [496]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 34191--34191
[] \T1/pcr/m/n/10 print. = TRUE, echo = TRUE, max.deparse.length
= Inf,[]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 34193--34193
[] \T1/pcr/m/n/10 deparseCtrl = c("keepInteger", "showAttributes"
, "keepNA"),[]
[497]
Underfull \hbox (badness 10000) in paragraph at lines 34236--34242
[][][]\T1/pcr/m/n/10 character[][][] \T1/ptm/m/n/10 vec-tor, passed as \T1/pcr/
m/n/10 control \T1/ptm/m/n/10 to [][]\T1/pcr/m/n/10 deparse[][][]()\T1/ptm/m/n/
10 , see
Underfull \hbox (badness 10000) in paragraph at lines 34236--34242
\T1/ptm/m/n/10 also [][]\T1/pcr/m/n/10 .deparseOpts[][][]\T1/ptm/m/n/10 . In \T
1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion <= 3.3.x, this was hard-
Underfull \hbox (badness 10000) in paragraph at lines 34236--34242
\T1/ptm/m/n/10 coded to \T1/pcr/m/n/10 "showAttributes"\T1/ptm/m/n/10 , which i
s the de-fault cur-rently;
Underfull \hbox (badness 2512) in paragraph at lines 34251--34253
[]\T1/ptm/m/n/10 integer; how many com-ment lines at the start of the file to s
kip if
[498]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 34347--34347
[]\T1/pcr/m/n/9 ## (all should look "as if on top level", e.g. non-assignments
should print:)[]
[499] [500] [501] [502] [503]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 34675--34675
[]\T1/pcr/m/n/9 ### Calculate \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 z-scores\TS1/pcr/m
/n/9 ' \T1/pcr/m/n/9 by group (standardize to mean zero, variance one)[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 34690--34690
[]\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is
being added[]
[504] [505] [506] [507] [508] [509]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 35129--35129
[]\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un
known")
Overfull \hbox (12.78088pt too wide) in paragraph at lines 35130--35130
[]\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile =
FALSE)[]
[510] [511] [512] [513]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 35394--35394
[]\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS
E, nowadays often three
[514]
Underfull \hbox (badness 10000) in paragraph at lines 35478--35488
[]\T1/ptm/m/n/10 A func-tion \T1/pcr/m/n/10 .First \T1/ptm/m/n/10 (and [][]\T1/
pcr/m/n/10 .Last[][][]\T1/ptm/m/n/10 ) can be de-fined in ap-pro-pri-ate `\T1/p
cr/m/n/10 .Rprofile\T1/ptm/m/n/10 '
Underfull \hbox (badness 10000) in paragraph at lines 35478--35488
\T1/ptm/m/n/10 or `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' files or have b
een saved in `\T1/pcr/m/n/10 .RData\T1/ptm/m/n/10 '. If you want
Underfull \hbox (badness 8113) in paragraph at lines 35478--35488
\T1/ptm/m/n/10 a dif-fer-ent set of pack-ages than the de-fault ones when you s
tart, in-sert a call
Underfull \hbox (badness 10000) in paragraph at lines 35478--35488
\T1/ptm/m/n/10 to [][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 in the `\T1/p
cr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n
/10 ' file. For ex-am-ple,
Underfull \hbox (badness 6542) in paragraph at lines 35478--35488
\T1/pcr/m/n/10 options(defaultPackages = character()) \T1/ptm/m/n/10 will at-ta
ch no ex-tra pack-ages on
Underfull \hbox (badness 5189) in paragraph at lines 35478--35488
\T1/ptm/m/n/10 startup (only the \T1/ptm/b/n/10 base \T1/ptm/m/n/10 pack-age) (
or set \T1/pcr/m/n/10 R_DEFAULT_PACKAGES=NULL \T1/ptm/m/n/10 as an en-vi-
Underfull \hbox (badness 4193) in paragraph at lines 35478--35488
\T1/ptm/m/n/10 ron-ment vari-able be-fore run-ning \T1/phv/m/n/10 R\T1/ptm/m/n/
10 ). Us-ing \T1/pcr/m/n/10 options(defaultPackages = "") \T1/ptm/m/n/10 or
[515]
Underfull \hbox (badness 10000) in paragraph at lines 35522--35528
[]\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 35522--35528
\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 35522--35528
\T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/i386/R
environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/pcr/m/n/10 .Renviron.i386\T1/ptm/m/
n/10 ' will be
Underfull \hbox (badness 1728) in paragraph at lines 35534--35541
[]\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 here is a
lso a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/Renviron\T1/ptm
/m/n/10 ' which is read
Underfull \hbox (badness 1038) in paragraph at lines 35534--35541
\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 35534--35541
\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
[516] [517] [518] [519] [520]
Underfull \hbox (badness 10000) in paragraph at lines 35875--35881
[]\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/pcr/m/n/10 form
at \T1/ptm/m/n/10 meth-ods is
[521] [522] [523]
Underfull \hbox (badness 1163) in paragraph at lines 36064--36071
[]\T1/ptm/m/n/10 Specific to \T1/phv/m/n/10 R \T1/ptm/m/n/10 is \T1/pcr/m/n/10
%OSn\T1/ptm/m/n/10 , which for out-put gives the sec-onds trun-cated to \T1/pcr
/m/n/10 0 <= n <= 6
Underfull \hbox (badness 8132) in paragraph at lines 36064--36071
\T1/ptm/m/n/10 dec-i-mal places (and if \T1/pcr/m/n/10 %OS \T1/ptm/m/n/10 is no
t fol-lowed by a digit, it uses the set-ting of
[524] [525] [526] [527]
Underfull \hbox (badness 1142) in paragraph at lines 36346--36352
[]\T1/ptm/m/n/10 Note that split-ting into sin-gle char-ac-ters can be done \T1
/ptm/m/it/10 via \T1/pcr/m/n/10 split = character(0) \T1/ptm/m/n/10 or
Overfull \hbox (0.78088pt too wide) in paragraph at lines 36361--36361
[] \T1/pcr/m/n/10 add the string to the left of the match to the ou
tput.[]
[528] [529] [530] [531]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 36609--36609
[] \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p
refix)[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 36653--36653
[]\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll
apse = "\n")[]
[532] [533] [534] [535] [536] [537] [538]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 37087--37087
[]\T1/pcr/m/n/9 ## In fact, you can pass vectors into several arguments, and e
verything gets added.[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 37090--37090
[]\T1/pcr/m/n/9 ## If there are missing values, the sum is unknown, i.e., also
missing, ....[]
[539]
Underfull \hbox (badness 10000) in paragraph at lines 37141--37148
[]\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 37141--37148
\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 37192--37192
[]\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau
lt precision
[540] [541] [542] [543]
Underfull \hbox (badness 2762) in paragraph at lines 37431--37440
\T1/ptm/m/n/10 of the el-e-ments in \T1/pcr/m/n/10 ...\T1/ptm/m/n/10 . If there
is a match then that el-e-ment is eval-u-ated un-less
Underfull \hbox (badness 1466) in paragraph at lines 37431--37440
\T1/ptm/m/n/10 it is miss-ing, in which case the next non-missing el-e-ment is
eval-u-ated, so for ex-am-ple
[544]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 37493--37493
[] \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw
ise: last"),"\n")[]
[545] [546]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 37658--37658
[]\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.
[547]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 37696--37696
[]\T1/pcr/m/n/9 if(.Platform$OS.type == "unix") ## on Unix-alikes such Linux,
macOS, FreeBSD:[]
[548]
Underfull \hbox (badness 3219) in paragraph at lines 37745--37750
[]\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 37745--37750
\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
[549]
Underfull \hbox (badness 2452) in paragraph at lines 37835--37838
\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 37835--37838
\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
[550] [551] [552]
Underfull \hbox (badness 10000) in paragraph at lines 38022--38026
[]\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 38037--38040
[]\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
[553] [554]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 38169--38169
[]\T1/pcr/m/n/9 is.symlink <- function(paths) isTRUE(nzchar(Sys.readlink(paths
), keepNA=TRUE))[]
[555]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 38239--38239
[]\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
[556] [557] [558]
Underfull \hbox (badness 1082) in paragraph at lines 38377--38380
[]\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
[559] [560]
Underfull \hbox (badness 1038) in paragraph at lines 38564--38567
[]\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
[561] [562] [563] [564] [565] [566]
Underfull \hbox (badness 1515) in paragraph at lines 38928--38931
[]\T1/ptm/m/n/10 Because of the way it is im-ple-mented, on a Unix-alike \T1/pc
r/m/n/10 stderr = TRUE \T1/ptm/m/n/10 im-plies
[567] [568] [569]
Underfull \hbox (badness 4096) in paragraph at lines 39169--39172
[]\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 ,
[570] [571]
Underfull \hbox (badness 10000) in paragraph at lines 39283--39287
[]\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.,
[572] [573]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 39437--39437
[] \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 39439--39439
[] \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),[]
[574]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 39441--39441
[] \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 39454--39456
[]\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
[575]
Underfull \hbox (badness 10000) in paragraph at lines 39534--39537
[][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$https : / / developer .
[576] [577]
Underfull \hbox (badness 1867) in paragraph at lines 39652--39656
[][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getTaskCallbackNames
[][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 https : / /
Underfull \hbox (badness 5475) in paragraph at lines 39714--39718
[][][]\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 \ [][]$\T1/pcr/m/n/10 https : / /
[578] [579] [580] [581] [582] [583] [584]
Underfull \hbox (badness 10000) in paragraph at lines 40132--40139
\T1/ptm/m/n/10 is also known as `\T1/pcr/m/n/10 GB\T1/ptm/m/n/10 ', `\T1/pcr/m/
n/10 GB-Eire\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 Europe/Belfast\T1/ptm/m/n/10 ', `
\T1/pcr/m/n/10 Europe/Guernsey\T1/ptm/m/n/10 ',
Underfull \hbox (badness 4467) in paragraph at lines 40188--40197
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 OlsonNames \T1/ptm/m/n/10 re-turn
s the time-zone names known to the cur-rently se-
Underfull \hbox (badness 3954) in paragraph at lines 40188--40197
\T1/ptm/m/n/10 lected Ol-son/IANA database. The system-specific lo-ca-tion in t
he file sys-tem varies,
Underfull \hbox (badness 10000) in paragraph at lines 40198--40206
[]\T1/ptm/m/n/10 Where \T1/phv/m/n/10 R \T1/ptm/m/n/10 was con-fig-ured with op
-tion `\T1/pcr/m/n/10 --with-internal-tzcode\T1/ptm/m/n/10 ' (the de-
Underfull \hbox (badness 10000) in paragraph at lines 40198--40206
\T1/ptm/m/n/10 fault on ma-cOS and Win-dows: rec-om-mended on So-laris), the da
tabase at
Underfull \hbox (badness 1303) in paragraph at lines 40198--40206
\T1/pcr/m/n/10 file.path(R.home("share"), "zoneinfo") \T1/ptm/m/n/10 is used by
de-fault: file `\T1/pcr/m/n/10 VERSION\T1/ptm/m/n/10 '
[585]
Underfull \hbox (badness 1337) in paragraph at lines 40264--40272
\T1/ptm/m/n/10 a file `\T1/pcr/m/n/10 localtime\T1/ptm/m/n/10 ', usu-ally un-de
r `\T1/pcr/m/n/10 /etc\T1/ptm/m/n/10 ' (but pos-si-bly un-der `\T1/pcr/m/n/10 /
usr/local/etc\T1/ptm/m/n/10 ' or
Underfull \hbox (badness 10000) in paragraph at lines 40273--40276
[]\T1/ptm/m/n/10 `Because the time zone iden-ti-fier is ex-tracted from the sym
-link tar-get name of
[586]
Underfull \hbox (badness 4429) in paragraph at lines 40330--40332
[][][]$\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-
Overfull \hbox (31.3804pt too wide) in paragraph at lines 40339--40339
[]\T1/pcr/m/n/9 ## typically some acronyms/aliases such as "UTC", "NZ", "MET",
"Eire", ..., but[]
[587] [588] [589]
Underfull \hbox (badness 10000) in paragraph at lines 40556--40558
[]\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
[590] [591]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 40678--40678
[]\T1/pcr/m/n/9 trace(pt, tracer = quote(cat(sprintf("tracing pt(*, ncp = %.15
g)\n", ncp))),[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 40680--40680
[]\T1/pcr/m/n/9 power.t.test(20, 1, power=0.8, sd=NULL) ##--> showing the ncp
root finding:[]
Underfull \vbox (badness 10000) has occurred while \output is active [592]
[593] [594] [595] [596]
Underfull \hbox (badness 6542) in paragraph at lines 41042--41044
[]\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
[597] [598] [599]
Underfull \hbox (badness 3460) in paragraph at lines 41208--41211
[]\T1/ptm/m/n/10 a [][]con-nec-tion[][][], or a char-ac-ter string nam-ing the
file to print to (via
Underfull \hbox (badness 1708) in paragraph at lines 41215--41223
[]\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 41215--41223
\T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][
]\T1/pcr/m/n/10 stderr[][][] \T1/ptm/m/n/10 con-nec-tion un-less
Underfull \hbox (badness 10000) in paragraph at lines 41224--41228
[]\T1/pcr/m/n/10 try \T1/ptm/m/n/10 is im-ple-mented us-ing [][]\T1/pcr/m/n/10
tryCatch[][][]\T1/ptm/m/n/10 ; for pro-gram-ming, in-
Underfull \hbox (badness 10000) in paragraph at lines 41224--41228
\T1/ptm/m/n/10 stead of \T1/pcr/m/n/10 try(expr, silent = TRUE)\T1/ptm/m/n/10 ,
some-thing like
Underfull \hbox (badness 3281) in paragraph at lines 41224--41228
\T1/pcr/m/n/10 tryCatch(expr, error = function(e) e) \T1/ptm/m/n/10 (or other s
im-ple er-ror han-dler func-
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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;
[600]
Underfull \hbox (badness 3895) in paragraph at lines 41307--41319
[]\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 41307--41319
\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 ,
[601] [602] [603]
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[]\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an
d sock-ets.
[604] [605]
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[]\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp
ression(1+x))[]
[606] [607] [608] [609] [610] [611]
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[]\T1/pcr/m/n/9 (xx <- intToUtf8(x, , TRUE)) # will only display in some local
es and fonts[]
[612]
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[]\T1/pcr/m/n/9 system(paste("od -x", foo)) # 2-byte units, correct on little-
endian platform[]
[613]
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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
[614]
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[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 is.vector\T1/ptm/m/n/10 , \T1/pcr/m/n/10 TR
UE \T1/ptm/m/n/10 or \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 . \T1/pcr/m/n/10 is.vec
tor(x, mode = "numeric") \T1/ptm/m/n/10 can be
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\T1/ptm/m/n/10 true for vec-tors of types \T1/pcr/m/n/10 "integer" \T1/ptm/m/n/
10 or \T1/pcr/m/n/10 "double" \T1/ptm/m/n/10 whereas \T1/pcr/m/n/10 is.vector(x
, mode =
[615] [616]
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[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di-
ately, even if
[617] [618]
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[] \T1/pcr/m/n/10 header = ngettext(n, "Warning message:\n", "Warning mes
sages:\n"),[]
[619]
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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 ...[]
[620] [621]
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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/pcr/m/n/10 which(*, arr.ind=TRUE)\T1/ptm/m/n/10 ). If [][]\T1/pcr/m/n/10 na
mes[][][](.dimnames) \T1/ptm/m/n/10 is not empty,
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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
[622]
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[][][]\T1/pcr/m/n/10 Logic[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 which.min[]
[][] \T1/ptm/m/n/10 for the in-dex of the min-i-mum or max-i-mum, and [][]\T1/p
cr/m/n/10 match[][][] \T1/ptm/m/n/10 for the
[623]
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[]\T1/ptm/m/n/10 If this ex-tremum is unique (or empty), the re-sults are the s
ame as
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\T1/ptm/m/n/10 (but more ef-fi-cient than) \T1/pcr/m/n/10 which(x == min(x, na.
rm = TRUE)) \T1/ptm/m/n/10 or
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[]\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:[]
[624] [625]
Underfull \hbox (badness 1622) in paragraph at lines 42993--42995
[]\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 .
[626] [627] [628] [629]
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[]\T1/ptm/m/n/10 This is a spe-cial case of rank-ing, but as a less gen-eral fu
nc-tion than [][]\T1/pcr/m/n/10 rank[][][]
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\T1/ptm/m/n/10 is more suit-able to be made generic. The de-fault method is sim
-i-lar to
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\T1/pcr/m/n/10 rank(x, ties.method = "min", na.last = "keep")\T1/ptm/m/n/10
, so \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 val-ues are
[630]
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[]\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
[631]
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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
[632]) (./compiler-pkg.tex
Chapter 2.
[633]
Underfull \hbox (badness 2884) in paragraph at lines 101--115
[]\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
[634] [635] [636]) (./datasets-pkg.tex
Chapter 3.
Underfull \hbox (badness 10000) in paragraph at lines 12--14
[]\T1/ptm/m/n/10 This pack-age con-tains a va-ri-ety of datasets. For a com-ple
te list, use
[637] [638] [639] [640] [641]
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[] \T1/pcr/m/n/9 plot(ff, data = anscombe, col = "red", pch = 21, bg = "orang
e", cex = 1.2,[]
[642]
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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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[644] [645] [646] [647]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[648] [649]
Overfull \hbox (66.81013pt 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", "nfGrou
pedData", "groupedData", "data.frame")
[650] [651]
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.
[652] [653]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[654] [655] [656] [657] [658]
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[]\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption
time (sec)")[]
[659] [660]
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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
[661] [662] [663]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[664]
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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)[]
[665] [666]
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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]]))))[]
[667] [668] [669] [670]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[671] [672] [673]
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[674] [675] [676] [677] [678]
Overfull \hbox (66.81013pt too wide) in paragraph at lines 2708--2711
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[679]
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[680]
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[682]
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[683] [684]
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[685]
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[]\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main =
1.2, pch = ".")[]
[686] [687] [688] [689] [690] [691] [692]
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[] \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t
he monthly one:[]
[693] [694]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[695]
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[696]
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\T1/ptm/m/it/10 Ed-u-ca-tion\T1/ptm/m/n/10 , \T1/ptm/b/n/10 3\T1/ptm/m/n/10 . [
][]$\T1/pcr/m/n/10 https : / / www . amstat . org / publications / jse / v3n3 /
datasets .
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[697]
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[] \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of
supplement")[]
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[]\T1/ptm/m/n/10 Time Se-ries Data Li-brary: [][]$\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 /
[698] [699] [700] [701] [702] [703] [704] [705] [706] [707] [708] [709]
[710] [711]) (./grDevices-pkg.tex [712]
Chapter 4.
[713] [714] [715] [716] [717] [718]
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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/pcr/m/n/10 quantile[][][](x, c(1,3)/4)\T1/ptm/m/n/10 . The hinges equal
the quar-tiles for odd $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 (where
[719]
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[]\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d
.pdf",[]
[720] [721] [722] [723] [724] [725] [726] [727] [728]
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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
[729]
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\T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 make.rgb[][][]\T1/ptm/m/n/10 . Built-in co
lor spaces may be ref-er-enced by strings: \T1/pcr/m/n/10 "XYZ"\T1/ptm/m/n/10 ,
\T1/pcr/m/n/10 "sRGB"\T1/ptm/m/n/10 ,
[730]
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[]\T1/ptm/m/n/10 For the white points [][]$\T1/pcr/m/n/10 http : / / www . efg2
. com / Lab / Graphics / Colors /
[731]
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[]\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab",
scale.in = 255))[]
[732]
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[]\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
[733] [734] [735]
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[]\T1/ptm/m/n/10 character: Which events can be gen-er-ated on
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\T1/ptm/m/n/10 this de-vice? Cur-rently this will be a sub-set of
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\T1/pcr/m/n/10 c("MouseDown", "MouseMove", "MouseUp", "Keybd")\T1/ptm/m/n/10
,
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[]\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 if the de-vice does not sup-port cap-ture,
oth-er-wise a ma-trix of color names (for
[736]
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[]\T1/ptm/m/n/10 logical; if \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion
also re-turns \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 when
Underfull \hbox (badness 10000) in paragraph at lines 1608--1612
[][]\T1/pcr/m/n/10 .Device[][][] == "null device" \T1/ptm/m/n/10 and [][]\T1/pc
r/m/n/10 getOption[][][]("device") \T1/ptm/m/n/10 is
[737] [738] [739]
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[]\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 1767--1772
\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
[740]
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[]\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res
= 72,[]
[741]
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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 ,
[742]
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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
[743] [744]
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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
[745] [746]
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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
[747] [748]
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[]\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r"
, yaxs = "r") {[]
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[750] [751] [752] [753] [754]
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[756] [757] [758] [759] [760]
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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))[]
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[]\T1/ptm/m/n/10 A length two in-te-ger vec-tor \T1/pcr/m/n/10 nr, nc \T1/ptm/m
/n/10 giv-ing the num-ber of rows and columns, ful-fill-ing
[761]
Underfull \hbox (badness 10000) in paragraph at lines 3248--3253
[]\T1/pcr/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas
ed on the inter-quartile range
[762] [763] [764]
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[]\T1/pcr/m/n/10 rainbow(n, s = 1, v = 1, start = 0, end = max(1, n - 1)/n, al
pha = 1)
[765]
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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 C in-te-ger for-mat such as
[766]
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[]\T1/ptm/m/n/10 title string to em-bed as the `\T1/pcr/m/n/10 /Title\T1/ptm/m/
n/10 ' field in the file. De-faults to
[767] [768] [769] [770]
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[]\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 ,
[771] [772] [773] [774] [775]
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\T1/pcr/m/n/10 / / www . adobe . com / products / postscript / pdfs / PLRM . pd
f$[][] \T1/ptm/m/n/10 or PDF [][]$\T1/pcr/m/n/10 https : / /
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\T1/pcr/m/n/10 www . adobe . com / devnet / acrobat / pdfs / pdf _ reference _
1-[]7 . pdf$[][] \T1/ptm/m/n/10 and in dec-i-
[776]
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[] \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz
w+p", "zip+p"),[]
[778]
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[]\T1/ptm/m/n/10 for \T1/pcr/m/n/10 type = "cairo"\T1/ptm/m/n/10 , giv-ing the
type of anti-aliasing (if any) to be
[779] [780]
Underfull \hbox (badness 1348) in paragraph at lines 4515--4518
[]\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
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[][][]\T1/pcr/m/n/10 capabilities[][][] \T1/ptm/m/n/10 to see if these de-vices
are sup-ported by this build of \T1/phv/m/n/10 R\T1/ptm/m/n/10 , and if
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[]\T1/pcr/m/n/9 ## Not run: dev.print(png, file = "myplot.png", width = 1024,
height = 768)[]
[781]
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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
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[]\T1/ptm/m/n/10 title string to em-bed as the \T1/pcr/m/n/10 Title \T1/ptm/m/n
/10 com-ment in the file. De-faults to
[782]
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\T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/pcr/
m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as
[783]
Underfull \hbox (badness 1755) in paragraph at lines 4739--4741
[]\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East
Asian lan-guages -- see
[784] [785]
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[]\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
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[][][]\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
[786] [787]
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\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
[788]
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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
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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 /
[789] [790]
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[]\T1/pcr/m/n/9 ## time ranges in diverse scales:% also in ../../../../tests/r
eg-tests-1c.R[]
[791]
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[]\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100
, ...)[]
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[]\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on
ly), de-fault
[792] [793]
Underfull \hbox (badness 10000) in paragraph at lines 5401--5403
[]\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
Underfull \hbox (badness 1072) in paragraph at lines 5437--5443
[]\T1/ptm/m/n/10 A fairly com-mon Mac prob-lem is no text ap-pear-ing on plots
due to cor-rupted or du-pli-
[794] [795] [796] [797] [798]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5759--5759
[]\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 5772--5775
[]\T1/pcr/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red
/green/blue) into HSV space
[799] [800] [801] [802] [803] [804] [805]
Underfull \hbox (badness 1189) in paragraph at lines 6169--6171
[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
[806]
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[]\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK
lan-guages and
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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
[807]
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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
[808]
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[] \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height
= 6, xpos = 0,[]
[809]
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[]\T1/ptm/m/n/10 These func-tions ap-ply only to an [][]\T1/pcr/m/n/10 X11[][][
] \T1/ptm/m/n/10 de-vice with \T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 --
[810]
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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 /
[811] [812] [813]
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\T1/ptm/m/n/10 ity of co-or-di-nates. These are com-pared af-ter round-ing them
via
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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
[814] [815] [816]) (./graphics-pkg.tex
Chapter 5.
Underfull \hbox (badness 10000) in paragraph at lines 16--18
[]\T1/ptm/m/n/10 For a com-plete list of func-tions with in-di-vid-ual help pag
es, use
[817] [818] [819] [820]
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[]\T1/ptm/m/n/10 Friendly, M. (1992), Graph-i-cal meth-ods for cat-e-gor-i-cal
data. \T1/ptm/m/it/10 SAS User Group In-ter-na-
[821] [822] [823]
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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
[824] [825] [826]
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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
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[]\T1/pcr/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p
tm/m/n/10 in-ter-face to the C func-tion \T1/pcr/m/n/10 CreateAtVector() \T1/pt
m/m/n/10 in
[827]
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[] \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n
intLog = 5))[]
[828] [829]
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[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , the lines whic
h di-vide ad-ja-cent (non-stacked!) bars
[830] [831] [832] [833] [834] [835] [836]
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[] \T1/pcr/m/n/10 horizontal = FALSE, add = FALSE, at = NULL, show.names =
NULL,[]
[837]
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\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 width, point char-ac-ter, point size ex-pan-sion, color, and bac
k-ground
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\T1/ptm/m/n/10 color. The de-fault \T1/pcr/m/n/10 medpch = NA \T1/ptm/m/n/10 su
p-presses the point, and
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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 ),
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[]\T1/ptm/m/n/10 When \T1/pcr/m/n/10 add = FALSE\T1/ptm/m/n/10 , \T1/pcr/m/n/10
xlim \T1/ptm/m/n/10 now de-faults to \T1/pcr/m/n/10 xlim = range(at, *) +
c(-0.5, 0.5)\T1/ptm/m/n/10 .
[838]
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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",[]
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[] \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl
ty = 1, outpch = NA)[]
[839] [840] [841] [842] [843]
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[][][]\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
[844]
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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 = "")[]
[845]
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[]\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col
umns,
[846] [847]
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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))[]
[848] [849] [850] [851]
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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
[852] [853] [854] [855] [856] [857]
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[]\T1/pcr/m/n/9 ## maybe change the desired number of tick marks: par(lab = c
(mx, my, 7))[]
[858] [859]
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\T1/ptm/m/n/10 they are the rel-a-tive fre-quen-cies \T1/pcr/m/n/10 counts/n \T
1/ptm/m/n/10 and in gen-eral sat-isfy
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[]\T1/ptm/m/n/10 Typical plots with ver-ti-cal bars are \T1/ptm/m/it/10 not \T1
/ptm/m/n/10 his-tograms. Con-sider [][]\T1/pcr/m/n/10 barplot[][][] \T1/ptm/m/n
/10 or
[860]
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[]\T1/pcr/m/n/9 ## Extreme outliers; the "FD" rule would take very large numbe
r of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 breaks\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[]
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[]\T1/pcr/m/n/9 length(hh$breaks) ## typically 1 million -- though 1e6 was "a
suggestion only"[]
[861]
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[][][]\T1/ptm/m/n/10 graphical pa-ram-e-ters[][][], or ar-gu-ments to [][]\T1/p
cr/m/n/10 hist.default[][][] \T1/ptm/m/n/10 such as
[862] [863] [864]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 3091--3091
[]\T1/pcr/m/n/9 identifyPch <- function(x, y = NULL, n = length(x), plot = FAL
SE, pch = 19, ...)[]
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[] \T1/pcr/m/n/9 ans <- identify(x[!sel], y[!sel], labels = which(!sel)
, n = 1, plot = plot, ...)[]
[865]
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[]\T1/ptm/m/n/10 a list of col-ors such as that gen-er-ated by [][]\T1/pcr/m/n/
10 rainbow[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 heat.colors[][][]\T1/ptm/m/
n/10 ,
[866]
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 useRaster \T1/ptm/m/n/10 is not spec-i-fied,
raster im-ages are used when the
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[][]\T1/pcr/m/n/10 getOption[][][]("preferRaster") \T1/ptm/m/n/10 is true, the
grid is reg-u-lar and ei-ther
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[][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage \T1/ptm/m/
n/10 is \T1/pcr/m/n/10 "yes" \T1/ptm/m/n/10 or it is
[867] [868] [869]
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[]\T1/pcr/m/n/9 barplot(yhist$counts, axes = FALSE, xlim = c(0, top), space =
0, horiz = TRUE)[]
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[] \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col =
par("fg"),[]
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[] \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace =
FALSE,[]
[870] [871] [872]
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[] \T1/pcr/m/n/9 text (1, y.leg[i] - 0.1, paste("cex=", formatC(cexv[i])), c
ex = 0.8, adj = 0)[]
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[] \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce
x = cexv[i])[]
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[] \T1/pcr/m/n/9 "text(c(3,3),2:3,\"c(rect(...)\")"), adj
= c(0, 0.3))[]
Underfull \vbox (badness 10000) has occurred while \output is active [873]
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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)[]
Underfull \vbox (badness 10000) has occurred while \output is active [874]
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[] \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste
("text.font =",i))[]
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[][][]\T1/pcr/m/n/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
[875] [876]
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[] \T1/pcr/m/n/10 log = "", ..., add = FALSE, verbose = getOption("verb
ose"))[]
[877]
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[]\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol
s given by
[878] [879]
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[]\T1/ptm/m/n/10 The mag-ni-fi-ca-tion to be used for axis an-no-ta-tion, as a
mul-ti-ple of
[880] [881] [882] [883]
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[]\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat
a con-tain
[884]
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\T1/ptm/m/n/10 which draws the ti-tle. You may want to spec-ify \T1/pcr/m/n/10
oma \T1/ptm/m/n/10 when chang-ing
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[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are
to be used, see
[885] [886]
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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))[]
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[]\T1/pcr/m/n/9 pairs(swiss, panel = panel.smooth, lwd = 2, cex = 1.5, col = "
blue") # hmm...[]
[887]
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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 ,
[888] [889]
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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.
[890] [891]
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[892 </usr/src/RPM/BUILD/R-3.5.3/library/graphics/help/figures/mai.pdf>]
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[893 </usr/src/RPM/BUILD/R-3.5.3/library/graphics/help/figures/oma.pdf>]
[894]
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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
[895]
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[]\T1/pcr/m/n/9 c(prof.pilots = 16, lawyers = 11, farmers = 10, salesmen = 9,
physicians = 9,[]
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[] \T1/pcr/m/n/9 mechanics = 6, policemen = 6, managers = 6, engineers = 5, t
eachers = 4,[]
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[897]
Underfull \hbox (badness 3954) in paragraph at lines 5325--5328
[]\T1/ptm/m/n/10 a ex-pan-sion fac-tor ap-plied to the \T1/pcr/m/n/10 z \T1/ptm
/m/n/10 co-or-di-nates. Of-ten used with
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\T1/ptm/m/n/10 are con-trolled by graph-ics pa-ram-e-ters \T1/pcr/m/n/10 "cex.l
ab"\T1/ptm/m/n/10 /\T1/pcr/m/n/10 "font.lab" \T1/ptm/m/n/10 and
[898] [899] [900] [901]
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[]\T1/pcr/m/n/9 pie(c(Sky = 78, "Sunny side of pyramid" = 17, "Shady side of p
yramid" = 5),[]
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[] \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow
3"), border = FALSE)[]
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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.,
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\T1/pcr/m/n/10 type = "punkte" \T1/ptm/m/n/10 be-ing equiv-a-lent to \T1/pcr/m/
n/10 type = "p" \T1/ptm/m/n/10 for S com-
[902] [903] [904] [905] [906] [907] [908]
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[]\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth) # numeric v
ector ~ factor[]
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[]\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes") # ext
remely silly[]
[909] [910] [911] [912] [913] [914]
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[]\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see
[915] [916]
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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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[][]
[917 </usr/src/RPM/BUILD/R-3.5.3/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,[]
[918]
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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 [919]
[920]
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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)))))[]
[921]
Underfull \hbox (badness 2600) in paragraph at lines 6978--6980
[]\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
[922] [923] [924]
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[]\T1/ptm/m/n/10 color for rect-an-gle bor-der(s). The de-fault means \T1/pcr/m
/n/10 par("fg")\T1/ptm/m/n/10 . Use
[925]
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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))[]
[926] [927] [928] [929] [930] [931]
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[]\T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), sp
ace = "Lab")[]
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[]\T1/pcr/m/n/9 ## label the 20 very lowest-density points,the "outliers" (wit
h obs.number):[]
[932]
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[]\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0
, add = TRUE),[]
[933] [934] [935] [936] [937]
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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,[]
[938]
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[] \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10
, key.loc = 0:1,[]
[939] [940]
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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, ...)[]
[941] [942]
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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
[943] [944]
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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),[]
[945] [946]
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[]\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll
apse = ","),[]
[947] [948] [949]
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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...")[]
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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
[950]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit
s}) has been already used, duplicate ignored
<to be read again>
\relax
l.8805 \HeaderA{units}{Graphical Units}{units}
[951]
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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
[952] [953]
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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)[]
[954]) (./grid-pkg.tex
Chapter 6.
[955] [956] [957] [958] [959] [960]
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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
[961] [962] [963] [964] [965] [966] [967] [968] [969] [970]
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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-
[971] [972] [973] [974]
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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
[975] [976] [977] [978] [979] [980]
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[] \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75)
, list(...)))[]
[981] [982] [983]
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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")[]
[984]
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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 ,
[985]
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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
[986] [987] [988]
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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
[989] [990] [991]
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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-
[992] [993] [994]
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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)[]
[995] [996] [997] [998]
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[] \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1
, "inches"),[]
[999] [1000] [1001] [1002]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3179--3179
[] \T1/pcr/m/n/9 children=vpList(viewpor
t(name="vp2"))))[]
[1003] [1004]
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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")))[]
[1005]
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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
[1006]
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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,[]
[1007] [1008] [1009]
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[] \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant
i-clockwise")[]
[1010]
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[] \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other
anti-clockwise")[]
[1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021]
[1022]
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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
[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-
[1024] [1025] [1026]
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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 to add and sub-tract unit ob-jects (e.g., \T1/pcr/m/n/10 unit(1,
"npc") - unit(1, "inches")\T1/ptm/m/n/10 ),
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\T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob-
jects (e.g.,
[1046] [1047] [1048] [1049] [1050]
Underfull \hbox (badness 1867) in paragraph at lines 6187--6189
[]\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
[1051]
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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 ,
[1052] [1053]
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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
[1054] [1055] [1056]
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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"))))[]
[1057]) (./methods-pkg.tex [1058]
Chapter 7.
[1059] [1060]
Underfull \hbox (badness 1688) in paragraph at lines 166--171
\T1/ptm/m/n/10 func-tion. See that doc-u-men-ta-tion also for de-tails of how c
o-erce meth-ods work. Use
[1061] [1062] [1063]
Underfull \hbox (badness 1348) in paragraph at lines 392--395
[][][]\T1/pcr/m/n/10 GroupGenericFunctions[][][] \T1/ptm/m/n/10 for other in-fo
r-ma-tion about group generic func-tions; [][]Meth-
[1064] [1065]
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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[]
[1066]
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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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[1069]
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[]\T1/ptm/m/n/10 A ma-trix (or ma-trix like ob-ject) com-bin-ing the columns (o
r rows) of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y\T1/ptm/m/n/10 .
Note
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\T1/ptm/m/n/10 that meth-ods must con-struct [][]\T1/pcr/m/n/10 colnames[][][]
\T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 rownames[][][] \T1/ptm/m/n/10 from the co
r-re-spond-ing col-
Underfull \hbox (badness 1789) in paragraph at lines 791--797
\T1/ptm/m/n/10 umn and row names of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr
/m/n/10 y \T1/ptm/m/n/10 (but not from de-pars-ing ar-gu-ment names such as in
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[1081] [1082]
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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[]
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[]\T1/pcr/m/n/10 signature(from = "ANY", to = "environment")\T1/ptm/m/n/10 : ca
lls
[1083] [1084]
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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
[1085] [1086] [1087]
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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 =
[1088] [1089]
Underfull \hbox (badness 10000) in paragraph at lines 2328--2332
[]\T1/ptm/m/n/10 To see the ac-tual ta-ble (an en-vi-ron-ment) used for meth-od
s dis-patch, call
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[]\T1/pcr/m/n/10 ## Deprecated in 2010 and defunct in 2015 for \code{table = F
ALSE}:[]
[1090] [1091] [1092]
Underfull \hbox (badness 3792) in paragraph at lines 2574--2577
[]\T1/ptm/m/n/10 As you might ex-pect [][]\T1/pcr/m/n/10 setGeneric[][][] \T1/p
tm/m/n/10 and [][]\T1/pcr/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o
b-jects of class
Underfull \hbox (badness 1194) in paragraph at lines 2605--2609
[]\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
[1093]
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[]\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin
g(where))[]
[1094] [1095] [1096]
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[]\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers
ions visible:[]
[1097] [1098] [1099] [1100] [1101] [1102] [1103]
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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,
Underfull \hbox (badness 6268) in paragraph at lines 3403--3408
\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
[1104] [1105]
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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
[1106]
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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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[]
[1107] [1108]
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[] \T1/pcr/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric",
longitude = "numeric", altitude = "numeric"))
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Underfull \hbox (badness 10000) in paragraph at lines 3809--3810
[]\T1/pcr/m/n/10 setMethod("plot", c("Pos", "missing"), function(x, y, ...) {
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[]\T1/pcr/m/n/10 GPS <- setClass("GPS", slots = c(time = "POSIXt"), contains =
"Pos")
[1109]
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[]\T1/pcr/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character")
, contains = "numeric")
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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
[1110] [1111] [1112]
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[]\T1/pcr/m/n/10 signature(from = "ANY", to = "call")\T1/ptm/m/n/10 . A method
ex-ists for
[1113] [1114]
Underfull \hbox (badness 1629) in paragraph at lines 4247--4256
\T1/pcr/m/n/10 x$ensureLocal() \T1/ptm/m/n/10 on the ob-ject. The other way is
to mod-ify a field ex-plic-itly by
[1115]
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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,[]
[1116]
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[]\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w
here)
[1117] [1118]
Underfull \hbox (badness 1033) in paragraph at lines 4531--4538
\T1/ptm/m/n/10 se-lect-ing class \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/10 for \T
1/pcr/m/n/10 y \T1/ptm/m/n/10 would pro-duce a method as-so-ci-ated with the si
g-na-ture
[1119]
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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 ,
[1120] [1121] [1122]
Underfull \hbox (badness 10000) in paragraph at lines 4811--4820
[]\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
[1123] [1124] [1125] [1126]
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[]\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate
inheritance[]
[1127]
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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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[1129]
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[]\T1/pcr/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...)
[1130]
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[]\T1/pcr/m/n/10 signature(method = "MethodWithNext")\T1/ptm/m/n/10 : used in-t
er-nally by
[1131]
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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
[1132] [1133] [1134]
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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
[1135]
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
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\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1136]
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
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\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1137] [1138] [1139] [1140]
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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
[1141] [1142]
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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
[1143]
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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
[1144]
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[]\T1/ptm/m/n/10 Establish a traced ver-sion of method
[1145]
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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
[1146]
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[1148] [1149]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}
[1150]
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[]\T1/pcr/m/n/10 ## Create a new object from the class or use the replacement
version of as().[]
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\T1/ptm/m/n/10 i-nat-ing all the for-mally de-fined slots and turn-ing off the
S4 bit of the ob-ject. With
[1151] [1152]
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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")[]
[1153]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}
pdfTeX warning (ext4): destination wi
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
[1154]
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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 ,
[1155] [1156]
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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
[1157] [1158]
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[]\T1/ptm/m/n/10 If no sub-class/superclass re-la-tion-ship pro-vides a method,
\T1/pcr/m/n/10 as \T1/ptm/m/n/10 looks for an in-her-
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\T1/ptm/m/n/10 ited method, but ap-ply-ing, in-her-i-tance for the ar-gu-ment \
T1/pcr/m/n/10 from \T1/ptm/m/n/10 only, not for the
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\T1/ptm/m/n/10 ar-gu-ment \T1/pcr/m/n/10 to \T1/ptm/m/n/10 (if you think about
it, you'll prob-a-bly agree that you wouldn't
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\T1/ptm/m/n/10 want the re-sult to be from some class other than the \T1/pcr/m/
n/10 Class \T1/ptm/m/n/10 spec-i-fied). Thus,
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\T1/pcr/m/n/10 selectMethod("coerce", sig, useInherited= c(from=TRUE, to= FALSE
))
[1159] [1160] [1161] [1162] [1163] [1164] [1165] [1166] [1167] [1168] [1169]
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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
[1170]
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[]\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact
er(),
[1171]
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[] \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class
Def =,[]
[1172] [1173] [1174] [1175]
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[]
[1176] [1177] [1178]
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")[]
[1179] [1180]
Underfull \vbox (badness 2302) has occurred while \output is active [1181]
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[]
[1182] [1183] [1184] [1185]
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[]
[1186]
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[]\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][]
[1187]
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][]
[1188] [1189] [1190] [1191] [1192] [1193] [1194] [1195] [1196]
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
[1197] [1198] [1199] [1200]) (./parallel-pkg.tex
Chapter 8.
Underfull \hbox (badness 2418) in paragraph at lines 14--16
[]\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/pcr
/m/n/10 "L\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[
][][]: see
[1201]
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
[1202] [1203]
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
[1204]
Underfull \hbox (badness 10000) in paragraph at lines 318--326
[]\T1/ptm/m/n/10 On Sparc So-laris \T1/pcr/m/n/10 logical = FALSE \T1/ptm/m/n/1
0 re-turns the num-ber of phys-i-cal cores and
[1205] [1206]
Underfull \hbox (badness 10000) in paragraph at lines 443--445
[]\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
[1207] [1208] [1209] [1210]
Underfull \hbox (badness 1917) in paragraph at lines 742--751
[]\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 742--751
\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
[1211] [1212]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 824--824
[] \T1/pcr/m/n/10 mc.cleanup = TRUE, mc.allow.recursive = TRUE, affini
ty.list = NULL)[]
[1213]
Underfull \hbox (badness 10000) in paragraph at lines 884--887
[]\T1/pcr/m/n/10 mclapply \T1/ptm/m/n/10 is a par-al-lelized ver-sion of [][]\T
1/pcr/m/n/10 lapply[][][]\T1/ptm/m/n/10 , pro-vided \T1/pcr/m/n/10 mc.cores > 1
\T1/ptm/m/n/10 : for
[1214]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 1005--1005
[]\T1/pcr/m/n/9 mclapply(list(A, A, A), first, mc.preschedule = FALSE, affinit
y.list = affL)[]
[1215]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 1009--1009
[]\T1/pcr/m/n/9 # To optimize the overall execution time elements of X are sch
eduled to suitable CPUs[]
[1216]
Underfull \hbox (badness 5388) in paragraph at lines 1119--1124
[]\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 1143--1151
[]\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
[1217]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1180--1180
[]\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)[]
[1218] [1219]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1296--1296
[] \T1/pcr/m/n/9 as.integer(runif(N, 1, 12)), as.integer(runif
(N, 1, 28)))[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1310--1310
[]\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 1339--1342
[]\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
[1220]
Underfull \hbox (badness 3375) in paragraph at lines 1385--1387
[]\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
[1221] [1222]) (./splines-pkg.tex
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
[1223] [1224] [1225] [1226] [1227] [1228] [1229]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 492--492
[]\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height, women, bSpl
ine = TRUE))[]
[1230] [1231] [1232] [1233]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 706--706
[]\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37,
sparse = TRUE)))[]
[1234] [1235] [1236]) (./stats-pkg.tex
Chapter 10.
[1237]
Underfull \hbox (badness 2781) in paragraph at lines 65--68
[]\T1/pcr/m/n/10 .MFclass \T1/ptm/m/n/10 re-turns a char-ac-ter string, one of
\T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ordered"\T1/ptm/m/n/10
, \T1/pcr/m/n/10 "factor"\T1/ptm/m/n/10 ,
[1238] [1239] [1240] [1241] [1242]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 417--417
[]\T1/pcr/m/n/9 add1(glm.D93, scope = ~outcome*treatment, test = "Rao") ## Pea
rson Chi-square[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 438--438
[]\T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet =
FALSE)
[1243] [1244] [1245] [1246] [1247] [1248] [1249]
Underfull \hbox (badness 1024) in paragraph at lines 847--849
[]\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
[1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257]
Underfull \hbox (badness 10000) in paragraph at lines 1391--1393
[]\T1/ptm/m/n/10 an es-ti-mate of the ra-tio of scales. (Only present if ar-gu-
ment
[1258]
Underfull \hbox (badness 10000) in paragraph at lines 1508--1512
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("aov", "lm") \T1/ptm/m/n/
10 or for mul-ti-ple re-sponses of class
Underfull \hbox (badness 10000) in paragraph at lines 1508--1512
\T1/pcr/m/n/10 c("maov", "aov", "mlm", "lm") \T1/ptm/m/n/10 or for mul-ti-ple e
r-ror strata of class
Underfull \hbox (badness 1490) in paragraph at lines 1508--1512
\T1/pcr/m/n/10 c("aovlist", "[][]listof[][][]")\T1/ptm/m/n/10 . There are [][]\
T1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 summary[][][] \
T1/ptm/m/n/10 meth-ods avail-able for
[1259] [1260] [1261] [1262]
Underfull \hbox (badness 10000) in paragraph at lines 1773--1777
[]\T1/ptm/m/n/10 function to be called to han-dle miss-ing val-ues. Cur-rently,
via
Underfull \hbox (badness 2197) in paragraph at lines 1773--1777
\T1/pcr/m/n/10 na.action = na.pass\T1/ptm/m/n/10 , only Yule-Walker method can
han-dle miss-
[1263] [1264]
Underfull \hbox (badness 4303) in paragraph at lines 1874--1876
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 x \T1/ptm/m/n/10 con-tains miss-ing val-ues,
see [][]\T1/pcr/m/n/10 NA[][][]\T1/ptm/m/n/10 , also con-sider us-ing [][]\T1/
pcr/m/n/10 arima[][][]()\T1/ptm/m/n/10 , pos-si-bly with
[1265] [1266] [1267]
Underfull \hbox (badness 10000) in paragraph at lines 2096--2101
[]\T1/ptm/m/n/10 logical; if true, the AR pa-ram-e-ters are trans-formed to en-
sure
Underfull \hbox (badness 10000) in paragraph at lines 2096--2101
\T1/ptm/m/n/10 that they re-main in the re-gion of sta-tion-ar-ity. Not used fo
r
Underfull \hbox (badness 1371) in paragraph at lines 2096--2101
\T1/pcr/m/n/10 method = "CSS"\T1/ptm/m/n/10 . For \T1/pcr/m/n/10 method = "ML"\
T1/ptm/m/n/10 , it has been ad-van-ta-geous
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[]\T1/ptm/m/n/10 optional nu-meric vec-tor of the same length as the to-tal num
-ber of pa-
Underfull \hbox (badness 4608) in paragraph at lines 2102--2108
\T1/ptm/m/n/10 ram-e-ters. If sup-plied, only \T1/pcr/m/n/10 NA \T1/ptm/m/n/10
en-tries in \T1/pcr/m/n/10 fixed \T1/ptm/m/n/10 will be var-ied.
[1268] [1269]
Underfull \hbox (badness 3965) in paragraph at lines 2183--2185
[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
[1270] [1271] [1272]
Underfull \hbox (badness 1221) in paragraph at lines 2457--2462
[]\T1/ptm/m/n/10 optional nu-meric vec-tor of the same length as the to-tal num
-ber of pa-
Underfull \hbox (badness 4608) in paragraph at lines 2457--2462
\T1/ptm/m/n/10 ram-e-ters. If sup-plied, only \T1/pcr/m/n/10 NA \T1/ptm/m/n/10
en-tries in \T1/pcr/m/n/10 fixed \T1/ptm/m/n/10 will be var-ied.
[1273]
Underfull \hbox (badness 3965) in paragraph at lines 2534--2536
[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
[1274] [1275]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2679--2679
[]\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F
ALSE)
[1276] [1277] [1278] [1279]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2919--2919
[]\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co
l = "green")[]
[1280] [1281] [1282]
Overfull \hbox (19.88992pt too wide) in paragraph at lines 3128--3130
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Bartlett test of homoge
neity of variances"\T1/ptm/m/n/10 .
[1283]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3176--3176
[]\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 3177--3177
[]\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p =
FALSE)[]
[1284]
Underfull \hbox (badness 2726) in paragraph at lines 3260--3276
\T1/ptm/m/n/10 We have slightly tweaked the orig-i-nal ``TOMS 708'' al-go-rithm
, and en-hanced for
[1285] [1286] [1287] [1288] [1289]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3568--3568
[]\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = "
log density",[]
[1290] [1291] [1292] [1293]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 3846--3846
[]\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit
df = 0)
[1294] [1295] [1296] [1297] [1298]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4135--4135
[]\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 4136--4136
[]\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p
= FALSE)[]
[1299] [1300] [1301]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4374--4374
[]\T1/pcr/m/n/9 chisq.test(x, p = p) # maybe doubtful
, but is ok![]
[1302] [1303] [1304]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4542--4542
[] \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df =
df, ncp = L)),[]
[1305]
Underfull \hbox (badness 3989) in paragraph at lines 4634--4641
[]\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 =
[1306] [1307]
Underfull \hbox (badness 2080) in paragraph at lines 4754--4756
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 "aov" \T1/ptm/m/n/10 method does not re-por
t aliased co-ef-fi-cients (see [][]\T1/pcr/m/n/10 alias[][][]\T1/ptm/m/n/10 ) b
y de-fault where
Underfull \hbox (badness 2050) in paragraph at lines 4757--4763
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 complete \T1/ptm/m/n/10 ar-gu-ment also ex-
ists for com-pat-i-bil-ity with [][]\T1/pcr/m/n/10 vcov[][][] \T1/ptm/m/n/10 me
th-ods, and \T1/pcr/m/n/10 coef
Underfull \hbox (badness 4954) in paragraph at lines 4757--4763
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 aov \T1/ptm/m/n/10 meth-ods for other classes
should typ-i-cally also keep the \T1/pcr/m/n/10 complete = *
Underfull \hbox (badness 4726) in paragraph at lines 4757--4763
\T1/ptm/m/n/10 be-hav-ior in sync. By that, with \T1/pcr/m/n/10 p <- length(coe
f(obj, complete = TF))\T1/ptm/m/n/10 ,
[1308] [1309] [1310] [1311]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5019--5019
[]\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 5021--5021
[]\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))[]
[1312]
Underfull \hbox (badness 7397) in paragraph at lines 5108--5112
[]\T1/ptm/m/n/10 For con-sis-tency, \T1/pcr/m/n/10 sparse \T1/ptm/m/n/10 is an
ar-gu-ment to all these con-trast func-tions, how-ever
Underfull \hbox (badness 7326) in paragraph at lines 5108--5112
\T1/pcr/m/n/10 sparse = TRUE \T1/ptm/m/n/10 for \T1/pcr/m/n/10 contr.poly \T1/p
tm/m/n/10 is typ-i-cally point-less and is rarely use-ful for
[1313] [1314]
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[]\T1/pcr/m/n/9 ## using sparse contrasts: % useful, once model.matrix() works
with these :[]
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[]\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil
ter"))
Underfull \hbox (badness 2680) in paragraph at lines 5287--5289
[]\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
[1315]
Underfull \hbox (badness 10000) in paragraph at lines 5292--5294
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 r <- convolve(x, y, type = "open") \T1/ptm/m
/n/10 and \T1/pcr/m/n/10 n <- length(x)\T1/ptm/m/n/10 ,
[1316] [1317]
Underfull \hbox (badness 1436) in paragraph at lines 5470--5475
[]\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 5470--5475
\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 5470--5475
\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 ,
[1318] [1319] [1320]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5668--5668
[] \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE,
...)[]
[1321]
Underfull \hbox (badness 1168) in paragraph at lines 5740--5745
[]\T1/ptm/m/n/10 For Spear-man's test, p-values are com-puted us-ing al-go-rith
m AS 89 for $\OML/cmm/m/it/10 n < \OT1/cmr/m/n/10 1290$ \T1/ptm/m/n/10 and
[1322] [1323]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5835--5835
[]\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center =
TRUE,
[1324] [1325] [1326]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 6020--6020
[]\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter =
NULL)
[1327] [1328]
Underfull \hbox (badness 10000) in paragraph at lines 6183--6188
[]\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
[1329] [1330] [1331]
Underfull \hbox (badness 5954) in paragraph at lines 6379--6381
[]\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn
, see
[1332]
Underfull \hbox (badness 2503) in paragraph at lines 6461--6464
[]\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 6465--6467
[]\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 6468--6473
\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,
[1333]
Underfull \hbox (badness 7238) in paragraph at lines 6504--6507
[][][]\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
[1334]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6539--6539
[]\T1/pcr/m/n/9 plot(dend2$lower[[3]], nodePar = list(col = 4), horiz = TRUE,
type = "tr")[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6554--6554
[]\T1/pcr/m/n/9 ## merge() all parts back (using default \TS1/pcr/m/n/9 '\T1/p
cr/m/n/9 height\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 instead of original one):[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6569--6569
[]\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h
oriz = TRUE)[]
[1335] [1336] [1337] [1338]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6813--6813
[] \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker
n = TRUE))))[]
[1339] [1340]
Underfull \vbox (badness 10000) has occurred while \output is active [1341]
[1342] [1343] [1344]
Underfull \hbox (badness 10000) in paragraph at lines 7211--7215
\T1/pcr/m/n/10 "maximum"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "manhattan"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "canberra"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "binary" \T1/ptm/
m/n/10 or
[1345]
Underfull \hbox (badness 6493) in paragraph at lines 7310--7313
[]\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T
1/pcr/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the
[1346] [1347]
Underfull \hbox (badness 10000) in paragraph at lines 7447--7450
[]\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/pcr/m/n/10 ht
tps : / / CRAN . R-[]project . org / view =
[1348] [1349] [1350] [1351] [1352] [1353]
Underfull \hbox (badness 10000) in paragraph at lines 7857--7862
[]\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 , ...,
[1354] [1355]
Overfull \hbox (33.6622pt too wide) in paragraph at lines 7995--7997
[]\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 (
\OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1
\OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1
/cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/pcr/m/n/10 -pexp(t, r, lower = FALSE, log
= TRUE)\T1/ptm/m/n/10 .
[1356] [1357] [1358]
Underfull \hbox (badness 1210) in paragraph at lines 8212--8214
[]\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
[1359] [1360] [1361] [1362] [1363] [1364] [1365]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 8687--8687
[]\T1/pcr/m/n/9 ## Not run: glm(y ~ x, family = quasi(variance = "mu^3", link
= "log")) # fails[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 8690--8690
[]\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit
"), start = c(0,1))[]
[1366] [1367]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 8828--8828
[]\T1/pcr/m/n/9 quantile(rel.err(qf(2*p - 1, df1 = 1, df2 = df), qt(p, df)^2),
.90) # ~= 7e-9[]
[1368]
Underfull \hbox (badness 1859) in paragraph at lines 8867--8872
\T1/ptm/m/n/10 If \T1/pcr/m/n/10 inverse \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\
T1/ptm/m/n/10 , the (un-nor-mal-ized) in-verse Fourier trans-form is re-turned,
i.e., if
[1369] [1370] [1371]
Underfull \hbox (badness 2865) in paragraph at lines 9113--9122
[]\T1/ptm/m/n/10 For larger than $\OT1/cmr/m/n/10 2 \OMS/cmsy/m/n/10 ^^B \OT1/c
mr/m/n/10 2$ \T1/ptm/m/n/10 ta-bles and \T1/pcr/m/n/10 hybrid = TRUE\T1/ptm/m/n
/10 , asymp-totic chi-squared prob-a-bil-i-
Underfull \hbox (badness 1331) in paragraph at lines 9113--9122
\T1/ptm/m/n/10 ties are only used if the `Cochran con-di-tions' (or mod-i-fied
ver-sion thereof) spec-i-fied by
[1372] [1373]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 9255--9255
[] \T1/pcr/m/n/9 dimnames = list(income = c("< 15k", "15-25k", "25-4
0k", "> 40k"),[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 9256--9256
[] \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Mod
erateS", "VeryS")))[]
[1374] [1375] [1376]
Overfull \hbox (61.88992pt too wide) in paragraph at lines 9435--9437
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Fligner-Killeen test of
homogeneity of variances"\T1/ptm/m/n/10 .
[1377] [1378] [1379] [1380] [1381] [1382] [1383]
Underfull \hbox (badness 2443) in paragraph at lines 9888--9894
[][][]\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);
[1384] [1385] [1386]
Underfull \hbox (badness 3758) in paragraph at lines 10101--10104
[]\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
[1387] [1388] [1389] [1390]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 10337--10337
[] \T1/pcr/m/n/10 x = FALSE, y = TRUE, singular.ok = TRUE, contrasts = NULL
, ...)[]
Underfull \hbox (badness 4518) in paragraph at lines 10363--10368
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1391]
Underfull \hbox (badness 4132) in paragraph at lines 10402--10406
[]\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth
od
[1392]
Underfull \hbox (badness 10000) in paragraph at lines 10507--10510
[]\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
[1393] [1394] [1395]
Underfull \hbox (badness 2142) in paragraph at lines 10711--10714
[]\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 ^^@
[1396]
Underfull \hbox (badness 1708) in paragraph at lines 10792--10796
[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
[1397]
Underfull \hbox (badness 10000) in paragraph at lines 10834--10840
[][][]\T1/pcr/m/n/10 glm[][][] \T1/ptm/m/n/10 for com-put-ing \T1/pcr/m/n/10 gl
m.obj\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 anova.glm[][][]\T1/ptm/m/n/10 ; the co
r-re-spond-ing \T1/ptm/m/it/10 generic \T1/ptm/m/n/10 func-tions,
Underfull \hbox (badness 1418) in paragraph at lines 10872--10877
\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 (=
[1398] [1399]
Underfull \hbox (badness 2635) in paragraph at lines 11005--11008
\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
[1400] [1401] [1402]
Underfull \hbox (badness 1694) in paragraph at lines 11190--11193
[]\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these
de-fault to
Underfull \hbox (badness 1337) in paragraph at lines 11209--11218
[]\T1/ptm/m/n/10 If ei-ther is a vec-tor (of `weights') then the ap-pro-pri-ate
den-dro-gram is re-ordered ac-cord-
Underfull \hbox (badness 3049) in paragraph at lines 11209--11218
\T1/ptm/m/n/10 ing to the sup-plied val-ues sub-ject to the con-straints im-pos
ed by the den-dro-gram, by
[1403]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 11291--11291
[]\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col
SideColors = cc,[]
[1404]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11324--11324
[] \T1/pcr/m/n/10 optim.start = c(alpha = 0.3, beta = 0.1, gamma =
0.1),[]
Underfull \hbox (badness 10000) in paragraph at lines 11337--11341
[]\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
[1405] [1406] [1407]
Underfull \hbox (badness 7379) in paragraph at lines 11517--11520
[]\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds
[][]\T1/pcr/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq
uiv-a-lent of
[1408] [1409]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11656--11656
[]\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4)
, DEV.FUN = nD)[]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has
been already used, duplicate ignored
<to be read again>
\relax
l.11671 \aliasA{hat}{influence.measures}{hat}
[1410]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11724--11724
[]\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA
LSE),[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11736--11736
[]\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE),
...)[]
[1411]
Underfull \hbox (badness 1062) in paragraph at lines 11785--11790
[]\T1/ptm/m/n/10 The op-tional \T1/pcr/m/n/10 infl\T1/ptm/m/n/10 , \T1/pcr/m/n/
10 res \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sd \T1/ptm/m/n/10 ar-gu-ments are ther
e to en-cour-age the use of these di-
Underfull \hbox (badness 1052) in paragraph at lines 11802--11804
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main
ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing
[1412] [1413]
Underfull \hbox (badness 3623) in paragraph at lines 11956--11958
[]\T1/pcr/m/n/10 rel.tol \T1/ptm/m/n/10 can-not be less than \T1/pcr/m/n/10 max
(50*.Machine$double.eps, 0.5e-28) \T1/ptm/m/n/10 if
[1414] [1415]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12052--12052
[] \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend =
TRUE,[]
[1416]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12145--12145
[] \T1/pcr/m/n/9 interaction.plot(agegp, tobgp, ncases/ncontrols, trace.label
= "tobacco",[]
[1417]
Underfull \hbox (badness 10000) in paragraph at lines 12193--12196
[]\T1/ptm/m/n/10 For nor-mally $\OML/cmm/m/it/10 N\OT1/cmr/m/n/10 (\OML/cmm/m/i
t/10 m; \OT1/cmr/m/n/10 1)$ \T1/ptm/m/n/10 dis-tributed $\OML/cmm/m/it/10 X$\T1
/ptm/m/n/10 , the ex-pected value of \T1/pcr/m/n/10 IQR(X) \T1/ptm/m/n/10 is
[1418] [1419] [1420]
Underfull \hbox (badness 4441) in paragraph at lines 12388--12390
[]\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is
fit-ted to
Underfull \hbox (badness 10000) in paragraph at lines 12395--12397
[]\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
[1421]
Underfull \hbox (badness 4739) in paragraph at lines 12418--12420
[]\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
[1422]
Underfull \hbox (badness 2753) in paragraph at lines 12487--12489
[]\T1/ptm/m/n/10 R bug re-port PR#14682 (2011-2013) [][]$\T1/pcr/m/n/10 https :
/ / bugs . r-[]project . org / bugzilla3 /
[1423] [1424]
Underfull \hbox (badness 1292) in paragraph at lines 12612--12616
\T1/ptm/m/n/10 than one, it means the con-vo-lu-tion of ker-nels of di-men-sion
\T1/pcr/m/n/10 m[j]\T1/ptm/m/n/10 , for
[1425]
Underfull \hbox (badness 10000) in paragraph at lines 12725--12727
[]\T1/ptm/m/n/10 an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of class \T1/pcr/m/
n/10 "kmeans"\T1/ptm/m/n/10 , typ-i-cally the re-sult \T1/pcr/m/n/10 ob \T1/ptm
/m/n/10 of
Underfull \hbox (badness 2894) in paragraph at lines 12731--12735
[]\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 12731--12735
\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
[1426] [1427] [1428] [1429] [1430] [1431] [1432] [1433] [1434] [1435] [1436]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13438--13438
[]\T1/pcr/m/n/9 dimnames(cAS) <- list(paste("it =", format(1:10)), c("intercep
t", "slope"))[]
[1437]
Underfull \hbox (badness 4518) in paragraph at lines 13481--13486
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1438] [1439]
Underfull \hbox (badness 10000) in paragraph at lines 13680--13684
[]\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
,
[1440] [1441] [1442]
Underfull \hbox (badness 6995) in paragraph at lines 13865--13867
[][][]\T1/pcr/m/n/10 naresid[][][] \T1/ptm/m/n/10 is ap-plied to the re-sults a
nd so will fill in with \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 s it the fit had
[1443] [1444]
Underfull \hbox (badness 1163) in paragraph at lines 14013--14021
\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 ,
[1445] [1446]
Underfull \hbox (badness 4518) in paragraph at lines 14133--14138
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1447] [1448]
Underfull \hbox (badness 10000) in paragraph at lines 14271--14275
[]\T1/ptm/m/n/10 Only for the (de-fault) case \T1/pcr/m/n/10 (surface =
Underfull \hbox (badness 7133) in paragraph at lines 14271--14275
\T1/pcr/m/n/10 "interpolate", statistics = "approximate")\T1/ptm/m/n/10 : shoul
d the
[1449]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 14319--14319
[]\T1/pcr/m/n/10 plogis(q, location = 0, scale = 1, lower.tail = TRUE, log.p =
FALSE)[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 14320--14320
[]\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p =
FALSE)[]
[1450]
Underfull \hbox (badness 10000) in paragraph at lines 14375--14378
[]\T1/ptm/m/n/10 The dis-tri-bu-tion func-tion is a rescaled hy-per-bolic tan-g
ent,
Underfull \hbox (badness 1715) in paragraph at lines 14375--14378
\T1/pcr/m/n/10 plogis(x) == (1+ [][]tanh[][][](x/2))/2\T1/ptm/m/n/10 , and it i
s called a \T1/ptm/m/it/10 sig-moid func-tion \T1/ptm/m/n/10 in con-texts
[1451] [1452] [1453] [1454]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 14663--14663
[]\T1/pcr/m/n/10 plnorm(q, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p =
FALSE)[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 14664--14664
[]\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p =
FALSE)[]
[1455]
Overfull \hbox (45.6622pt too wide) in paragraph at lines 14714--14716
[]\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 (
\OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1
\OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1
/cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/pcr/m/n/10 -plnorm(t, r, lower = FALSE, l
og = TRUE)\T1/ptm/m/n/10 .
Overfull \hbox (18.78088pt too wide) in paragraph at lines 14757--14757
[]\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra
nge(x)))
[1456] [1457] [1458] [1459] [1460] [1461] [1462]
Underfull \hbox (badness 2726) in paragraph at lines 15164--15167
[]\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 ,
[1463] [1464] [1465] [1466] [1467] [1468] [1469] [1470] [1471] [1472] [1473]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 15879--15879
[]\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc
gp, data = esoph)
[1474] [1475]
Underfull \hbox (badness 1014) in paragraph at lines 16017--16022
\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
[1476]
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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
[1477]
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[]\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts = list(a = "contr.sum", b
= "contr.poly"))[]
[1478] [1479] [1480] [1481] [1482] [1483] [1484] [1485]
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[]\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[]
[1486] [1487] [1488] [1489]
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[]\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x,
s, prob = 0.4)),[]
[1490] [1491] [1492] [1493] [1494] [1495] [1496] [1497]
Underfull \hbox (badness 2359) in paragraph at lines 17533--17535
[]\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For-
tran code used by
[1498] [1499]
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Overfull \hbox (15.18042pt too wide) in paragraph at lines 17705--17705
[] \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21
), th = b[1]))[]
[1501]
Underfull \hbox (badness 10000) in paragraph at lines 17785--17789
[]\T1/ptm/m/n/10 Fits the asymp-totic re-gres-sion model, in the form \T1/pcr/m
/n/10 b0 +
[1502] [1503]
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[]\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 )[]
[1504]
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[]\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[]
[1505] [1506] [1507] [1508] [1509] [1510] [1511] [1512]
Underfull \hbox (badness 1248) in paragraph at lines 18450--18453
[]\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 value by a fac-tor of \T1/pcr/m/n/10 reltol * (abs(val) + reltol
) \T1/ptm/m/n/10 at a step. De-faults to
[1513]
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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 18529--18531
[]\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
[1514] [1515]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 18635--18635
[] \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",[]
Overfull \hbox (96.18033pt too wide) in paragraph at lines 18698--18698
[]\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 18718--18718
[]\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),[]
[1517]
Underfull \hbox (badness 2564) in paragraph at lines 18756--18767
[]\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 18756--18767
\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
[1518]
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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)[]
[1519] [1520] [1521]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 19044--19044
[]\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp =
1, lty = 1:6,[]
[1522]
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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
[1523] [1524] [1525] [1526] [1527] [1528]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19439--19439
[] \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd =
1.5),[]
[1529]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 19527--19527
[] \T1/pcr/m/n/10 expression("Cook\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s dist
vs Leverage " * h[ii] / (1 - h[ii]))),[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 19530--19530
[] \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact
ive(),[]
[1530]
Underfull \hbox (badness 3049) in paragraph at lines 19609--19613
[]\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
[1531] [1532] [1533] [1534]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19857--19857
[] \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3,
...)[]
Underfull \hbox (badness 4779) in paragraph at lines 19864--19866
[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read
y ex-ist-ing plot. Only valid for
Underfull \hbox (badness 1194) in paragraph at lines 19867--19870
[]\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting
of the con-fi-dence
[1535]
Underfull \hbox (badness 1107) in paragraph at lines 19925--19927
[]\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
[1536]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 19980--19980
[]\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange
") # all colors[]
[1537]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 19987--19987
[]\T1/pcr/m/n/9 legend(2.5, 1.9, paste("f =", c(0, 0.2, 1)), col = 1:3, lty =
1, y.intersp = 1)[]
Underfull \hbox (badness 10000) in paragraph at lines 20037--20040
[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 function(x, col, bg, pch, type, ...) \T1/ptm/
m/n/10 which gives
Underfull \hbox (badness 10000) in paragraph at lines 20037--20040
\T1/ptm/m/n/10 the ac-tion to be car-ried out in each panel of the dis-play for
[1538]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 20081--20081
[]\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma
r..., oma...)")[]
[1539] [1540]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20206--20206
[] \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE) # no
cancellation[]
[1541]
Underfull \hbox (badness 10000) in paragraph at lines 20269--20271
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Exact Poisson test" \T1
/ptm/m/n/10 or
Overfull \hbox (6.78088pt too wide) in paragraph at lines 20317--20317
[]\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple =
FALSE)
[1542]
Underfull \hbox (badness 10000) in paragraph at lines 20372--20374
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 poly(*, simple=TRUE)\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 polym(*, coefs=<non-NULL>)\T1/ptm/m/n/10 , and
[1543]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20409--20409
[] \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 20414--20414
[]\T1/pcr/m/n/9 ## poly(<matrix>, df) --- used to fail till July 14 (vive la F
rance!), 2017:[]
[1544] [1545] [1546] [1547] [1548] [1549] [1550] [1551] [1552] [1553] [1554]
[1555] [1556]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 21264--21264
[] \T1/pcr/m/n/9 all.equal(pz3$sdev, pZ$sdev, tol = 1e-15)) # exactly
equal typically[]
[1557]
Underfull \hbox (badness 6859) in paragraph at lines 21331--21338
[][][]\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 21342--21348
[]\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 ,
[1558] [1559] [1560] [1561] [1562] [1563] [1564] [1565] [1566] [1567] [1568]
[1569]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 22080--22080
[] \T1/pcr/m/n/10 subset = rep_len(TRUE, nrow(as.matrix(x))), fix_sign
= TRUE, ...)[]
[1570] [1571] [1572] [1573] [1574]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 22364--22364
[] \T1/pcr/m/n/10 has.Pvalue = nc >= 4L && length(cn <- colnames(x
)) &&[]
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[] \T1/pcr/m/n/10 substr(cn[nc], 1L, 3L) %in% c("Pr("
, "p-v"),[]
[1575] [1576] [1577] [1578] [1579]
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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
[1580] [1581] [1582] [1583] [1584] [1585] [1586] [1587]
Overfull \hbox (133.98029pt too wide) in paragraph at lines 23251--23251
[] \T1/pcr/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty
p, ...), quantile(x, prob, type=1)))[]
[1588] [1589]
Underfull \hbox (badness 1028) in paragraph at lines 23392--23395
[]\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
[1590] [1591]
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[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by
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\T1/pcr/m/n/10 cutree(hclust.obj, k = k)\T1/ptm/m/n/10 , can be spec-i-fied for
ef-fi-ciency if
[1592]
Underfull \hbox (badness 10000) in paragraph at lines 23557--23559
[]\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
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[]\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
[1593] [1594]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 23721--23721
[]\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd,
10:1, mean)")[]
[1595] [1596] [1597]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 23941--23941
[]\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide
", v.names = "x")[]
[1598] [1599] [1600]
Underfull \hbox (badness 10000) in paragraph at lines 24087--24090
[]\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
Underfull \hbox (badness 2134) in paragraph at lines 24139--24143
[][][]\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
[1601]
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[]\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi
ans Example")[]
[1602] [1603] [1604] [1605] [1606] [1607] [1608]
Underfull \hbox (badness 6268) in paragraph at lines 24616--24621
[][]\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 ,
[1609]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 24644--24644
[] \T1/pcr/m/n/9 setNames(pars[c(".lin", "xmid", "scal")], nm = mCall[c("As
ym", "xmid", "scal")])[]
[1610] [1611]
Underfull \hbox (badness 1867) in paragraph at lines 24821--24823
[]\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 24834--24838
\T1/ptm/m/n/10 where \T1/pcr/m/n/10 NN <- [][]nobs[][][](object, use.fallback =
use.fallback) \T1/ptm/m/n/10 and
Underfull \hbox (badness 10000) in paragraph at lines 24834--24838
\T1/pcr/m/n/10 PP <- sum(!is.na([][]coef[][][](object))) \T1/ptm/m/n/10 -- wher
e in older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was
[1612]
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[]\T1/pcr/m/n/9 sigma(lm1) # ~= 7.165 = "Residual standard error" printed fr
om summary(lm1)[]
[1613] [1614] [1615]
Underfull \hbox (badness 2495) in paragraph at lines 25060--25069
[]\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 .
[1616]
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[] \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends
= FALSE)[]
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[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui
red; de-faults to
[1617]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 25236--25236
[]\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS
S"), smooth(x)))[]
[1618]
Overfull \hbox (84.78088pt too wide) in paragraph at lines 25261--25261
[]\T1/pcr/m/n/10 smooth.spline(x, y = NULL, w = NULL, df, spar = NULL, lambda
= NULL, cv = FALSE,
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[] \T1/pcr/m/n/10 control.spar = list(), tol = 1e-6 * IQR(x), kee
p.stuff = FALSE)[]
[1619]
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[]\T1/ptm/m/n/10 integer or [][]\T1/pcr/m/n/10 function[][][] \T1/ptm/m/n/10 gi
v-ing the num-ber of knots to use when
Underfull \hbox (badness 2435) in paragraph at lines 25306--25311
\T1/pcr/m/n/10 all.knots = FALSE\T1/ptm/m/n/10 . If a func-tion (as by de-fault
), the num-ber of
[1620]
Underfull \hbox (badness 2980) in paragraph at lines 25451--25453
[]\T1/ptm/m/n/10 the value of \T1/pcr/m/n/10 spar \T1/ptm/m/n/10 com-puted or g
iven, un-less it has been given as
[1621]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 25487--25487
[] \T1/pcr/m/n/10 nx <- length(x) - sum(duplicated( round((x - mean(x)) /
tol) ))[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 25536--25536
[]\T1/pcr/m/n/9 plot(dist ~ speed, data = cars, main = "data(cars) & smoothi
ng splines")[]
[1622]
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[]\T1/pcr/m/n/9 with(cars.spl$fit, min + range * knot[-c(1:3, nk+1 +1:3)]) # =
= unique(cars$speed)[]
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[1624]
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[]\T1/pcr/m/n/9 legend(1, 470, paste("endrule", c("keep","constant","median"),
sep = " = "),[]
[1625]
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[]\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na.
fail,
[1626] [1627] [1628] [1629] [1630] [1631]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 26107--26107
[] \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC"
, "hyman"),[]
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[]\T1/ptm/m/n/10 Method \T1/pcr/m/n/10 "hyman" \T1/ptm/m/n/10 com-putes a \T1/p
tm/m/it/10 mono-tone \T1/ptm/m/n/10 cu-bic spline us-ing Hy-man fil-ter-ing of
an
[1632] [1633]
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[]\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 26293--26293
[]\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman") (x), add = TRUE, c
ol = 4, n = 1001)[]
Underfull \vbox (badness 10000) has occurred while \output is active [1634]
Underfull \hbox (badness 2922) in paragraph at lines 26362--26367
[]\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
[1635]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 26399--26399
[] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5.2), xlim
= c(-.3, 5),[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 26402--26402
[] \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 26411--26411
[] \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 26412--26412
[] \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 26416--26416
[] \T1/pcr/m/n/9 axis(2, at = c(1,AR2,5), labels= expression(phi[2], frac(phi
[1]+phi[2],2), phi[1]),[]
[1636]
Underfull \hbox (badness 2922) in paragraph at lines 26458--26463
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
Underfull \hbox (badness 3240) in paragraph at lines 26470--26473
[][][]\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
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[] \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 26494--26494
[] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(-.5,6), xlim
= c(-1, 8),[]
[1637]
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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
[1638]
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[] \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 26581--26581
[] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5), xlim =
c(-1/4, 5),[]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 26591--26591
[] \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 26596--26596
[] \T1/pcr/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5]
== frac(log(2), e^{phi[2]})}),[]
[1639]
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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
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26654--26654
[]\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 26670--26670
[] \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 =
1.5 * exp(-x)"),[]
[1640] [1641]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 26784--26784
[]\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK
a)*input))
[1642]
Underfull \hbox (badness 2922) in paragraph at lines 26846--26851
[]\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
[1643]
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[] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "A", phi[2] == "B", phi[3] == "xm
id", phi[4] == "scal")))[]
[1644]
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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
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26964--26964
[]\T1/pcr/m/n/9 lines(x, do.call(SSgompertz, c(list(x=x), coef(fm1))), col = "
red", lwd=2)[]
[1645]
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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 ## 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")))[]
[1646]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 27057--27057
[] \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[]
Underfull \hbox (badness 2922) in paragraph at lines 27092--27097
[]\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
[1647]
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[]\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt),
digits = 3)[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 27132--27132
[] \T1/pcr/m/n/9 ann = FALSE, axes = FALSE, main = "Parameters in the SS
micmen model")[]
[1648]
Underfull \hbox (badness 6493) in paragraph at lines 27184--27189
[]\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
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27211--27211
[]\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 27213--27213
[]\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 27216--27216
[]\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 27219--27219
[]\T1/pcr/m/n/9 As <- coef(fm1)[["Asym"]]; abline(v = 0, h = c(As, As - coef(f
m1)[["Drop"]]), lty = 3)[]
[1649] [1650] [1651] [1652] [1653] [1654] [1655] [1656]
Underfull \hbox (badness 10000) in paragraph at lines 27714--27717
[]\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex-
Underfull \hbox (badness 10000) in paragraph at lines 27714--27717
\T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/pcr/m/n/10 NULL\T1/ptm/m/
n/10 , the de-fault,
[1657] [1658] [1659] [1660] [1661] [1662] [1663]
Underfull \hbox (badness 3396) in paragraph at lines 28143--28145
[]\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
[1664] [1665] [1666]
Underfull \hbox (badness 2237) in paragraph at lines 28320--28322
[]\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
[1667] [1668]
Underfull \hbox (badness 2591) in paragraph at lines 28484--28486
[]\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
[1669]
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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
[1670]
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[]\T1/pcr/m/n/10 supsmu(x, y, wt =, span = "cv", periodic = FALSE, bass = 0, t
race = FALSE)
[1671] [1672]
Underfull \hbox (badness 3407) in paragraph at lines 28711--28715
[]\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)
[1673] [1674]
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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
[1675] [1676]
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[]\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/
10 ; cur-rently ex-cept for \T1/pcr/m/n/10 rt()\T1/ptm/m/n/10 , only for
[1677] [1678]
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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,[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 29118--29118
[] \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com
mon",[]
[1679]
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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
[1680]
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[]\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s
pan.smth = 1/4)[]
[1681]
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[]\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out =
TRUE,[]
[1682]
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[]\T1/ptm/m/n/10 A [][]\T1/pcr/m/n/10 terms.object[][][] \T1/ptm/m/n/10 ob-ject
is re-turned. The ob-ject it-self is the re-ordered (un-less
[1683]
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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
[1684] [1685] [1686] [1687] [1688] [1689] [1690] [1691]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 29984--29984
[]\T1/pcr/m/n/10 ptukey(q, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
FALSE)
[1692]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 29985--29985
[]\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
FALSE)[]
[1693] [1694] [1695] [1696]
Underfull \hbox (badness 10000) in paragraph at lines 30274--30278
[]\T1/ptm/m/n/10 Setting \T1/pcr/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/p
cr/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect
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\T1/pcr/m/n/10 interval = c(lower,upper) \T1/ptm/m/n/10 if \T1/pcr/m/n/10 sign(
f(x)) \T1/ptm/m/n/10 does not sat-isfy the re-quire-ments at
Overfull \hbox (30.78088pt too wide) in paragraph at lines 30285--30285
[] \T1/pcr/m/n/10 extendInt = c("no", "yes", "downX", "upX"), check.con
v = FALSE,[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 30286--30286
[] \T1/pcr/m/n/10 tol = .Machine$double.eps^0.25, maxiter = 1000, trace
= 0)[]
[1697] [1698]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 30412--30412
[]\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:[]
[1699] [1700] [1701] [1702]
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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
[1703] [1704] [1705] [1706] [1707] [1708] [1709] [1710]
Underfull \hbox (badness 1337) in paragraph at lines 31165--31169
[]\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
[1711]
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[]\T1/ptm/m/n/10 When \T1/pcr/m/n/10 x \T1/ptm/m/n/10 (and \T1/pcr/m/n/10 y \T1
/ptm/m/n/10 if ap-pli-ca-ble) are valid, the func-tion now al-ways re-turns, al
so in the
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[]\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if
ar-gu-ment
[1712] [1713] [1714] [1715] [1716]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 31590--31590
[]\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F
ALSE,
[1717]
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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
[1718]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 31710--31710
[]\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 "")[]
[1719]) (./stats4-pkg.tex [1720]
Chapter 11.
[1721] [1722] [1723]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 192--192
[] \T1/pcr/m/n/9 -sum(stats::dpois(y, lambda = exp(lymax)/(1+x/exp(lxhalf))
, log = TRUE))[]
[1724] [1725] [1726]pdfTeX warning (ext4): destination with the same identifier
(name{Rfn.show.Rdash.methods}) has been already used, duplicate ignored
<to be read again>
\relax
l.407 ...Package \pkg{stats4}}{show.Rdash.methods}
[1727]
Underfull \hbox (badness 10000) in paragraph at lines 440--443
[]\T1/ptm/m/n/10 Generate a sum-mary as an ob-ject of class
[1728] [1729]) (./tcltk-pkg.tex [1730]
Chapter 12.
[1731] [1732] [1733] [1734]
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[]\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all = TRUE) # .Tcl.args put a callback
ref in here[]
[1735] [1736] [1737]
Underfull \vbox (badness 10000) has occurred while \output is active [1738]
Underfull \hbox (badness 1292) in paragraph at lines 664--671
[]\T1/pcr/m/n/10 tcl \T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-ing
any Tk or Tcl com-mand by sim-ply run-ning
[1739] [1740] [1741] [1742] [1743] [1744] [1745] [1746] [1747] [1748] [1749]
Underfull \hbox (badness 1189) in paragraph at lines 1407--1410
[][][]\T1/pcr/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept
on Win-dows and the ma-cOS GUI), [][]\T1/pcr/m/n/10 menu[][][] \T1/ptm/m/n/10 (
whose
[1750]) (./tools-pkg.tex
Chapter 13.
[1751]
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[]\T1/pcr/m/n/9 ## is used for simple print methods in R, and as prototype for
new methods.[]
[1752]
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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
[1753]
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[]\T1/pcr/m/n/9 assertCondition(ff(), "error", "warning") # ok (quietly, catch
ing warning)[]
[1754]
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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 ,
[1755]
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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
[1756] [1757] [1758] [1759] [1760] [1761] [1762]
Overfull \vbox (7.18602pt too high) has occurred while \output is active
[1763] [1764]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 905--905
[]\T1/pcr/m/n/10 resaveRdaFiles(paths, compress = c("auto", "gzip", "bzip2", "
xz"),[]
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[]\T1/pcr/m/n/9 bad <- is.na(res$ASCII) | res$ASCII | (res$size > 1e4 & res$co
mpress == "none")[]
[1765] [1766]
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[]\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i
g-nored when
[1767]
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[]\T1/ptm/m/n/10 a named list of char-ac-ter vec-tors with ar-gu-ments to be pa
ssed to
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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-
[1768]
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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
[1769]
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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
[1770] [1771]
Underfull \hbox (badness 10000) in paragraph at lines 1360--1363
[]\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/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S
up-port func-tion for
[1772] [1773] [1774] [1775] [1776]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 1683--1683
[] \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 .
[1777] [1778] [1779]pdfTeX warning (ext4): destination with the same identifier
(name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored
<to be read again>
\relax
l.1897 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD}
[1780] [1781] [1782]
[1783]
Underfull \hbox (badness 1142) in paragraph at lines 2165--2171
[]\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}",[]
[1784]
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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
[1785]
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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
[1786]
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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 .
[1787]
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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"),[]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 2427--2427
[] \T1/pcr/m/n/10 align = TRUE, character_only = TRUE, include_declarations
= TRUE)[]
[1788] [1789] [1790] [1791]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2692--2692
[] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macros", "system.
Rd"),[]
[1792]
Underfull \hbox (badness 2486) in paragraph at lines 2737--2745
[]\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
[1793] [1794] [1795] [1796] [1797]
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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
[1798] [1799] [1800] [1801] [1802]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 3451--3451
[] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macro
s", "system.Rd"))[]
[1803] [1804] [1805] [1806]
Underfull \hbox (badness 4108) in paragraph at lines 3695--3702
[]\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
[1807] [1808]
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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
[1809] [1810]
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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
[1811]
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[] \T1/pcr/m/n/10 depLevel = c("Depends", "Imports", "Sugg
ests"))[]
[1812]
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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
[1813] [1814] [1815]
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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
Underfull \hbox (badness 6859) in paragraph at lines 4253--4258
[]\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
[1816]
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 reduce \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE
\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/pcr/m/n/10 De
pendsList
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\T1/ptm/m/n/10 ob-ject such that a min-i-mal set of de-pen-den-cies are spec-i-
fied (for in-stance if
Underfull \hbox (badness 10000) in paragraph at lines 4341--4346
\T1/ptm/m/n/10 there was `\T1/pcr/m/n/10 foo, foo (>= 1.0.0), foo (>= 1.3.0)\T1
/ptm/m/n/10 ', it would only re-turn
[1817] [1818]
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[] \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F
ALSE,[]
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[] \T1/pcr/m/n/10 latestOnly = TRUE, addFiles = FALSE, rds_compr
ess = "xz")[]
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[]\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 ',
[1819]
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\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 4525--4531
[]\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
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\T1/ptm/m/n/10 each pack-age's `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file
, and writes this in-for-ma-tion into the `\T1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/1
0 ',
Underfull \hbox (badness 1571) in paragraph at lines 4553--4557
[]\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
[1820] [1821] [1822]) (./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 ',
[1823] [1824] [1825]
Underfull \hbox (badness 6316) in paragraph at lines 212--216
[]\T1/pcr/m/n/10 find \T1/ptm/m/n/10 is a dif-fer-ent user in-ter-face for a si
m-i-lar task to \T1/pcr/m/n/10 apropos\T1/ptm/m/n/10 . By de-fault
[1826]
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[]\T1/pcr/m/n/9 find("cor", numeric = TRUE) # numbers with
these names[]
[1827]
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[] \T1/pcr/m/n/10 prompts = getOption("askYesNo", gettext(c("Yes", "No
", "Cancel"))),[]
[1828] [1829] [1830]
Underfull \hbox (badness 1946) in paragraph at lines 527--531
\T1/ptm/m/n/10 28. [][]$\T1/pcr/m/n/10 https : / / journal . r-[]project . org
/ archive / 2011-[]2 / RJournal _ 2011-[]2 _
Overfull \hbox (0.78088pt too wide) in paragraph at lines 577--577
[]\T1/pcr/m/n/10 aspell_package_Rd_files(dir, drop = c("\\author", "\\referenc
es"),
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[]\T1/pcr/m/n/10 aspell_package_R_files(dir, ignore = character(), control = l
ist(),[]
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[] \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 585--585
[]\T1/pcr/m/n/10 aspell_package_C_files(dir, ignore = character(), control = l
ist(),[]
[1831]
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[] \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[]
Underfull \hbox (badness 10000) in paragraph at lines 620--626
[]\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 620--626
\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-
[1832]
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[] \T1/pcr/m/n/10 ignore_repo_cache = FALSE, max_repo_cache
_age,[]
[1833]
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\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
[1834]
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\T1/ptm/m/n/10 ory avail-able and con-trol-ling the load/save pro-cess. If \T1/
pcr/m/n/10 infile \T1/ptm/m/n/10 starts
Underfull \hbox (badness 3029) in paragraph at lines 870--876
\T1/ptm/m/n/10 with a `\T1/pcr/m/n/10 -\T1/ptm/m/n/10 ', use `\T1/pcr/m/n/10 --
\T1/ptm/m/n/10 ' as the fi-nal op-tion. The de-fault op-tions are
[1835]
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[]\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer =
NULL,
[1836]
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\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 1003--1005
[]\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing
[1837] [1838]
Underfull \hbox (badness 10000) in paragraph at lines 1111--1114
[]\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org
/ wiki / Digital _ Object _
[1839]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 1194--1194
[] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[]
[1840] [1841] [1842] [1843] [1844]
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[]\T1/ptm/m/n/10 For ex-am-ple, sup-pose that on a data set which you know to b
e quite large the com-
[1845] [1846]
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[] \T1/pcr/m/n/9 data = infert, family = b
inomial())))[]
[1847]
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[]\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b
efore$timestamp,[]
[1848]
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[]\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp"
), md5sum=TRUE)[]
[1849]
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[]\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind =
NULL,
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[]\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind =
NULL,
[1850]
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[]\T1/pcr/m/n/10 ind \T1/ptm/m/n/10 chooses a row in the list of cur-rent mir-r
ors, by num-ber. It is best used with
[1851] [1852]
Underfull \hbox (badness 10000) in paragraph at lines 2054--2056
[]\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the
`\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' file via
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[] \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")[]
[1853]
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[]\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after =
NULL,[]
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[]\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w
hen
[1854]
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[] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[]
[1855]
Underfull \hbox (badness 1082) in paragraph at lines 2305--2309
[][][]\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;
[1856]
Underfull \hbox (badness 10000) in paragraph at lines 2342--2344
[]\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
Underfull \hbox (badness 1057) in paragraph at lines 2374--2381
\T1/ptm/m/n/10 a [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 ); if FALSE, the
func-tion re-turns a [][]\T1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 . Note that w
hen
[1857] [1858] [1859]
Underfull \hbox (badness 10000) in paragraph at lines 2563--2565
[]\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see
[1860] [1861] [1862] [1863]
Underfull \hbox (badness 10000) in paragraph at lines 2800--2804
[]\T1/ptm/m/n/10 files end-ing `\T1/pcr/m/n/10 .tab\T1/ptm/m/n/10 ', `\T1/pcr/m
/n/10 .txt\T1/ptm/m/n/10 ' or `\T1/pcr/m/n/10 .TXT\T1/ptm/m/n/10 ' are read us-
ing
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[][]\T1/pcr/m/n/10 read.table[][][](..., header = TRUE, as.is=FALSE)\T1/ptm/m/n
/10 , and hence re-sult in a
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[]\T1/ptm/m/n/10 files end-ing `\T1/pcr/m/n/10 .csv\T1/ptm/m/n/10 ' or `\T1/pcr
/m/n/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/pcr/m/n/10 read.table[][][
](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 2854--2857
[]\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
[1864]
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[]\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 '[]
[1865]
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[]\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
[1866] [1867] [1868] [1869] [1870] [1871] [1872]
Underfull \hbox (badness 1072) in paragraph at lines 3499--3507
[]\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
[1873]
Underfull \hbox (badness 1231) in paragraph at lines 3548--3554
[]\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 3555--3560
[]\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 3555--3560
\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 3555--3560
\T1/pcr/m/n/10 [user:password@]machine[:port] \T1/ptm/m/n/10 where the parts in
brack-ets are op-tional. See
[1874] [1875]
Underfull \hbox (badness 4660) in paragraph at lines 3677--3680
\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 3701--3703
[]\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
[1876] [1877] [1878]
Underfull \hbox (badness 1565) in paragraph at lines 3886--3890
[]\T1/ptm/m/n/10 Data frame columns are co-erced on in-put to \T1/ptm/m/it/10 c
har-ac-ter \T1/ptm/m/n/10 un-less nu-meric (in the sense of
Underfull \hbox (badness 10000) in paragraph at lines 3907--3913
[]\T1/ptm/m/n/10 For a data frame, the row names will be taken from the orig-i-
nal ob-ject if
[1879]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 3969--3969
[] \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F
ALSE,[]
Overfull \hbox (2.55087pt too wide) in paragraph at lines 3997--4004
\T1/pcr/m/n/10 setRNG = {RNGkind("default", "default"); set.seed(1)}\T1/ptm/m/n
/10 .
[1880] [1881] [1882] [1883] [1884]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4324--4324
[]\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o
ne is in the[]
[1885]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for
mat}) has been already used, duplicate ignored
<to be read again>
\relax
l.4395 ...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.4395 ...mat Unordered and Ordered Lists}{format}
[1886] [1887] [1888]
[1889] [1890] [1891] [1892] [1893] [1894] [1895] [1896] [1897] [1898] [1899]
[1900]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5348--5348
[] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h
elp(dgamma):[]
[1901]
Underfull \hbox (badness 10000) in paragraph at lines 5432--5434
[]\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
[1902]
Underfull \hbox (badness 1502) in paragraph at lines 5481--5486
[]\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 5481--5486
\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are
listed in file
[1903] [1904]
Underfull \hbox (badness 10000) in paragraph at lines 5654--5663
[]\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 5654--5663
\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
[1905]
Underfull \hbox (badness 2150) in paragraph at lines 5717--5720
[]\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 5733--5736
[]\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
[1906] [1907]
Underfull \hbox (badness 3118) in paragraph at lines 5854--5856
[]\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
[1908]
Underfull \hbox (badness 2409) in paragraph at lines 5887--5891
[]\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the
sub-architecture used by
[1909]
Underfull \hbox (badness 5091) in paragraph at lines 5991--5993
[]\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
Overfull \hbox (44.55087pt too wide) in paragraph at lines 6007--6012
\T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/
ptm/m/n/10 .
Overfull \hbox (48.30977pt too wide) in paragraph at lines 6020--6027
[]\T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 means to use \T1/pcr/m/n/10 c("Depends", "
Imports", "LinkingTo", "Suggests")
[1910]
Underfull \hbox (badness 10000) in paragraph at lines 6078--6081
[]\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to
be passed
Underfull \hbox (badness 10000) in paragraph at lines 6078--6081
\T1/ptm/m/n/10 to \T1/pcr/m/n/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pack
-age in-stall. E.g.,
[1911]
Underfull \hbox (badness 10000) in paragraph at lines 6137--6141
[]\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 ,
Underfull \hbox (badness 2376) in paragraph at lines 6151--6158
[]\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 6151--6158
\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 6151--6158
\T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com
-piled is con-trolled by
[1912]
Underfull \hbox (badness 1314) in paragraph at lines 6210--6217
[]\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 6251--6256
[][][]\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 ,
[1913]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 6274--6274
[] \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc
lude/udunits2"))[]
Underfull \hbox (badness 5133) in paragraph at lines 6310--6314
[]\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 6324--6327
[]\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
[1914]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6371--6371
[]\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields
= "License")[]
[1915] [1916]
Underfull \hbox (badness 4132) in paragraph at lines 6490--6492
[]\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
[1917] [1918] [1919]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6648--6648
[]\T1/pcr/m/n/9 ls.str(mode = "list") #- what are the structured objects I h
ave defined?[]
[1920] [1921]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 6791--6791
[]\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F
ALSE)
[1922]
Underfull \hbox (badness 10000) in paragraph at lines 6831--6833
[]\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
[1923] [1924]
Underfull \hbox (badness 10000) in paragraph at lines 6972--6974
[]\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 6977--6979
[]\T1/ptm/m/n/10 typically the re-sult of \T1/pcr/m/n/10 methods(..)\T1/ptm/m/n
/10 , an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of class
[1925] [1926] [1927]
Underfull \hbox (badness 1859) in paragraph at lines 7200--7203
[]\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br
owser (by
[1928]
Underfull \hbox (badness 1655) in paragraph at lines 7282--7285
[]\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 7293--7293
[]\T1/pcr/m/n/9 db3 <- news(Version == "3.0.1" & grepl("^BUG", Category) & gre
pl("PR#", Text),[]
[1929]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7297--7297
[]\T1/pcr/m/n/9 ## News from a date range (\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 Matri
x\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is there in a regular R installation):[]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 7305--7305
[]\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st
andardize a bit more[]
[1930]
Underfull \hbox (badness 10000) in paragraph at lines 7390--7394
[]\T1/ptm/m/n/10 For all stan-dards, \T1/pcr/m/n/10 unit = "auto" \T1/ptm/m/n/1
0 is also al-lowed. If
[1931] [1932] [1933] [1934]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 7654--7654
[] \T1/pcr/m/n/10 date.fields = c("Date", "Packaged", "Date/Publica
tion", "Built"),[]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 7655--7655
[] \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 7656--7656
[] \T1/pcr/m/n/10 desc = packageDescription(pkg, lib.loc=lib.loc, f
ields=date.fields))[]
[1935]
Underfull \hbox (badness 10000) in paragraph at lines 7684--7686
[]\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 7698--7700
[]\T1/pcr/m/n/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut,
al-low-ing things like
Underfull \hbox (badness 1259) in paragraph at lines 7706--7711
[]\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,
[1936]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7752--7752
[] \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 7753--7753
[] \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[]
[1937] [1938]
Underfull \hbox (badness 10000) in paragraph at lines 7882--7887
[]\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 7882--7887
[][]\T1/pcr/m/n/10 installed.packages[][][] \T1/ptm/m/n/10 plus \T1/pcr/m/n/10
"Status"\T1/ptm/m/n/10 , a fac-tor with lev-els
Underfull \hbox (badness 10000) in paragraph at lines 7889--7892
[]\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 7889--7892
[][]\T1/pcr/m/n/10 available.packages[][][] \T1/ptm/m/n/10 plus \T1/pcr/m/n/10
"Status"\T1/ptm/m/n/10 , a fac-tor with lev-els
[1939]
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[] \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme
nt"),[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 8006--8006
[] \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<",
">"),[]
[1940] [1941] [1942]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8177--8177
[] \T1/pcr/m/n/9 "S original, <http://statwww.epfl.ch/davison/BMA/libr
ary.html>"),[]
[1943]
Underfull \hbox (badness 1789) in paragraph at lines 8300--8302
[]\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
[1944]
Underfull \hbox (badness 10000) in paragraph at lines 8358--8362
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
Underfull \hbox (badness 10000) in paragraph at lines 8358--8362
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1945] [1946]
Underfull \hbox (badness 10000) in paragraph at lines 8473--8477
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
Underfull \hbox (badness 10000) in paragraph at lines 8473--8477
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1947]
Underfull \hbox (badness 10000) in paragraph at lines 8538--8542
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
Underfull \hbox (badness 10000) in paragraph at lines 8538--8542
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1948] [1949] [1950] [1951]
Underfull \hbox (badness 5203) in paragraph at lines 8869--8872
[]\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
[1952] [1953] [1954]
Underfull \hbox (badness 1776) in paragraph at lines 9095--9102
[]\T1/ptm/m/n/10 If you are un-com-fort-able with un-so-licited eval-u-a-tion o
f pieces of code, you should set
[1955]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 9119--9119
[] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "
no.loss"),[]
[1956] [1957]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 9280--9280
[]\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr
anspose = TRUE)[]
[1958] [1959]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9461--9461
[]\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[]
[1960] [1961]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 9547--9547
[] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss",
"no.loss"),[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 9550--9550
[] \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines.
skip,[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 9555--9555
[] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski
pNul = FALSE)[]
[1962]
Underfull \hbox (badness 1077) in paragraph at lines 9627--9630
[]\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
[1963] [1964] [1965] [1966] [1967] [1968]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10067--10067
[] \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c
(1, 0)))
[1969]
Underfull \hbox (badness 10000) in paragraph at lines 10154--10156
[]\T1/ptm/m/n/10 To re-move from the li-brary tree \T1/ptm/m/sl/10 lib \T1/ptm/
m/n/10 in-stead of the de-fault one, use
[1970] [1971]
Underfull \hbox (badness 2181) in paragraph at lines 10277--10281
[]\T1/pcr/m/n/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/pcr/m/n
/10 "roman" \T1/ptm/m/n/10 which are in-ter-nally rep-re-sented as in-te-
Underfull \hbox (badness 2269) in paragraph at lines 10277--10281
\T1/ptm/m/n/10 gers, and have suit-able meth-ods for print-ing, for-mat-ting, s
ub-set-ting, co-er-cion, etc, see
Underfull \hbox (badness 10000) in paragraph at lines 10289--10293
\T1/pcr/m/n/10 en . wikipedia . org / w / index . php ? title = Roman _ numeral
s & oldid = 78252134$[][]\T1/ptm/m/n/10 .
[1972]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 10307--10307
[]\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 10311--10311
[]\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in
{1,2,..,3899} :[]
[1973] [1974]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 10443--10443
[]\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold
= 0)
[1975]
Underfull \hbox (badness 1917) in paragraph at lines 10566--10569
[]\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 10566--10569
\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
[1976]
Overfull \hbox (106.98032pt too wide) in paragraph at lines 10589--10589
[]\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 '[]
[1977]
Underfull \hbox (badness 8075) in paragraph at lines 10652--10654
[]\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
[1978]
Underfull \hbox (badness 6725) in paragraph at lines 10702--10711
\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 10702--10711
\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 10702--10711
\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 10702--10711
\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
[1979]
Underfull \hbox (badness 3646) in paragraph at lines 10828--10830
[][][]$\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 /
[1980]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 10866--10866
[] \T1/pcr/m/n/10 split = FALSE, quiet = FALSE, drop.evalFALSE = F
ALSE, ...)[]
[1981] [1982] [1983]
Underfull \hbox (badness 10000) in paragraph at lines 11047--11051
[]\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 11078--11084
[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
[1984]
Underfull \hbox (badness 2012) in paragraph at lines 11173--11179
\T1/ptm/m/n/10 and `\T1/pcr/m/n/10 \includegraphics\T1/ptm/m/n/10 ' state-ments
for fig-ures should be auto-generated. Use
[1985]
Underfull \hbox (badness 2096) in paragraph at lines 11186--11188
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w
hether EPS fig-ures should be gen-er-ated. Ig-nored if
Underfull \hbox (badness 2698) in paragraph at lines 11189--11191
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ), in-di-cat-ing wh
ether PDF fig-ures should be gen-er-ated. Ig-nored if
Underfull \hbox (badness 1527) in paragraph at lines 11196--11199
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w
hether PNG fig-ures should be gen-er-ated. Ig-nored if
Underfull \hbox (badness 1067) in paragraph at lines 11200--11203
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w
hether JPEG fig-ures should be gen-er-ated. Ig-nored if
Overfull \hbox (6.78088pt too wide) in paragraph at lines 11254--11254
[] \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa
rent")[]
[1986]
Underfull \hbox (badness 1009) in paragraph at lines 11272--11283
[]\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
[1987]
Underfull \hbox (badness 2846) in paragraph at lines 11359--11369
\T1/ptm/m/n/10 con-trols the num-ber of lines that are saved (de-fault 512), an
d \T1/pcr/m/n/10 R_HISTFILE \T1/ptm/m/n/10 (de-fault
[1988] [1989]
Underfull \hbox (badness 10000) in paragraph at lines 11498--11501
[]\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the plat-form \T1/phv/m/n/10
R \T1/ptm/m/n/10 was built un-
Underfull \hbox (badness 10000) in paragraph at lines 11498--11501
\T1/ptm/m/n/10 der. Where sub-architectures are in use this is of the form
Underfull \hbox (badness 10000) in paragraph at lines 11515--11518
[]\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in
g
[1990]
Underfull \hbox (badness 2158) in paragraph at lines 11594--11597
[]\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
[1991] [1992] [1993]
Underfull \hbox (badness 3333) in paragraph at lines 11774--11776
[]\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-
[1994] [1995]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 11939--11939
[] \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing =
TRUE, ...))[]
[1996]
Underfull \hbox (badness 5970) in paragraph at lines 11972--11975
[]\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 11972--11975
[][]\T1/pcr/m/n/10 options[][][]("width")\T1/ptm/m/n/10 ; note that this has on
ly a weak ef-fect, un-less
Underfull \hbox (badness 1052) in paragraph at lines 11983--11992
\T1/ptm/m/n/10 (see [][]\T1/pcr/m/n/10 options[][][]\T1/ptm/m/n/10 ) which de-f
aults to \T1/pcr/m/n/10 "no" \T1/ptm/m/n/10 for back com-pat-i-bil-ity rea-sons
;
[1997]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 12027--12027
[]\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification
of binary numbers[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 12058--12058
[]\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 12065--12065
[]\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 12067--12067
[]\T1/pcr/m/n/9 invisible(lapply(60:66, function(N) str( ch , nchar.max = N)))
# "1 is 1" here[]
[1998] [1999] [2000]
Underfull \hbox (badness 10000) in paragraph at lines 12235--12237
[]\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
[2001] [2002]
Underfull \hbox (badness 4492) in paragraph at lines 12392--12399
[]\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 12392--12399
\T1/ptm/m/n/10 turn, and se-lected if their \T1/pcr/m/n/10 extension \T1/ptm/m/
n/10 com-po-nent matches (as a reg-exp) the file
Underfull \hbox (badness 2452) in paragraph at lines 12392--12399
\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
[2003] [2004] [2005]
Underfull \hbox (badness 2020) in paragraph at lines 12555--12571
\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 12555--12571
\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
[2006]
Underfull \hbox (badness 2809) in paragraph at lines 12675--12679
[]\T1/ptm/m/n/10 NetBSD prior to 8.0 used flag `\T1/pcr/m/n/10 --xz\T1/ptm/m/n/
10 ' rather than `\T1/pcr/m/n/10 -J\T1/ptm/m/n/10 ', so this should be used \T1
/ptm/m/it/10 via
Underfull \hbox (badness 1596) in paragraph at lines 12675--12679
\T1/pcr/m/n/10 extra_flags = "--xz" \T1/ptm/m/n/10 rather than \T1/pcr/m/n/10 c
ompression = "xz"\T1/ptm/m/n/10 . The com-mands from
Underfull \hbox (badness 5022) in paragraph at lines 12690--12694
[]\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 12697--12700
[][][]$\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 12697--12700
\T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht
ml # tag _ 20 _
[2007] [2008] [2009]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 12862--12862
[] \T1/pcr/m/n/10 numerals = c("allow.loss", "warn.loss", "no.loss
"), ...)[]
[2010] [2011] [2012] [2013] [2014] [2015]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 13246--13246
[] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc,
...),[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 13252--13252
[] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc,
...),[]
Underfull \hbox (badness 4467) in paragraph at lines 13273--13275
[]\T1/ptm/m/n/10 Download method, see [][]\T1/pcr/m/n/10 download.file[][][]\T1
/ptm/m/n/10 . Un-used if a non-\T1/pcr/m/n/10 NULL
Underfull \hbox (badness 4660) in paragraph at lines 13286--13290
\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
Overfull \hbox (36.87935pt too wide) in paragraph at lines 13300--13304
[]\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][]\T1/pcr/m/n/10 insta
lled.packages[][][](lib.loc = lib.loc)\T1/ptm/m/n/10 .
Underfull \hbox (badness 10000) in paragraph at lines 13306--13311
[]\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 13306--13311
\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 13306--13311
\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[][][]
[2016]
Underfull \hbox (badness 1052) in paragraph at lines 13312--13314
[]\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and
in-stall. See
Underfull \hbox (badness 10000) in paragraph at lines 13342--13347
[]\T1/ptm/m/n/10 For how the list of suit-able avail-able pack-ages is de-ter-m
ined see
Underfull \hbox (badness 10000) in paragraph at lines 13342--13347
[][]\T1/pcr/m/n/10 available.packages[][][]\T1/ptm/m/n/10 . \T1/pcr/m/n/10 avai
lable = NULL \T1/ptm/m/n/10 make a call to
Underfull \hbox (badness 10000) in paragraph at lines 13342--13347
\T1/pcr/m/n/10 available.packages(contriburl = contriburl, method = method) \T1
/ptm/m/n/10 and
Underfull \hbox (badness 10000) in paragraph at lines 13363--13368
[]\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 13371--13374
[][][]\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 ,
[2017]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13425--13425
[]\T1/pcr/m/n/9 ## Not run: url.show("http://www.stats.ox.ac.uk/pub/datasets/c
sb/ch3a.txt")
[2018] [2019] [2020]
Underfull \hbox (badness 10000) in paragraph at lines 13613--13616
[][][]\T1/pcr/m/n/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi-
gnette browser;
Overfull \hbox (42.18039pt too wide) in paragraph at lines 13629--13629
[]\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:[]
[2021]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 13696--13696
[] \T1/pcr/m/n/9 lm(weight ~ (Time + I(Time^2)) * Diet, d
ata = DAT)))[]
[2022]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13718--13718
[] \T1/pcr/m/n/9 nls(weight ~ SSlogis(Time, Asym, xmid, scal),
data = DD)))[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 13737--13737
[]\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep =
" ",
[2023]
Underfull \hbox (badness 1454) in paragraph at lines 13764--13768
[]\T1/ptm/m/n/10 the char-ac-ter(s) to print at the end of each line (row). For
ex-am-ple,
Underfull \hbox (badness 1715) in paragraph at lines 13789--13792
[]\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 13834--13836
[]\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec-
tion
[2024]
Underfull \hbox (badness 3271) in paragraph at lines 13846--13850
\T1/ptm/m/n/10 set \T1/pcr/m/n/10 sep \T1/ptm/m/n/10 and \T1/pcr/m/n/10 dec \T1
/ptm/m/n/10 (see be-low), \T1/pcr/m/n/10 qmethod = "double"\T1/ptm/m/n/10 , and
\T1/pcr/m/n/10 col.names \T1/ptm/m/n/10 to \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 if
[2025] [2026]) [2027] [2028] (./KernSmooth-pkg.tex
Chapter 15.
[2029]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 124--124
[]\T1/pcr/m/n/10 bkde2D(x, bandwidth, gridsize = c(51L, 51L), range.x, truncat
e = TRUE)
[2030] [2031] [2032] [2033] [2034]
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,
[2035] [2036] [2037] [2038]) (./MASS-pkg.tex
Chapter 16.
[2039] [2040] [2041] [2042] [2043] [2044] [2045] [2046] [2047] [2048] [2049]
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))[]
[2050] [2051] [2052] [2053] [2054] [2055] [2056] [2057] [2058] [2059] [2060]
[2061]
Underfull \hbox (badness 7256) in paragraph at lines 1604--1606
[]\T1/ptm/m/n/10 logical. If true and the re-sult would be sparse (only true fo
r
[2062] [2063] [2064] [2065] [2066] [2067] [2068] [2069] [2070] [2071] [2072]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2412--2412
[]\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq",
"F"),[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2416--2416
[]\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq",
"F"),[]
[2073] [2074] [2075] [2076]
Underfull \hbox (badness 6559) in paragraph at lines 2694--2697
[]\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
[2077] [2078] [2079]
Underfull \hbox (badness 10000) in paragraph at lines 2864--2869
\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 8189) in paragraph at lines 2864--2869
\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 ,
Underfull \hbox (badness 3557) in paragraph at lines 2900--2908
[]\T1/ptm/m/n/10 For the fol-low-ing named dis-tri-bu-tions, rea-son-able start
-ing val-ues will be com-puted if
Underfull \hbox (badness 3118) in paragraph at lines 2900--2908
\T1/pcr/m/n/10 start \T1/ptm/m/n/10 is omit-ted or only par-tially spec-i-fied:
\T1/pcr/m/n/10 "cauchy"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 ,
\T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 ,
[2080] [2081]
Underfull \hbox (badness 4686) in paragraph at lines 3032--3034
[]\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i-
na-tor ex-ceeds
Underfull \hbox (badness 1515) in paragraph at lines 3046--3050
[]\T1/ptm/m/n/10 where \T1/pcr/m/n/10 p1\T1/ptm/m/n/10 , \T1/pcr/m/n/10 p2\T1/p
tm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/pcr/m/n
/10 cycles \T1/ptm/m/n/10 terms or when a
[2082] [2083] [2084]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3227--3227
[] \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL
SE, ...)[]
Underfull \hbox (badness 5817) in paragraph at lines 3234--3236
[]\T1/ptm/m/n/10 Fitted model ob-ject from a \T1/pcr/m/n/10 Gamma \T1/ptm/m/n/1
0 fam-ily or \T1/pcr/m/n/10 quasi \T1/ptm/m/n/10 fam-ily with
[2085]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3357--3357
[]\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist =
"exponential")[]
[2086] [2087] [2088] [2089] [2090] [2091] [2092] [2093] [2094] [2095] [2096]
[2097]
Underfull \hbox (badness 1845) in paragraph at lines 4143--4145
[]\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
[2098] [2099] [2100] [2101] [2102] [2103] [2104]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4639--4639
[] \T1/pcr/m/n/10 col = 5, xlab = deparse(substitute(data)), bty = "n",
...)[]
[2105] [2106]
Underfull \hbox (badness 10000) in paragraph at lines 4791--4794
[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[2107]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4861--4861
[]\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model
= FALSE,
Underfull \hbox (badness 10000) in paragraph at lines 4869--4872
[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[2108] [2109] [2110] [2111] [2112]
Underfull \hbox (badness 5681) in paragraph at lines 5269--5271
[]\T1/ptm/m/n/10 the quan-tile to be used: see \T1/pcr/m/n/10 Details\T1/ptm/m/
n/10 . This is over-ridden if
Underfull \hbox (badness 5022) in paragraph at lines 5273--5276
[]\T1/ptm/m/n/10 the cut-off / tun-ing con-stant used for $\OML/cmm/m/it/10 ^^_
\OT1/cmr/m/n/10 ()$ \T1/ptm/m/n/10 and $\OML/cmm/m/it/10 \OT1/cmr/m/n/10 ()$ \
T1/ptm/m/n/10 func-tions when
[2113]
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[]\T1/ptm/m/n/10 the value of the cri-te-rion for the best so-lu-tion found, in
the case of
[2114] [2115] [2116] [2117] [2118] [2119] [2120] [2121]
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[]\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP
ACK = FALSE)
[2122]
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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")
[2123] [2124]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.npk}) has been already used, duplicate ignored
<to be read again>
\relax
l.6111 ...sical N, P, K Factorial Experiment}{npk}
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l.6111 ...sical N, P, K Factorial Experiment}{npk}
[2125]
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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
[2126] [2127] [2128] [2129]
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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)))[]
[2131]
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[] \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr
ellis"))[]
[2132] [2133] [2134] [2135] [2136] [2137]
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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"))[]
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[2138]
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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 ) =
[2139]
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[]\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da
ta = housing)[]
[2140] [2141]
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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
[2142] [2143]
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[]\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam
p = "exact")[]
[2144]
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[] \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC
V"), ...)[]
[2145] [2146] [2147] [2148] [2149] [2150]
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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
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[]\T1/ptm/m/n/10 where \T1/pcr/m/n/10 p1\T1/ptm/m/n/10 , \T1/pcr/m/n/10 p2\T1/p
tm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/pcr/m/n
/10 cycles \T1/ptm/m/n/10 terms or when a
[2151] [2152]
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[] \T1/pcr/m/n/10 maxit = 20, acc = 1e-4, test.vec = "resid", lqs.control =
NULL)[]
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[]\T1/ptm/m/n/10 A func-tion to spec-ify the ac-tion to be taken if \T1/pcr/m/n
/10 NA\T1/ptm/m/n/10 s are found. The
[2153] [2154] [2155] [2156] [2157] [2158] [2159] [2160] [2161] [2162] [2163]
[2164] [2165] [2166] [2167] [2168] [2169] [2170] [2171] [2172]
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[]\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS
E, ...)[]
[2173]
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[]\T1/ptm/m/n/10 how much the stu-dent smokes. (Fac-tor, lev-els \T1/pcr/m/n/10
"Heavy"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Regul" \T1/ptm/m/n/10 (reg-u-larly),
[2174]
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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)[]
[2175] [2176] [2177] [2178] [2179] [2180] [2181] [2182] [2183] [2184] [2185]
[2186] [2187]) (./Matrix-pkg.tex [2188]
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
[2189]
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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
[2190]
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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
[2191]
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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
[2192] [2193]
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[]\T1/pcr/m/n/10 bandSparse(n, m = n, k, diagonals, symmetric = FALSE, giveCsp
arse = TRUE)
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[]\T1/ptm/m/n/10 integer vec-tor of ``di-ag-o-nal num-bers'', with iden-ti-cal
mean-ing as in
[2194]
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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)],[]
[2195] [2196]
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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)[]
[2197]
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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 .
[2198] [2199] [2200]
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[]\T1/pcr/m/n/10 ## solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D
","P","Pt"), ...)[]
[2201]
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[]\T1/pcr/m/n/10 signature(from = "CHMfactor", to = "sparseMatrix") \T1/ptm/m/n
/10 (or equiv-a-
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[]\T1/pcr/m/n/10 signature(x = "CHMfactor"): \T1/ptm/m/n/10 Plot the im-age of
the lower tri-
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\T1/ptm/m/n/10 an-gu-lar fac-tor, $\OML/cmm/m/it/10 L$\T1/ptm/m/n/10 , from the
de-com-po-si-tion. This method is equiv-a-lent to
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\T1/pcr/m/n/10 image(as(x, "sparseMatrix")) \T1/ptm/m/n/10 so the com-ments in
the above de-scrip-tion of
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[]\T1/pcr/m/n/10 signature(x = "CHMfactor", logarithm = "logical")
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l}) has been already used, duplicate ignored
<to be read again>
\relax
l.1134 ...- 'Matrix' S4 Generic and Methods}{chol}
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ation with the same identifier (name{Rfn.chol.1}) has been already used, duplic
ate ignored
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\relax
l.1134 ...- 'Matrix' S4 Generic and Methods}{chol}
[2203pdfTeX 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'
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tion with the same identifier (name{Rfn.chol,lsCMatrix.Rdash.method}) has been
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\AtBegShi@Output ...ipout \box \AtBeginShipoutBox
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l.1163 ## S4 method for signature 'dsparseMatrix'
pdfTeX warning (ext4): destina
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\AtBegShi@Output ...ipout \box \AtBeginShipoutBox
\fi \fi
l.1163 ## S4 method for signature 'dsparseMatrix'
] [2204]
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[]\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur
e & factorization[]
[2205]
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[]\T1/pcr/m/n/10 Cholesky(A, perm = TRUE, LDL = !super, super = FALSE, Imult =
0, ...)
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[]\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
[2206]
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[]\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
[2207]
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[]\T1/pcr/m/n/9 ## hence, the identical() check *should* work, but fails on so
me GOTOblas:[]
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[]\T1/pcr/m/n/9 dq <- function(ch) paste(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/p
cr/m/n/9 '\T1/pcr/m/n/9 ,ch,\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/pcr/m/n/9 '\T1/
pcr/m/n/9 , sep="") ## dQuote(<UTF-8>) gives bad plots[]
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[]\T1/pcr/m/n/9 (opts <- expand.grid(perm = c(TRUE,FALSE), LDL = c(TRUE,FALSE)
, super = c(FALSE,TRUE)))[]
[2208]
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[]\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
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\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
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[]\T1/ptm/m/n/10 Both these fac-tor-iza-tions can \T1/ptm/m/it/10 di-rectly \T1
/ptm/m/n/10 be treated as (tri-an-gu-lar) ma-tri-ces, as they ex-tend
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\T1/ptm/m/n/10 ply an $\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10
n$ \T1/ptm/m/n/10 nu-meric [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 . Hen
ce, for com-pat-i-bil-ity, the \T1/pcr/m/n/10 "Cholesky" \T1/ptm/m/n/10 and
[2209]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col
Sums}) has been already used, duplicate ignored
<to be read again>
\relax
l.1623 ... Row and Column Sums and Means}{colSums}
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l.1623 ... Row and Column Sums and Means}{colSums}
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l.1624 \aliasA{colMeans}{colSums}{colMeans}
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ith the same identifier (name{Rfn.rowMeans}) has been already used, duplicate i
gnored
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l.1645 \aliasA{rowMeans}{colSums}{rowMeans}
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nored
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l.1656 \aliasA{rowSums}{colSums}{rowSums}
[2210]
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sparse, i.e., i
n-her-it-ing from
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\T1/ptm/m/n/10 class [][]\T1/pcr/m/n/10 sparseVector[][][]\T1/ptm/m/n/10 . Only
ap-pli-ca-ble when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is in-her-it-ing from a
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[][][]\T1/pcr/m/n/10 dimnames[][][](x) \T1/ptm/m/n/10 are only kept (as [][]\T1
/pcr/m/n/10 names[][][](v)\T1/ptm/m/n/10 ) when the re-sult-ing \T1/pcr/m/n/10
v \T1/ptm/m/n/10 is [][]\T1/pcr/m/n/10 numeric[][][]\T1/ptm/m/n/10 , since
[2211]
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[]\T1/pcr/m/n/10 signature(x = "compMatrix", value = "list")\T1/ptm/m/n/10 : se
t the
[2212]
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[]\T1/ptm/m/n/10 a num-ber $\OML/cmm/m/it/10 > \OT1/cmr/m/n/10 0$\T1/ptm/m/n/10
, the es-ti-mated (1-norm) con-di-tion num-ber $[]$; when
[2213] [2214] [2215]
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[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "ddenseMatrix
", where =
[2216] [2217]
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[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "denseMatrix"
, where =
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\T1/ptm/m/n/10 i-cally via \T1/pcr/m/n/10 as(*, "CsparseMatrix") \T1/ptm/m/n/10
or sim-i-lar. Of-ten how-ever, more eas-ily via
[2218]
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[]\T1/pcr/m/n/10 signature(x = "dgCMatrix")\T1/ptm/m/n/10 : com-putes the LU de
-com-po-si-tion of a square
[2219]
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[]\T1/pcr/m/n/10 signature(x = "dgeMatrix", norm = "character") \T1/ptm/m/n/10
or
[2220]
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[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("dgTMatrix", ...)\T1/ptm/m/n/10 ,
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\T1/ptm/m/n/10 but more typ-i-cally via \T1/pcr/m/n/10 as(*, "dgTMatrix")\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 spMatrix[][][]()\T1/ptm/m/n/10 , or
[2221]
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[]\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
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[]\T1/ptm/m/n/10 However this means that a ma-trix typ-i-cally can tbe stored i
n more than one pos-si-ble
Underfull \hbox (badness 10000) in paragraph at lines 2617--2620
[]\T1/ptm/m/n/10 Class [][]\T1/pcr/m/n/10 dgCMatrix[][][] \T1/ptm/m/n/10 or the
su-per-classes [][]\T1/pcr/m/n/10 dsparseMatrix[][][] \T1/ptm/m/n/10 and [][]\
T1/pcr/m/n/10 TsparseMatrix[][][]\T1/ptm/m/n/10 ;
[2222]
Underfull \hbox (badness 2689) in paragraph at lines 2673--2675
[]\T1/ptm/m/n/10 integer spec-i-fy-ing the di-men-sion of the (square) ma-trix.
If miss-ing,
Underfull \hbox (badness 10000) in paragraph at lines 2677--2682
[]\T1/ptm/m/n/10 for \T1/pcr/m/n/10 .symDiagonal \T1/ptm/m/n/10 (\T1/pcr/m/n/10
.trDiagonal\T1/ptm/m/n/10 ), the re-sult-ing sparse
Underfull \hbox (badness 3482) in paragraph at lines 2677--2682
[][]\T1/pcr/m/n/10 symmetricMatrix[][][] \T1/ptm/m/n/10 (or [][]\T1/pcr/m/n/10
triangularMatrix[][][]\T1/ptm/m/n/10 ) will have slot \T1/pcr/m/n/10 uplo
[2223]
Underfull \hbox (badness 1097) in paragraph at lines 2700--2703
[]\T1/pcr/m/n/10 Diagonal() \T1/ptm/m/n/10 re-turns an ob-ject of class [][]\T1
/pcr/m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 ldiMatrix[][][
] \T1/ptm/m/n/10 (with ``su-per-class''
Underfull \hbox (badness 1142) in paragraph at lines 2713--2718
[][]\T1/pcr/m/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 (the re-sult-ing class de
-pend-ing on \T1/pcr/m/n/10 shape \T1/ptm/m/n/10 and \T1/pcr/m/n/10 kind\T1/ptm
/m/n/10 ) rep-re-sen-ta-tion of
[2224]
Underfull \hbox (badness 3646) in paragraph at lines 2951--2954
[]\T1/ptm/m/n/10 the [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , a [][]\T
1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 , see the [][]\T1/pcr/m/n/10 Matrix[][][]
\T1/ptm/m/n/10 class de-scrip-tion. Typ-i-cally
Underfull \hbox (badness 10000) in paragraph at lines 2973--2974
[]\T1/pcr/m/n/10 signature(from = "diagonalMatrix", to = "triangularMatrix")\T1
/ptm/m/n/10 :
Underfull \hbox (badness 1810) in paragraph at lines 2980--2982
[]\T1/pcr/m/n/10 signature(a = "diagonalMatrix", b, ...)\T1/ptm/m/n/10 : is tri
v-ially im-ple-mented, of
Underfull \hbox (badness 10000) in paragraph at lines 2983--2985
[]\T1/pcr/m/n/10 signature(x = "nMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv
-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
Underfull \hbox (badness 3803) in paragraph at lines 2986--2990
[]\T1/pcr/m/n/10 signature(x = "diagonalMatrix")\T1/ptm/m/n/10 : all these grou
p meth-ods re-turn a
[2225]
Underfull \hbox (badness 1371) in paragraph at lines 2995--3001
[]\T1/pcr/m/n/10 signature(e1 = "ddiMatrix", e2="denseMatrix")\T1/ptm/m/n/10 :
the re-sult is from class
Underfull \hbox (badness 10000) in paragraph at lines 3002--3006
[]\T1/pcr/m/n/10 (object = "diagonalMatrix")\T1/ptm/m/n/10 : Re-turns an ob-jec
t of S3 class
Underfull \hbox (badness 2318) in paragraph at lines 3012--3016
[][][]\T1/pcr/m/n/10 Diagonal[][][]() \T1/ptm/m/n/10 as con-struc-tor of these
ma-tri-ces, and [][]\T1/pcr/m/n/10 isDiagonal[][][]\T1/ptm/m/n/10 . [][]\T1/pcr
/m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 and
[2226] [2227]
Underfull \hbox (badness 1859) in paragraph at lines 3196--3198
[]\T1/pcr/m/n/10 signature(x = "dMatrix", digits = "numeric")\T1/ptm/m/n/10 : t
his group con-tains
Underfull \hbox (badness 10000) in paragraph at lines 3243--3245
[][][]\T1/pcr/m/n/10 drop0[][][](x, tol=1e-10) \T1/ptm/m/n/10 is some-times pre
fer-able to (and more ef-fi-cient than)
[2228]
Underfull \hbox (badness 1168) in paragraph at lines 3363--3366
[]\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
[2229] [2230]
Underfull \hbox (badness 4967) in paragraph at lines 3528--3532
[]\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
[2231]
Overfull \hbox (2.39853pt too wide) in paragraph at lines 3533--3535
[]\T1/ptm/m/n/10 Creation ``from scratch'' most ef-fi-ciently hap-pens via [][]
\T1/pcr/m/n/10 sparseMatrix[][][](*, symmetric=TRUE)\T1/ptm/m/n/10 .
Underfull \hbox (badness 6364) in paragraph at lines 3575--3578
[]\T1/pcr/m/n/10 signature(a = "dsCMatrix", b = "....")\T1/ptm/m/n/10 : \T1/pcr
/m/n/10 x <- solve(a,b) \T1/ptm/m/n/10 solves
[2232] [2233]
Underfull \hbox (badness 10000) in paragraph at lines 3725--3730
[]\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 3725--3730
\T1/ptm/m/n/10 class \T1/pcr/m/n/10 "dsparseMatrix" \T1/ptm/m/n/10 or \T1/pcr/m
/n/10 "RsparseMatrix"\T1/ptm/m/n/10 ; class \T1/pcr/m/n/10 "compMatrix" \T1/ptm
/m/n/10 by class
Underfull \hbox (badness 10000) in paragraph at lines 3735--3737
[]\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "missing")\T1/ptm/m/n/10 : a
triv-ial
Underfull \hbox (badness 10000) in paragraph at lines 3737--3740
[]\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "character")\T1/ptm/m/n/10 :
if
[2234]
Underfull \hbox (badness 4967) in paragraph at lines 3813--3815
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 3852--3855
[]\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")\T1/ptm/m/n/10 ,
or
Underfull \hbox (badness 1735) in paragraph at lines 3852--3855
\T1/pcr/m/n/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 type = "missing
"\T1/ptm/m/n/10 : Com-putes the ma-trix norm of the
[2235]
Underfull \hbox (badness 10000) in paragraph at lines 3855--3858
[]\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")\T1/ptm/m/n/10 ,
or
Underfull \hbox (badness 2318) in paragraph at lines 3855--3858
\T1/pcr/m/n/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 type = "missing
"\T1/ptm/m/n/10 : Com-putes the re-cip-ro-cal con-di-tion
Underfull \hbox (badness 6364) in paragraph at lines 3859--3862
[]\T1/pcr/m/n/10 signature(a = "dsyMatrix", b = "....")\T1/ptm/m/n/10 : \T1/pcr
/m/n/10 x <- solve(a,b) \T1/ptm/m/n/10 solves
[2236]
Underfull \hbox (badness 4060) in paragraph at lines 3983--3986
[]\T1/pcr/m/n/10 signature(a = "dtCMatrix", b = "....")\T1/ptm/m/n/10 : sparse
tri-an-gu-lar solve (aka
[2237]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4023--4023
[]\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 4091--4095
[]\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
[2238]
Underfull \hbox (badness 10000) in paragraph at lines 4100--4103
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix", y = "dgeMatrix")\T1/ptm/m/n/10 : Ma
-
Underfull \hbox (badness 10000) in paragraph at lines 4100--4103
\T1/ptm/m/n/10 trix mul-ti-pli-ca-tion; ditto for sev-eral other sig-na-ture co
m-bi-na-tions, see
Underfull \hbox (badness 10000) in paragraph at lines 4105--4109
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix", logarithm = "logical")\T1/ptm/m/n/1
0 : the
[2239] [2240] [2241] [2242]
Underfull \hbox (badness 10000) in paragraph at lines 4393--4398
[]\T1/ptm/m/n/10 The ex-po-nen-tial of a ma-trix is de-fined as the in-fi-nite
Tay-lor se-ries
[2243] [2244]
Overfull \hbox (85.38034pt too wide) in paragraph at lines 4527--4527
[] \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 4530--4530
[] \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 4534--4534
[]\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 4537--4537
[]\T1/pcr/m/n/9 file.info(MMfile)[,c("size", "ctime")] # (some confirmation of
the file\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s)[]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 4547--4547
[]\T1/pcr/m/n/9 ## has columns (i, j, x) -> we can use via do.call() as argume
nts to sparseMatrix():[]
[2245] [2246]
Underfull \hbox (badness 10000) in paragraph at lines 4702--4704
[][][]\T1/pcr/m/n/10 symmpart[][][] \T1/ptm/m/n/10 for the sym-met-ric part of
a ma-trix, or the co-er-cions
[2247] [2248]
Underfull \hbox (badness 10000) in paragraph at lines 4849--4854
[]\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 ,
[2249]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4930--4930
[]\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 4932--4932
[] \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 4936--4936
[] \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE,
dimnames=dns))[]
[2250]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4943--4943
[] \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 '[]
[2251]
Underfull \hbox (badness 10000) in paragraph at lines 5068--5073
[]\T1/ptm/m/n/10 color for the bor-der of each rect-an-gle. \T1/pcr/m/n/10 NA \
T1/ptm/m/n/10 means
Underfull \hbox (badness 10000) in paragraph at lines 5068--5073
\T1/ptm/m/n/10 no bor-der is drawn. When \T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 as
by de-fault,
Underfull \hbox (badness 2644) in paragraph at lines 5068--5073
\T1/pcr/m/n/10 border.col <- if(lwd < .01) NA else NULL \T1/ptm/m/n/10 is used.
Con-
Underfull \hbox (badness 4108) in paragraph at lines 5068--5073
\T1/ptm/m/n/10 sider us-ing an opaque color in-stead of \T1/pcr/m/n/10 NULL \T1
/ptm/m/n/10 which cor-re-sponds to
[2252]
Underfull \hbox (badness 4120) in paragraph at lines 5087--5090
[]\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 5124--5124
[]\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 5130--5130
[] \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 5131--5131
[] \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 5134--5134
[]\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 5136--5136
[]\T1/pcr/m/n/9 if(doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CH
ECK_EXTRA")) ||[]
[2253]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5143--5143
[]\T1/pcr/m/n/9 image(USCounties, useRaster = TRUE) # should not suffer from a
nti-aliasing[]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 5146--5146
[] \T1/pcr/m/n/9 ## and now look at the *.png image in a viewer you can easi
ly zoom in and out[]
[2254]
Underfull \hbox (badness 1817) in paragraph at lines 5235--5244
[]\T1/ptm/m/n/10 While ``row-indexing'' (of more than one row \T1/ptm/m/it/10 o
r \T1/ptm/m/n/10 us-ing \T1/pcr/m/n/10 drop=FALSE\T1/ptm/m/n/10 ) stays within
the
Underfull \hbox (badness 5637) in paragraph at lines 5277--5279
[]\T1/pcr/m/n/10 signature(x = "matrix", y = "indMatrix") \T1/ptm/m/n/10 and ot
her sig-na-tures (use
[2255]
Underfull \hbox (badness 3138) in paragraph at lines 5303--5305
[]\T1/pcr/m/n/10 signature(x = "indMatrix")\T1/ptm/m/n/10 : re-turn the
[2256]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 5370--5370
[] \T1/pcr/m/n/9 if(getRversion() >= "3.2.0") identical(I12, rbind(I1
, I2)) else TRUE,[]
Underfull \hbox (badness 1603) in paragraph at lines 5391--5393
[]\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 p \T1/ptm/m/n/10 con-t
ains val-ues \T1/pcr/m/n/10 0:(n-1) \T1/ptm/m/n/10 or rather (by de-fault,
Underfull \hbox (badness 10000) in paragraph at lines 5399--5404
[]\T1/ptm/m/n/10 an in-te-ger vec-tor of the same length (\T1/pcr/m/n/10 n\T1/p
tm/m/n/10 ) as \T1/pcr/m/n/10 p\T1/ptm/m/n/10 . By de-fault,
Underfull \hbox (badness 10000) in paragraph at lines 5399--5404
\T1/ptm/m/n/10 (\T1/pcr/m/n/10 zero.p = FALSE, zero.res = FALSE\T1/ptm/m/n/10 )
, \T1/pcr/m/n/10 invPerm(p) \T1/ptm/m/n/10 is the same as
Underfull \hbox (badness 10000) in paragraph at lines 5399--5404
[][]\T1/pcr/m/n/10 order[][][](p) \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 sort.lis
t[][][](p) \T1/ptm/m/n/10 and for that case, the func-tion is equiv-a-lent to
[2257] [2258] [2259]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5628--5628
[]\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[]
[2260]
Underfull \hbox (badness 10000) in paragraph at lines 5709--5712
[][][]\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 5720--5720
[]\T1/pcr/m/n/9 isTriangular(as(M, "dgeMatrix")) # still triangular, even if n
ot "formally"[]
[2261]
Underfull \hbox (badness 1622) in paragraph at lines 5757--5762
[]\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 5757--5762
\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
[2262]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5818--5818
[]\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 5819--5819
[] \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 5826--5826
[] \T1/pcr/m/n/9 identical(dimnames(KhatriRao(m, d0, make.dimnames=TRUE)), di
mnames(Kmd)))[]
[2263]
Underfull \hbox (badness 1062) in paragraph at lines 5955--5958
[]\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
[2264]
Underfull \hbox (badness 2809) in paragraph at lines 5984--5987
[]\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
[2265]
Underfull \hbox (badness 2635) in paragraph at lines 6096--6101
[]\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 6096--6101
\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 6104--6107
[]\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.,
[2266]
Underfull \hbox (badness 10000) in paragraph at lines 6214--6224
\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 6214--6224
[][]\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
[2267]
Underfull \hbox (badness 1184) in paragraph at lines 6296--6299
[]\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
[2268]
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[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,
[2269]
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[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,
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[]\T1/pcr/m/n/9 str(lutp <- as(lutr, "ltpMatrix"))# packed matrix: only 10 = (
4+1)*4/2 entries[]
[2270]
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[]\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
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[][]\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,
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[]\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
[2271]
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[] \T1/pcr/m/n/9 # q is a 0-based permutation o
f the columns[]
[2272] [2273]
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[]\T1/ptm/m/n/10 Note that when the re-sult-ing ma-trix is di-ag-o-nal (``math-
e-mat-i-cally''),
[2274]
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[]\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,
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\T1/pcr/m/n/10 Matrix(0, nrow,ncol) \T1/ptm/m/n/10 di-rectly con-structs an ``e
mpty'' [][]sparse-Ma-trix[][][], as does
[2275]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det
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l.6868 \aliasA{det}{Matrix-class}{det}
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[]\T1/pcr/m/n/10 signature(x = "Matrix")\T1/ptm/m/n/10 : As [][]\T1/pcr/m/n/10
diff[][][]() \T1/ptm/m/n/10 for tra-di-tional ma-tri-ces, i.e., ap-ply-ing
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[]\T1/pcr/m/n/10 signature(x = "Matrix", value = "ANY")\T1/ptm/m/n/10 : where \
T1/pcr/m/n/10 value \T1/ptm/m/n/10 is
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\T1/ptm/m/n/10 in-te-ger of length 2. Al-lows to \T1/ptm/m/it/10 re-shape \T1/p
tm/m/n/10 Ma-trix ob-jects, but only when
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[]\T1/pcr/m/n/10 signature(from = "ANY", to = "Matrix")\T1/ptm/m/n/10 : This re
-lies on a cor-rect
[2276]pdfTeX warning (ext4): destination with the same identifier (name{Rfn..Rp
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\relax
l.7044 ...*\%}{matrix-products}{.Rpcent.*.Rpcent.}
pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.crossprod}) has been already used, dup
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\relax
l.7152 ...A{crossprod}{matrix-products}{crossprod}
pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.tcrossprod}) has been already used, du
plicate ignored
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\relax
l.7252 ...tcrossprod}{matrix-products}{tcrossprod}
[2277]
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\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
[2278pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cros
sprod.Rdash.methods}) has been already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox
\fi \fi
l.7412 \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.7412 \end{Details}
]
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[]\T1/pcr/m/n/10 signature(x = "dgeMatrix", y = "dgeMatrix")\T1/ptm/m/n/10 : Ma
-
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\T1/ptm/m/n/10 trix mul-ti-pli-ca-tion; ditto for sev-eral other sig-na-ture co
m-bi-na-tions, see
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[]\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") \T1/ptm/m/n/10 and ot
her sig-na-tures (use
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[]\T1/pcr/m/n/10 signature(x = "CsparseMatrix", y = "missing") \T1/ptm/m/n/10 r
e-turns
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[]\T1/pcr/m/n/10 signature(x = "TsparseMatrix", y = "missing") \T1/ptm/m/n/10 r
e-turns
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[]\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") \T1/ptm/m/n/10
and
[2279] [2280]
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[]\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
[2281]
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[]\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
[2282]
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 X <- (X + t(X))/2 \T1/
ptm/m/n/10 should be done, af-ter
[2283]
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[]\T1/ptm/m/n/10 Higham (2002) uses Dyk-stra's cor-rec-tion, but the ver-sion b
y Jens Oehlschlaegel did not
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\T1/ptm/m/n/10 use it (ac-ci-den-tally), and has still lead to good re-sults; t
his sim-pli-fi-ca-tion, now only via
[2284]
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[]\T1/pcr/m/n/9 stopifnot(all.equal(ncr, ncF))# norm type does not matter at a
ll in this example[]
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[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 , di-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 .
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\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "denseMatrix"\T1/ptm/m/n/10 , by class \T1/
pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 . Class \T1/pcr/m/n/10 "Matrix"\T1/ptm/
m/n/10 , by class
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[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ); us
e, e.g.,
[2286] [2287]
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[]\T1/ptm/m/n/10 fast
[2288]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.nor
m}) has been already used, duplicate ignored
<to be read again>
\relax
l.8153 \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.8153 \HeaderA{norm}{Matrix Norms}{norm}
[2289]
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[]\T1/pcr/m/n/9 A <- sparseMatrix(i, j, x = x) ## 8 x 10
"dgCMatrix"[]
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[]\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10
"dsCMatrix"[]
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[]\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10
"dtCMatrix"[]
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[]\T1/ptm/m/n/10 These can be stored in the ``triplet'' form ([][]\T1/pcr/m/n/1
0 TsparseMatrix[][][]\T1/ptm/m/n/10 , sub-classes \T1/pcr/m/n/10 ngTMatrix\T1/p
tm/m/n/10 ,
[2290]
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[]\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
[2291]
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[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,
[2292]
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[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,
[2293]
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[]\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
[2294]
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[]\T1/pcr/m/n/10 signature(x = "matrix", y = "pMatrix") \T1/ptm/m/n/10 and othe
r sig-na-tures (use
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[]\T1/pcr/m/n/10 signature(from = "pMatrix", to = "ngTMatrix")\T1/ptm/m/n/10 :
co-er-cion to sparse
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\T1/ptm/m/n/10 ma-trix; note that \T1/pcr/m/n/10 solve(P) \T1/ptm/m/n/10 is ide
n-ti-cal to \T1/pcr/m/n/10 t(P) \T1/ptm/m/n/10 for per-mu-ta-tion ma-tri-ces. S
ee
[2295] [2296]
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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 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[]
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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
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\T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro
m
[2297] [2298]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.qr}) has been already used, duplicate ignored
<to be read again>
\relax
l.8953 \aliasA{qr}{qr-methods}{qr}
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[]\T1/ptm/m/n/10 QR de-com-po-si-tion of a gen-eral sparse double-precision ma-
trix with
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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![]
[2299]
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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[]
[2300]
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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
[2301]
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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"[]
[2302]
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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.9249 ... the Reciprocal Condition Number}{rcond}
[2303]
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[]\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not
have full rank[]
[2304] [2305] [2306]
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[]\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 gets \T1/pcr/m/n/10 x <- rand.x(nnz) \T1/ptm/m/n/10 and calls []
[]\T1/pcr/m/n/10 sparseMatrix[][][](i=i, j=j, x=x, ..)\T1/ptm/m/n/10 . When
[2307] [2308]
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[]\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
[2309]
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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:[]
[2310]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sol
ve}) has been already used, duplicate ignored
<to be read again>
\relax
l.9826 \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[]
[2311]
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 solve \T1/ptm/m/n/10 meth-ods
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[]\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 basically com-putes uses tri-an-gu-lar
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[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list
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\T1/pcr/m/n/10 ( sparse = FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : U
ses the sparse
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[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list
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\T1/pcr/m/n/10 ( sparse=FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : Che
cks if \T1/pcr/m/n/10 a \T1/ptm/m/n/10 is sym-
[2312]
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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 , and sim-i-lar \T1/pcr/m/n/10 b\T1/ptm/m/n/10 , in-clud-ing
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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[]
[2313]
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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
[2314]
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[]\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for
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\T1/pcr/m/n/10 sparse.model.matrix \T1/ptm/m/n/10 has been changed to \T1/pcr/m
/n/10 FALSE\T1/ptm/m/n/10 , 2010-07, for
Underfull \hbox (badness 6592) in paragraph at lines 10178--10180
[]\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
[2315]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10255--10255
[] \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 10256--10256
[] \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 10257--10257
[] \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M)
== c(0,12),[]
[2316] [2317]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 10441--10441
[] \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)[]
[2318]
Underfull \hbox (badness 4621) in paragraph at lines 10482--10486
[]\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
[2319]
Underfull \hbox (badness 10000) in paragraph at lines 10558--10561
[]\T1/ptm/m/n/10 The stan-dard \T1/phv/m/n/10 R [][]\T1/pcr/m/n/10 xtabs[][][](
*, sparse=TRUE)\T1/ptm/m/n/10 , for sparse ta-bles and
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10570--10570
[]\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 10574--10574
[]\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 10575--10575
[]\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10
"dtCMatrix"[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10580--10580
[]\T1/pcr/m/n/9 (AA <- sparseMatrix(c(1,3:8), c(2,9,6:10), x = 7 * (1:7), dims
= c(10,20)))[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10583--10583
[]\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar
e consistent[]
[2320]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 10606--10606
[]\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted
if necessary:[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 10607--10607
[]\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 10633--10633
[]\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 10637--10637
[] \T1/pcr/m/n/9 XX <- sparseMatrix(j = X@ja, p = X@ia - 1L, x = X@ra, dims =
X@dimension)[]
[2321]
Underfull \hbox (badness 10000) in paragraph at lines 10730--10738
[]\T1/pcr/m/n/10 (object = "sparseMatrix")\T1/ptm/m/n/10 : Re-turns an ob-ject
of S3 class
Underfull \hbox (badness 1325) in paragraph at lines 10751--10755
[]\T1/pcr/m/n/10 signature(x = "sparseMatrix", value = "ANY")\T1/ptm/m/n/10 : a
l-lows to \T1/ptm/m/it/10 re-shape \T1/ptm/m/n/10 a
[2322]
Underfull \hbox (badness 10000) in paragraph at lines 10781--10785
[][][]\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.10821 \aliasA{qr.Q}{sparseQR-class}{qr.Q}
[2323] [2324]
Underfull \hbox (badness 1430) in paragraph at lines 10951--10953
[]\T1/pcr/m/n/10 signature(a = "sparseQR", b = "ANY")\T1/ptm/m/n/10 : For \T1/p
cr/m/n/10 solve(a,b)\T1/ptm/m/n/10 , sim-ply uses
Overfull \hbox (58.38037pt too wide) in paragraph at lines 10979--10979
[] \T1/pcr/m/n/9 qc <- qr.coef (qrm, y); qc. <- qr.coef (qrm, y.) # 2nd fai
led in Matrix <= 1.1-0[]
Underfull \hbox (badness 5036) in paragraph at lines 11007--11009
[]\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case
a
[2325]
Underfull \hbox (badness 2970) in paragraph at lines 11140--11146
[]\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 11140--11146
\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 ,
[2326]
Underfull \hbox (badness 10000) in paragraph at lines 11191--11194
[]\T1/pcr/m/n/10 signature(x = "sparseVector", mode = "character") \T1/ptm/m/n/
10 co-erces
Underfull \hbox (badness 10000) in paragraph at lines 11213--11216
[]\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
[2327]
Underfull \hbox (badness 10000) in paragraph at lines 11231--11236
[]\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 11246--11248
[][][]\T1/pcr/m/n/10 sparseVector[][][]() \T1/ptm/m/n/10 for friendly con-struc
-tion of sparse vec-tors (apart from
[2328] [2329]
Underfull \hbox (badness 3525) in paragraph at lines 11364--11368
[]\T1/ptm/m/n/10 The ma-trix $\OML/cmm/m/it/10 M$ \T1/ptm/m/n/10 will have \T1/
pcr/m/n/10 M[i[k], j[k]] == x[k]\T1/ptm/m/n/10 , for $\OML/cmm/m/it/10 k \OT1/c
mr/m/n/10 = 1\OML/cmm/m/it/10 ; \OT1/cmr/m/n/10 2\OML/cmm/m/it/10 ; [] ; n$\T1/
ptm/m/n/10 , where
Underfull \hbox (badness 1831) in paragraph at lines 11371--11377
[][][]\T1/pcr/m/n/10 Matrix[][][](*, sparse=TRUE) \T1/ptm/m/n/10 for the more u
sual con-struc-tor of such ma-tri-ces. Then,
[2330]
Underfull \hbox (badness 10000) in paragraph at lines 11466--11470
[]\T1/pcr/m/n/10 signature(object = "symmetricMatrix")\T1/ptm/m/n/10 : re-turns
\T1/ptm/m/it/10 sym-met-ric
Underfull \hbox (badness 1043) in paragraph at lines 11466--11470
[][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , even when the \T1/pcr/m/n/10
Dimnames \T1/ptm/m/n/10 slot only has row or col-umn names. This
Underfull \hbox (badness 10000) in paragraph at lines 11482--11487
[]\T1/ptm/m/n/10 The va-lid-ity checks do not re-quire a sym-met-ric \T1/pcr/m/
n/10 Dimnames \T1/ptm/m/n/10 slot, so it can be
Underfull \hbox (badness 1259) in paragraph at lines 11482--11487
\T1/pcr/m/n/10 list(NULL, <character>)\T1/ptm/m/n/10 , e.g., for ef-fi-ciency.
How-ever, [][]\T1/pcr/m/n/10 dimnames[][][]() \T1/ptm/m/n/10 and other
Underfull \hbox (badness 2591) in paragraph at lines 11490--11495
\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
[2331]
Underfull \hbox (badness 2057) in paragraph at lines 11562--11564
[]\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.,
[2332] [2333]
Underfull \hbox (badness 6641) in paragraph at lines 11648--11651
[]\T1/ptm/m/n/10 Currently, [][]\T1/pcr/m/n/10 Schur[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 isSymmetric[][][] \T1/ptm/m/n/10 and \T1/pcr/m/n/10 as() \T1/ptm
/m/n/10 (i.e. [][]\T1/pcr/m/n/10 coerce[][][]\T1/ptm/m/n/10 ) have meth-ods wit
h
Underfull \hbox (badness 5133) in paragraph at lines 11688--11692
[]\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 11688--11692
\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
[2334]
Underfull \hbox (badness 7649) in paragraph at lines 11795--11797
[]\T1/ptm/m/n/10 a sparse ma-trix stored in triplet form, i.e., in-her-it-ing f
rom class
[2335] [2336] [2337]
Underfull \hbox (badness 7362) in paragraph at lines 11996--11998
[]\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
[2338]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 12034--12034
[]\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted
if necessary:[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 12035--12035
[]\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)[]
[2339] [2340]
Underfull \hbox (badness 6910) in paragraph at lines 12285--12287
[]\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back
[2341] [2342] [2343]) (./boot-pkg.tex [2344]
Chapter 18.
[2345] [2346] [2347] [2348] [2349] [2350] [2351]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 530--530
[]\T1/pcr/m/n/10 boot(data, statistic, R, sim = "ordinary", stype = c("i", "f"
, "w"),
[2352]
Underfull \hbox (badness 1325) in paragraph at lines 568--575
[]\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sim-u-la-tion r
e-quired. Pos-si-ble
Underfull \hbox (badness 1275) in paragraph at lines 583--588
[]\T1/ptm/m/n/10 An in-te-ger vec-tor or fac-tor spec-i-fy-ing the strata for m
ulti-sample prob-
Underfull \hbox (badness 1264) in paragraph at lines 583--588
\T1/ptm/m/n/10 lems. This may be spec-i-fied for any sim-u-la-tion, but is ig-n
ored when
[2353]
Overfull \hbox (43.25928pt too wide) in paragraph at lines 643--649
[]\T1/ptm/m/n/10 logical, only al-lowed to be \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/1
0 for \T1/pcr/m/n/10 sim = "ordinary", stype = "i", n = 0
[2354]
Underfull \hbox (badness 6268) in paragraph at lines 797--807
\T1/ptm/m/n/10 or \T1/pcr/m/n/10 parallel = "snow" \T1/ptm/m/n/10 us-ing the de
-fault clus-ter, a sec-ond ap-proach is used if
[2355]
Underfull \hbox (badness 1881) in paragraph at lines 824--826
[]\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi
-cient boot-strap sim-u-la-tion.
Underfull \hbox (badness 6493) in paragraph at lines 851--855
[][][]\T1/pcr/m/n/10 boot.array[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.c
i[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 censboot[][][]\T1/ptm/m/n/10 , [][]\
T1/pcr/m/n/10 empinf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 tilt.boot[][][]\T1/ptm/m/n/10 ,
[2356]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 885--885
[]\T1/pcr/m/n/9 nuke.lm <- glm(log(cost) ~ date+log(cap)+ne+ct+log(cum.n)+pt,
data = nuke)[]
Underfull \vbox (badness 10000) has occurred while \output is active [2357]
[2358]
Underfull \hbox (badness 10000) in paragraph at lines 1066--1070
[]\T1/ptm/m/n/10 A vec-tor of char-ac-ter strings rep-re-sent-ing the type of i
n-ter-
Underfull \hbox (badness 10000) in paragraph at lines 1066--1070
\T1/ptm/m/n/10 vals re-quired. The value should be any sub-set of the val-ues
[2359]
Underfull \hbox (badness 1496) in paragraph at lines 1082--1091
[]\T1/ptm/m/n/10 If sup-plied, a value to be used as an es-ti-mate of the vari-
ance of the
Underfull \hbox (badness 2005) in paragraph at lines 1082--1091
\T1/ptm/m/n/10 statis-tic for the nor-mal ap-prox-i-ma-tion and stu-den-tized i
n-ter-vals. If it
Underfull \hbox (badness 2343) in paragraph at lines 1082--1091
\T1/ptm/m/n/10 is not sup-plied and \T1/pcr/m/n/10 length(index) \T1/ptm/m/n/10
is 2 then \T1/pcr/m/n/10 var.t0 \T1/ptm/m/n/10 de-faults to
Underfull \hbox (badness 2150) in paragraph at lines 1103--1109
[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa
ult value is
[2360] [2361] [2362] [2363]
Underfull \hbox (badness 1571) in paragraph at lines 1443--1445
[]\T1/ptm/m/n/10 Rawlings, J.O. (1988) \T1/ptm/m/it/10 Ap-plied Re-gres-sion An
al-y-sis\T1/ptm/m/n/10 . Wadsworth and Brooks/Cole Statis-
[2364] [2365] [2366] [2367] [2368]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1735--1735
[]\T1/pcr/m/n/10 censboot(data, statistic, R, F.surv, G.surv, strata = matrix(
1,n,2),
[2369] [2370] [2371]
Underfull \vbox (badness 10000) has occurred while \output is active [2372]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 2010--2010
[]\T1/pcr/m/n/9 mel.cox <- coxph(Surv(time, status == 1) ~ ns(thickness, df=4)
+ strata(ulcer),[]
[2373]
Underfull \hbox (badness 6268) in paragraph at lines 2081--2083
[]\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch
an-ning House.
[2374] [2375] [2376]
Underfull \hbox (badness 1565) in paragraph at lines 2335--2340
[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est on the ori
g-i-nal data set
[2377]
Underfull \hbox (badness 4595) in paragraph at lines 2360--2365
\T1/ptm/m/n/10 are passed un-changed ev-ery time \T1/pcr/m/n/10 boot.out$statis
tic \T1/ptm/m/n/10 is called.
Underfull \hbox (badness 1881) in paragraph at lines 2429--2431
[]\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi
-cient boot-strap sim-u-la-tion.
Underfull \hbox (badness 2057) in paragraph at lines 2437--2438
[][][]\T1/pcr/m/n/10 boot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 empinf[][][]
\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 k3.linear[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 linear.approx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 saddle.distn[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smooth.spline[][][]\T1/ptm/m/n/10 ,
[2378] [2379]
Underfull \hbox (badness 1077) in paragraph at lines 2533--2537
[]\T1/ptm/m/n/10 The un-bi-ased es-ti-ma-tor uses a mul-ti-plier of \T1/pcr/m/n
/10 n/((n-1)*(n-2)) \T1/ptm/m/n/10 where \T1/pcr/m/n/10 n \T1/ptm/m/n/10 is the
sam-ple
Underfull \hbox (badness 1112) in paragraph at lines 2533--2537
\T1/ptm/m/n/10 size, if \T1/pcr/m/n/10 unbiased \T1/ptm/m/n/10 is \T1/pcr/m/n/1
0 FALSE \T1/ptm/m/n/10 then a mul-ti-plier of \T1/pcr/m/n/10 1/n \T1/ptm/m/n/10
is used. This is mul-ti-plied by
[2380] [2381] [2382] [2383] [2384]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2892--2892
[]\T1/pcr/m/n/10 EEF.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t
= 25,
Overfull \hbox (18.78088pt too wide) in paragraph at lines 2894--2894
[]\T1/pcr/m/n/10 EL.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t
= 25,[]
[2385] [2386] [2387]
Underfull \hbox (badness 3861) in paragraph at lines 3102--3105
[][][]\T1/pcr/m/n/10 boot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.array[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.ci[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 control[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[][][
]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 linear.approx[][][]\T1/ptm/m/n/10 ,
[2388]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 3155--3155
[]\T1/pcr/m/n/10 envelope(boot.out = NULL, mat = NULL, level = 0.95, index = 1
:ncol(mat))
[2389] [2390] [2391]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3375--3375
[]\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t
he resampling
[2392] [2393] [2394] [2395] [2396] [2397] [2398]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3835--3835
[] \T1/pcr/m/n/10 t = boot.out$t[, index], w = NULL, def = TRUE, q
= NULL)[]
[2399] [2400]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3974--3974
[]\T1/pcr/m/n/9 grav.p <- imp.prob(grav.tilt.boot, w = grav.w, index = 3, t0 =
grav.z0[3])[]
[2401] [2402] [2403]
Underfull \hbox (badness 10000) in paragraph at lines 4187--4189
[]\T1/ptm/m/n/10 The quan-tiles at which the plots are re-quired. The de-fault
is
[2404]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4256--4256
[]\T1/pcr/m/n/9 # To draw the jackknife-after-bootstrap plot for the head siz
e data as in
[2405] [2406]
Underfull \hbox (badness 10000) in paragraph at lines 4359--4361
[]\T1/ptm/m/n/10 The in-dex of the vari-able of in-ter-est within the out-put o
f
Underfull \hbox (badness 1430) in paragraph at lines 4368--4372
\T1/ptm/m/n/10 If \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is sup-plied but nei-ther \T
1/pcr/m/n/10 t \T1/ptm/m/n/10 nor \T1/pcr/m/n/10 L \T1/ptm/m/n/10 are sup-plied
then \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is set to
Underfull \hbox (badness 2269) in paragraph at lines 4386--4389
[]\T1/ptm/m/n/10 The lin-ear ap-prox-i-ma-tion to a boot-strap repli-cate with
fre-quency vec-tor \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is given by
[2407] [2408] [2409] [2410] [2411] [2412] [2413] [2414] [2415]
Underfull \hbox (badness 3000) in paragraph at lines 4956--4959
[]\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put
of a call to
[2416] [2417] [2418] [2419]
Underfull \hbox (badness 2293) in paragraph at lines 5235--5238
[]\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the
boot-strap
Underfull \hbox (badness 1668) in paragraph at lines 5235--5238
\T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl
os-est to
[2420]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5314--5314
[]\T1/pcr/m/n/9 grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w", strat
a = grav1[, 2])[]
[2421] [2422] [2423] [2424] [2425] [2426] [2427] [2428]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5863--5863
[]\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c
ity.sp1$spa[1][]
[2429]
Underfull \hbox (badness 1127) in paragraph at lines 5985--6003
\T1/ptm/m/n/10 etc. un-til a point is found with a cdf ap-prox-i-ma-tion less t
han \T1/pcr/m/n/10 min(alpha)/10\T1/ptm/m/n/10 , then
[2430]
Underfull \hbox (badness 2837) in paragraph at lines 6018--6021
[]\T1/ptm/m/n/10 The re-turned value is an ob-ject of class \T1/pcr/m/n/10 "sad
dle.distn"\T1/ptm/m/n/10 . See the help file for
[2431] [2432] [2433] [2434]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6303--6303
[]\T1/pcr/m/n/9 # This example is taken from Exercise 7.5 of Gill, Murray and
Wright (1991).
[2435] [2436]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6492--6492
[]\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t
he resampling
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[]\T1/pcr/m/n/9 # value of the test statistic 1.84. In the book exponential t
ilting was used[]
[2437] [2438] [2439]
Underfull \hbox (badness 1596) in paragraph at lines 6739--6743
[]\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sec-ond ar-gu-m
ent ex-pected by
[2440] [2441]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6899--6899
[] \T1/pcr/m/n/9 stype = "i", sim = "balanced", alpha =
c(0.05, 0.95),[]
[2442] [2443] [2444] [2445] [2446] [2447] [2448] [2449]) (./class-pkg.tex
[2450]
Chapter 19.
[2451] [2452] [2453] [2454] [2455] [2456] [2457] [2458]
Underfull \hbox (badness 10000) in paragraph at lines 608--610
[]\T1/ptm/m/n/10 the size of the code-book. De-faults to
[2459] [2460] [2461] [2462] [2463] [2464] [2465] [2466]) (./cluster-pkg.tex
Chapter 20.
[2467]
Underfull \hbox (badness 3098) in paragraph at lines 133--142
[]\T1/ptm/b/n/10 Care \T1/ptm/m/n/10 and ex-per-tise is prob-a-bly needed when
us-ing \T1/pcr/m/n/10 method = "flexible" \T1/ptm/m/n/10 par-tic-u-
Underfull \hbox (badness 2253) in paragraph at lines 133--142
\T1/ptm/m/n/10 larly for the case when \T1/pcr/m/n/10 par.method \T1/ptm/m/n/10
is spec-i-fied of longer length than one. Since
Underfull \hbox (badness 3323) in paragraph at lines 133--142
\T1/ptm/b/n/10 clus-ter \T1/ptm/m/n/10 ver-sion 2.0, choices lead-ing to in-val
id \T1/pcr/m/n/10 merge \T1/ptm/m/n/10 struc-tures now sig-nal an er-ror
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\T1/ptm/m/n/10 as \T1/pcr/m/n/10 method="flexible", par.method = 0.5\T1/ptm/m/n
/10 . Fur-ther, \T1/pcr/m/n/10 method= "single"
Underfull \hbox (badness 10000) in paragraph at lines 133--142
\T1/ptm/m/n/10 is equiv-a-lent to \T1/pcr/m/n/10 method="flexible", par.method
= c(.5,.5,0,-.5)\T1/ptm/m/n/10 , and
Overfull \hbox (48.49016pt too wide) in paragraph at lines 133--142
\T1/pcr/m/n/10 method="complete" \T1/ptm/m/n/10 is equiv-a-lent to \T1/pcr/m/n/
10 method="flexible", par.method = c(.5,.5,0,+.5)\T1/ptm/m/n/10 .
[2468]
Underfull \hbox (badness 10000) in paragraph at lines 167--169
[]\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 method = "gaverage", par.method = 0 \
T1/ptm/m/n/10 (or \T1/pcr/m/n/10 par.method =
[2469]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 252--252
[] \T1/pcr/m/n/9 all.equal(a.wgt [iC], agnes(d.vr, method="flexible", par.met
hod = 0.5)[iC]) ,[]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 253--253
[] \T1/pcr/m/n/9 all.equal(a.sing[iC], agnes(d.vr, method="flex", par.method=
c(.5,.5,0, -.5))[iC]),[]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 254--254
[] \T1/pcr/m/n/9 all.equal(a.comp[iC], agnes(d.vr, method="flex", par.method=
c(.5,.5,0, +.5))[iC]))[]
[2470] [2471]
Underfull \vbox (badness 10000) has occurred while \output is active [2472]
[2473]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 518--518
[] \T1/pcr/m/n/10 col = c(2, 0), border = 0, axes = TRUE, frame.plot
= axes,[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 522--522
[] \T1/pcr/m/n/10 yaxRight = fromLeft, y.mar = 2.4 + max.strlen/2.5,
...)[]
[2474]
Underfull \hbox (badness 5374) in paragraph at lines 539--541
[]\T1/ptm/m/n/10 logical in-di-cat-ing the ban-ner should be framed; mainly use
d when
[2475]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 637--637
[] \T1/pcr/m/n/10 keep.data = medoids.x, rngR = FALSE, pamLike = FALSE, c
orrect.d = TRUE)[]
[2476]
Underfull \hbox (badness 3078) in paragraph at lines 688--691
[]\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
[2477] [2478]
Underfull \hbox (badness 2941) in paragraph at lines 778--781
[][][]\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 816--816
[]\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo
r this seed):[]
[2479]
Underfull \hbox (badness 10000) in paragraph at lines 863--865
[]\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p
le, see
[2480]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 928--928
[] \T1/pcr/m/n/10 arrowArgs = list(col="red3", length=1/16, angle=90, code
=3), ...)[]
[2481]
Underfull \hbox (badness 4872) in paragraph at lines 974--976
[]\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 988--992
[]\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in
2012,
[2482]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1095--1095
[] \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE.
factor = SEf)))[]
[2483]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 1112--1112
[]\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 1150--1150
[]\T1/pcr/m/n/9 plot(gsP.Z, main = "clusGap(<iid_rnorm_p=3>) ==> k = 1 clust
er is optimal")[]
[2484]
Underfull \hbox (badness 4144) in paragraph at lines 1182--1186
[]\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
[2485]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 1258--1258
[] \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 1264--1264
[] \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin
t variability."),[]
[2486] [2487]
Underfull \hbox (badness 10000) in paragraph at lines 1403--1408
[]\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 1451--1454
[2488]
Underfull \hbox (badness 10000) in paragraph at lines 1468--1472
[][][]\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 1492--1492
[]\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 1502--1502
[] \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i
dent. only points[]
[2489]
Underfull \hbox (badness 5741) in paragraph at lines 1542--1545
[]\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
[2490]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1608--1608
[] \T1/pcr/m/n/10 warnBin = warnType, warnAsym = warnType, warnConst = wa
rnType,[]
[2491]
Underfull \hbox (badness 5008) in paragraph at lines 1725--1733
\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
[2492] [2493]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1816--1816
[]\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 1835--1835
[]\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st
and = FALSE,
[2494] [2495] [2496] [2497]
Underfull \hbox (badness 10000) in paragraph at lines 2143--2145
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the con-verged. This is de-fined as
Underfull \hbox (badness 10000) in paragraph at lines 2154--2157
Underfull \hbox (badness 3179) in paragraph at lines 2168--2174
[][][]\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.
[2498] [2499] [2500]
Underfull \hbox (badness 10000) in paragraph at lines 2326--2329
[][][]\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 ,
[2501]
Underfull \hbox (badness 1292) in paragraph at lines 2394--2397
[]\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 2403--2405
[]\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 2426--2429
[][][]\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 ,
[2502] [2503] [2504] [2505]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2642--2642
[]\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 ):[]
[2506] [2507]
Underfull \hbox (badness 1067) in paragraph at lines 2829--2834
[]\T1/ptm/m/n/10 The de-fault \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 (or in-te-ger
\T1/pcr/m/n/10 0\T1/ptm/m/n/10 ) cor-re-sponds to the orig-i-nal ``swap'' al-g
o-rithm, whereas
[2508]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2888--2888
[]\T1/pcr/m/n/9 ## no _build_ *and* no _swap_ phase: just cluster all obs. aro
und (1, 16):[]
[2509] [2510]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 2991--2991
[]\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co
l.axis = "red")[]
[2511] [2512] [2513]
Overfull \hbox (78.78088pt too wide) in paragraph at lines 3187--3187
[] \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x
$ac, digits = 2)),[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3188--3188
[] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
= TRUE, ...)[]
[2514]
Underfull \hbox (badness 10000) in paragraph at lines 3255--3258
[]\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
[2515]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3305--3305
[] \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc,
digits = 2)),[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3306--3306
[] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
= TRUE, ...)[]
[2516] [2517] [2518]
Underfull \hbox (badness 10000) in paragraph at lines 3491--3494
[]\T1/ptm/m/n/10 when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 does not have a \T1/pcr/m
/n/10 diss \T1/ptm/m/n/10 com-po-nent as for
Underfull \hbox (badness 3471) in paragraph at lines 3491--3494
[][]\T1/pcr/m/n/10 pam[][][](*, keep.diss=FALSE)\T1/ptm/m/n/10 , \T1/pcr/m/n/10
dist \T1/ptm/m/n/10 must be the dis-sim-i-lar-ity if a
[2519]
Underfull \hbox (badness 10000) in paragraph at lines 3554--3559
[][][]\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 ,
[2520]
Underfull \hbox (badness 4621) in paragraph at lines 3616--3621
[]\T1/ptm/m/n/10 Note that cur-rently the method func-tion sim-ply calls \T1/pc
r/m/n/10 plot([][]as.hclust[][][](x), ...)\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1990) in paragraph at lines 3616--3621
\T1/ptm/m/n/10 which dis-patches to [][]\T1/pcr/m/n/10 plot.hclust[][][](..)\T1
/ptm/m/n/10 . If more flex-i-ble plots are needed, con-sider
Underfull \hbox (badness 6268) in paragraph at lines 3628--3631
[][][]\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 ,
[2521] [2522] [2523]
Underfull \hbox (badness 10000) in paragraph at lines 3813--3816
[][][]\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 3844--3847
[][][]\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 ,
[2524]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 3897--3897
[] \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right =
TRUE, ...)[]
Underfull \hbox (badness 2035) in paragraph at lines 3908--3910
[]\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
[2525] [2526] [2527] [2528]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 4101--4101
[] \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 4103--4103
[] \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat
= TRUE, ...)[]
Underfull \hbox (badness 1946) in paragraph at lines 4132--4137
[]\T1/ptm/m/n/10 arguments passed [][]\T1/pcr/m/n/10 barplot[][][]()\T1/ptm/m/n
/10 ; note that the de-fault used to be \T1/pcr/m/n/10 col
[2529]
Underfull \hbox (badness 10000) in paragraph at lines 4199--4207
\T1/pcr/m/n/10 attr(sil, "Ordered") \T1/ptm/m/n/10 is a log-i-cal in-di-cat-ing
if \T1/pcr/m/n/10 sil \T1/ptm/m/it/10 is \T1/ptm/m/n/10 or-dered as by
[2530]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4241--4241
[]\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 4250--4250
[] \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 4252--4252
[] \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 4255--4255
[]\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 4257--4257
[] \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 4264--4264
[]\T1/pcr/m/n/9 str(xc1k <- xclara[ sample(nrow(xclara), size = 1000) ,]) # ro
wnames == indices[]
[2531] [2532] [2533] [2534] [2535] [2536]
Underfull \hbox (badness 10000) in paragraph at lines 4622--4628
[]\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 4638--4640
[]\T1/ptm/m/n/10 Sample data set ac-com-pa-ny-ing the ref-er-ence be-low (file
`\T1/pcr/m/n/10 xclara.dat\T1/ptm/m/n/10 ' in side
Overfull \hbox (52.98038pt too wide) in paragraph at lines 4651--4651
[]\T1/pcr/m/n/9 ## Visualization: Assuming groups are defined as {1:1000}, {10
01:2000}, {2001:3000}
Overfull \hbox (9.78043pt too wide) in paragraph at lines 4653--4653
[]\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:[]
[2537]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4667--4667
[] \T1/pcr/m/n/9 ## Apart from these, what are the robust ranges of indices? -
- Robust range:[]
[2538]) (./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,[]
[2539]
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[]\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
[2540]
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[]\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e
nterInternal,[]
[2541] [2542] [2543]) (./foreign-pkg.tex [2544]
Chapter 22.
[2545]
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[]\T1/ptm/m/n/10 a char-ac-ter string with the name of the ARFF file to read fr
om, or a
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[]\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / /
www . cs . waikato . ac . nz / ~ml / weka / arff .
[2546] [2547]
Underfull \hbox (badness 3601) in paragraph at lines 235--243
[]\T1/ptm/m/n/10 A data frame with at-tributes. These will in-clude \T1/pcr/m/n
/10 "datalabel"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "time.stamp"\T1/ptm/m/n/10 ,
[2548]
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[]\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates =
FALSE,
[2549] [2550] [2551]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 462--462
[] \T1/pcr/m/n/10 trim_values = TRUE, reencode = NA, use.missings = t
o.data.frame,[]
[2552]
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[] \T1/pcr/m/n/10 sub = ".", add.undeclared.levels = c("sort", "appen
d", "no"),[]
Underfull \hbox (badness 10000) in paragraph at lines 506--515
[]\T1/ptm/m/n/10 character: what to do with du-pli-cated value la-bels for dif-
fer-
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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
Underfull \hbox (badness 10000) in paragraph at lines 506--515
\T1/ptm/m/n/10 la-bel is kept while fur-ther du-pli-cated la-bels are re-named
to
Underfull \hbox (badness 10000) in paragraph at lines 506--515
\T1/pcr/m/n/10 paste0(label, duplicated.value.labels.infix, level)\T1/ptm/m/n/1
0 ,
Underfull \hbox (badness 10000) in paragraph at lines 516--519
[]\T1/ptm/m/n/10 character: the in-fix used for la-bels of fac-tor lev-els with
du-
Underfull \hbox (badness 10000) in paragraph at lines 516--519
\T1/ptm/m/n/10 pli-cated value la-bels in SPSS (de-fault \T1/pcr/m/n/10 "_dupli
cated_"\T1/ptm/m/n/10 ) if
[2553]
Underfull \hbox (badness 10000) in paragraph at lines 551--559
[]\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 http : / / msdn . microsoft . com / en
-[]us / library / ms776446(VS . 85 ) .aspx$[][]
Underfull \hbox (badness 7613) in paragraph at lines 569--575
[]\T1/ptm/m/n/10 There may be at-tributes \T1/pcr/m/n/10 "label.table" \T1/ptm/
m/n/10 and \T1/pcr/m/n/10 "variable.labels"\T1/ptm/m/n/10 . At-tribute
[2554]
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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,[]
[2555]
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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 669--669
[]\T1/pcr/m/n/9 long.string <- apply(x[,c("string_500", "STRIN0")], 1, paste,
collapse="")[]
[2556] [2557]
Underfull \hbox (badness 10000) in paragraph at lines 813--814
Overfull \hbox (4.38043pt too wide) in paragraph at lines 823--823
[]\T1/pcr/m/n/9 iris.s <- read.systat(system.file("files/Iris.syd", package="f
oreign")[1])[]
[2558] [2559]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 899--899
[] \T1/pcr/m/n/10 data.restore(file, print = FALSE, verbose = FALSE, env = .G
lobalEnv)
[2560]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 963--963
[]\T1/pcr/m/n/10 write.arff(x, file, eol = "\n", relation = deparse(substitute
(x)))
Underfull \hbox (badness 6708) in paragraph at lines 989--992
[]\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / /
www . cs . waikato . ac . nz / ~ml / weka / arff .
[2561] [2562]
Underfull \hbox (badness 10000) in paragraph at lines 1073--1074
[][][]$\T1/pcr/m/n/10 http : / / www . clicketyclick . dk / databases / xbase /
format / data _ types .
Overfull \hbox (24.78088pt too wide) in paragraph at lines 1109--1109
[] \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric",
"codes"))[]
[2563]
Underfull \hbox (badness 1286) in paragraph at lines 1194--1198
[]\T1/ptm/m/n/10 Unless dis-abled by ar-gu-ment \T1/pcr/m/n/10 convert.dates =
FALSE\T1/ptm/m/n/10 , \T1/phv/m/n/10 R \T1/ptm/m/n/10 date and date-time ob-jec
ts
[2564]
Underfull \hbox (badness 10000) in paragraph at lines 1267--1273
[]\T1/ptm/m/n/10 The work for this func-tion is done by \T1/pcr/m/n/10 foreign:
::writeForeignStata\T1/ptm/m/n/10 ,
[2565]
Underfull \hbox (badness 6725) in paragraph at lines 1293--1296
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 package="SPSS"\T1/ptm/m/n/10 , as a side ef
-fect, the dec-i-mal in-di-ca-tor is al-ways set by
[2566]) (./lattice-pkg.tex
Chapter 23.
[2567] [2568] [2569]
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"),[]
[2570]
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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"),[]
[2571]
Underfull \hbox (badness 4060) in paragraph at lines 357--369
[]\T1/ptm/m/n/10 For the func-tions doc-u-mented here, the for-mula is gen-er-a
lly of the
Underfull \hbox (badness 10000) in paragraph at lines 357--369
\T1/ptm/m/n/10 form \T1/pcr/m/n/10 y ~ x | g1 * g2 * ... \T1/ptm/m/n/10 (or equ
iv-a-lently, \T1/pcr/m/n/10 y ~ x |
Underfull \hbox (badness 1028) in paragraph at lines 397--412
\T1/ptm/m/n/10 This for-mula would be taken to mean that the user wants to plot
both
Underfull \hbox (badness 10000) in paragraph at lines 413--415
[]\T1/ptm/m/n/10 To in-ter-pret \T1/pcr/m/n/10 y1 + y2 \T1/ptm/m/n/10 as a sum,
one can ei-ther set
[2572]
Underfull \hbox (badness 7631) in paragraph at lines 479--484
[]\T1/ptm/m/n/10 A po-ten-tially use-ful com-po-nent of \T1/pcr/m/n/10 scales \
T1/ptm/m/n/10 in this case may be
[2573] [2574]
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
[2575] [2576] [2577] [2578]
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.
[2579]
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
[2580] [2581]
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
[2582] [2583] [2584]
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 ,
[2585]
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 ,
[2586]
Underfull \vbox (badness 10000) has occurred while \output is active [2587]
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
[2588]
Underfull \hbox (badness 6808) in paragraph at lines 1755--1759
[]\T1/ptm/m/n/10 graphical ar-gu-ments, which are pro-cessed and even-tu-ally p
assed to
Underfull \hbox (badness 10000) in paragraph at lines 1772--1775
[]\T1/ptm/m/n/10 style set-tings be-yond the stan-dard \T1/pcr/m/n/10 col\T1/pt
m/m/n/10 , \T1/pcr/m/n/10 lty\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lwd\T1/ptm/m/n/10
, etc; see
[2589]
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
[2590] [2591] [2592]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2071--2071
[] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl
ot"),[]
Underfull \hbox (badness 10000) in paragraph at lines 2086--2093
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 formula \T1/ptm/m/n/10 method, \T1/pcr/
m/n/10 x \T1/ptm/m/n/10 can be a for-mula of the form
Underfull \hbox (badness 1997) in paragraph at lines 2086--2093
\T1/pcr/m/n/10 ~ x | g1 * g2 * ...\T1/ptm/m/n/10 , in-di-cat-ing that his-togra
ms or ker-nel den-sity
[2593]
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
[2594] [2595] [2596]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 2345--2345
[] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 2349--2349
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.qqmath"),[]
Underfull \hbox (badness 4441) in paragraph at lines 2362--2366
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 method, \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 should be a for-mula of the form
[2597] [2598] [2599]
Underfull \hbox (badness 4441) in paragraph at lines 2547--2554
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 method, \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 should be a for-mula of the form
[2600] [2601]
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"),[]
[2602]
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[]\T1/ptm/m/n/10 for the \T1/pcr/m/n/10 formula \T1/ptm/m/n/10 method, a for-mu
la of the form \T1/pcr/m/n/10 z ~ x * y
[2603]
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
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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 2877--2881
\T1/ptm/m/n/10 ren-dered as a raster im-age us-ing [][]\T1/pcr/m/n/10 grid.rast
er[][][]\T1/ptm/m/n/10 . See also
Underfull \hbox (badness 10000) in paragraph at lines 2883--2885
[]\T1/ptm/m/n/10 Logical flag, passed to [][]\T1/pcr/m/n/10 rasterGrob[][][] \T
1/ptm/m/n/10 when
[2604]
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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,
Underfull \hbox (badness 2772) in paragraph at lines 2935--2941
\T1/ptm/m/n/10 both for the false color im-age and the color key (if present).
Ef-
Underfull \hbox (badness 1400) in paragraph at lines 2935--2941
\T1/ptm/m/n/10 fec-tively, set-ting this to \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10
changes the de-fault panel func-tion from
Underfull \hbox (badness 2486) in paragraph at lines 2959--2963
[]\T1/ptm/m/n/10 Other use-ful ar-gu-ments are men-tioned in the help page for
the de-fault panel func-tion
[2605] [2606]
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[] \T1/pcr/m/n/10 xlim = if (is.factor(x)) levels(x) else range(x, finite
= TRUE),[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3061--3061
[] \T1/pcr/m/n/10 ylim = if (is.factor(y)) levels(y) else range(y, finite
= TRUE),[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3062--3062
[] \T1/pcr/m/n/10 zlim = if (is.factor(z)) levels(z) else range(z, finite
= TRUE),[]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3073--3073
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
cloud"),[]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 3085--3085
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.wireframe"),[]
[2607]
Underfull \hbox (badness 10000) in paragraph at lines 3110--3118
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 meth-ods, a fo
r-mula of the form \T1/pcr/m/n/10 z ~ x
Underfull \hbox (badness 2913) in paragraph at lines 3143--3150
[]\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix.
Underfull \hbox (badness 3058) in paragraph at lines 3143--3150
\T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p
tm/m/n/10 must have the same lengths as
[2608] [2609] [2610] [2611]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.parallel}) has been already used, duplicate ignored
<to be read again>
\relax
l.3431 \aliasA{parallel}{B\_08\_splom}{parallel}
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3473--3473
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
splom"),[]
[2612]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3496--3496
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.parallel"),[]
[2613] [2614] [2615] [2616] [2617]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3832--3832
[]\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt(
var(x)))
[2618]
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\T1/ptm/m/n/10 fy-ing \T1/pcr/m/n/10 lattice.options(default.theme = "col.white
bg")\T1/ptm/m/n/10 .
Underfull \hbox (badness 2435) in paragraph at lines 3922--3926
\T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa
ded) set to
[2619] [2620]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4052--4052
[]\T1/pcr/m/n/10 trellis.par.set(name, value, ..., theme, warn = TRUE, strict
= FALSE)
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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
Underfull \hbox (badness 1728) in paragraph at lines 4105--4109
\T1/pcr/m/n/10 theme\T1/ptm/m/n/10 ). These are used to mod-ify the cur-rent se
t-tings (ob-tained by
[2621]
Underfull \hbox (badness 5161) in paragraph at lines 4170--4174
[]\T1/ptm/m/n/10 The ac-tual list of the com-po-nents in \T1/pcr/m/n/10 trellis
.settings \T1/ptm/m/n/10 has not been fi-nal-ized,
Underfull \hbox (badness 4913) in paragraph at lines 4170--4174
\T1/ptm/m/n/10 so I'm not at-tempt-ing to list them here. The cur-rent value ca
n be ob-tained by
[2622] [2623]
Underfull \hbox (badness 1067) in paragraph at lines 4284--4294
[]\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. \T1/pcr/m/n/10 col \T1/ptm/m/n/10 i
s used for com-po-nents \T1/pcr/m/n/10 "plot.symbol"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 4284--4294
\T1/pcr/m/n/10 "plot.line"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "plot.polygon"\T1/ptm
/m/n/10 , \T1/pcr/m/n/10 "superpose.symbol"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1735) in paragraph at lines 4284--4294
\T1/pcr/m/n/10 "superpose.line"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "superpose.p
olygon"\T1/ptm/m/n/10 . \T1/pcr/m/n/10 col.points
Underfull \hbox (badness 10000) in paragraph at lines 4284--4294
\T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col\T1/ptm/m/n/10 , but is used only f
or \T1/pcr/m/n/10 "plot.symbol" \T1/ptm/m/n/10 and
Underfull \hbox (badness 5231) in paragraph at lines 4284--4294
\T1/pcr/m/n/10 "superpose.symbol"\T1/ptm/m/n/10 . Sim-i-larly, \T1/pcr/m/n/10 c
ol.line \T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col \T1/ptm/m/n/10 for
Underfull \hbox (badness 1701) in paragraph at lines 4309--4312
[]\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 plot
.symbol\T1/ptm/m/n/10 , \T1/pcr/m/n/10 plot.polygon\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 4312--4314
[]\T1/ptm/m/n/10 border color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 pl
ot.polygon \T1/ptm/m/n/10 and
[2624] [2625] [2626] [2627] [2628] [2629]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4716--4716
[]\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab
= "Height")[]
[2630] [2631]
Underfull \hbox (badness 10000) in paragraph at lines 4903--4906
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 trellis\T1/ptm/m/n/10 , by
de-fault plot-ted by \T1/pcr/m/n/10 print.trellis\T1/ptm/m/n/10 .
[2632] [2633]
Underfull \hbox (badness 1442) in paragraph at lines 5035--5038
[]\T1/pcr/m/n/10 plot.shingle \T1/ptm/m/n/10 dis-plays the ranges of shin-gles
via rect-an-gles. \T1/pcr/m/n/10 print.shingle \T1/ptm/m/n/10 and
[2634] [2635] [2636] [2637] [2638] [2639]
Underfull \hbox (badness 3646) in paragraph at lines 5367--5370
[][][]\T1/pcr/m/n/10 Lattice[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 draw.key[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 trellis.par.get[][][]\T1/ptm/m/n/10 ,
and [][]\T1/pcr/m/n/10 xyplot[][][]\T1/ptm/m/n/10 , specif-i-cally the en-try f
or
Overfull \hbox (36.78088pt too wide) in paragraph at lines 5397--5397
[] \T1/pcr/m/n/10 bg = trellis.par.get("strip.background")$col[wh
ich.given],[]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 5398--5398
[] \T1/pcr/m/n/10 fg = trellis.par.get("strip.shingle")$col[which
.given],[]
[2640]
Underfull \hbox (badness 10000) in paragraph at lines 5486--5489
[]\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i
-zon-tal.
Underfull \hbox (badness 2103) in paragraph at lines 5486--5489
\T1/pcr/m/n/10 horizontal=FALSE \T1/ptm/m/n/10 is use-ful for strips on the lef
t of pan-els us-ing
Underfull \hbox (badness 6412) in paragraph at lines 5503--5509
[]\T1/ptm/m/n/10 default strip func-tion for trel-lis func-tions. Use-ful mostl
y be-cause of the \T1/pcr/m/n/10 style
Underfull \hbox (badness 10000) in paragraph at lines 5503--5509
\T1/ptm/m/n/10 ar-gu-ment --- non-default styles are of-ten more in-for-ma-tive
, es-pe-cially when
Underfull \hbox (badness 10000) in paragraph at lines 5503--5509
\T1/ptm/m/n/10 the names of the lev-els of the fac-tor \T1/pcr/m/n/10 x \T1/ptm
/m/n/10 are small. Tra-di-tional use is as
Underfull \hbox (badness 10000) in paragraph at lines 5503--5509
\T1/pcr/m/n/10 strip = function(...) strip.default(style=2,...)\T1/ptm/m/n/10 ,
though this can be
[2641]
Underfull \hbox (badness 1635) in paragraph at lines 5512--5517
[]\T1/pcr/m/n/10 strip.default \T1/ptm/m/n/10 is called for its side-effect, wh
ich is to draw a strip ap-pro-pri-ate for
[2642]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5661--5661
[]\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la
bels,[]
[2643]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 5675--5675
[]\T1/pcr/m/n/10 panel.link.splom(threshold = 18, verbose = getOption("verbose
"), ...)[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 5676--5676
[]\T1/pcr/m/n/10 panel.brush.splom(threshold = 18, verbose = getOption("verbos
e"), ...)[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5679--5679
[]\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location"
, "toplevel",[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5682--5682
[] \T1/pcr/m/n/10 "xlab", "ylab", "xlab.top", "ylab.rig
ht", "page"),[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 5684--5684
[] \T1/pcr/m/n/10 side = c("left", "top", "right", "bottom", "in
side"),[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 5690--5690
[] \T1/pcr/m/n/10 which.given = lattice.getStatus("current.whi
ch.given",[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5691--5691
[] \T1/pcr/m/n/10 prefix = pre
fix),[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 5692--5692
[] \T1/pcr/m/n/10 which.panel = lattice.getStatus("current.whi
ch.panel",[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5693--5693
[] \T1/pcr/m/n/10 prefix = pre
fix),[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5694--5694
[] \T1/pcr/m/n/10 column = lattice.getStatus("current.focus.co
lumn",[]
Underfull \hbox (badness 10000) in paragraph at lines 5710--5712
[]\T1/ptm/m/n/10 variables defin-ing the con-tents of the panel. In the case of
[2644]
Underfull \hbox (badness 2376) in paragraph at lines 5721--5723
[]\T1/ptm/m/n/10 an op-tional vec-tor of la-bels as-so-ci-ated with each point.
De-faults to
[2645]
Underfull \hbox (badness 2538) in paragraph at lines 5846--5850
\T1/ptm/m/n/10 For \T1/pcr/m/n/10 trellis.focus\T1/ptm/m/n/10 , the de-fault is
\T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 in in-ter-ac-tive mode, and
Underfull \hbox (badness 4205) in paragraph at lines 5857--5864
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 panel.identify.qqmath\T1/ptm/m/n/10 , ex-tr
a pa-ram-e-ters are passed on to
Underfull \hbox (badness 4792) in paragraph at lines 5857--5864
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 trellis.switchFocus\T1/ptm/m/n/10 , these are
used (in com-bi-na-tion with
[2646] [2647]
Underfull \hbox (badness 10000) in paragraph at lines 6010--6014
[][][]\T1/pcr/m/n/10 identify[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Lattice[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.trellis[][][]\T1/ptm/m/n/10 , []
[]\T1/pcr/m/n/10 trellis.currentLayout[][][]\T1/ptm/m/n/10 ,
[2648] [2649]
Underfull \hbox (badness 4242) in paragraph at lines 6157--6162
[]\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li
s pa-ram-e-
[2650] [2651]
Underfull \hbox (badness 3601) in paragraph at lines 6273--6278
[]\T1/ptm/m/n/10 Creates Box and Whisker plot of \T1/pcr/m/n/10 x \T1/ptm/m/n/1
0 for ev-ery level of \T1/pcr/m/n/10 y \T1/ptm/m/n/10 (or the other way round
Underfull \hbox (badness 2486) in paragraph at lines 6273--6278
\T1/ptm/m/n/10 if \T1/pcr/m/n/10 horizontal=FALSE\T1/ptm/m/n/10 ). By de-fault,
the ac-tual box-plot statis-tics are cal-cu-lated us-ing
[2652] [2653]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 6360--6360
[] \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co
lors")$palette,[]
[2654]
Underfull \hbox (badness 1888) in paragraph at lines 6492--6499
\T1/pcr/m/n/10 at \T1/ptm/m/n/10 can be a nu-meric vec-tor, \T1/pcr/m/n/10 col.
regions \T1/ptm/m/n/10 a vec-tor of col-ors, and
[2655]
Underfull \hbox (badness 10000) in paragraph at lines 6549--6552
[]\T1/ptm/m/n/10 All three num-bers should be be-tween 0 and 1. The
Underfull \hbox (badness 1558) in paragraph at lines 6549--6552
\T1/pcr/m/n/10 shade.colors.palette \T1/ptm/m/n/10 func-tion should re-turn a v
alid color. The
[2656]
Underfull \hbox (badness 1005) in paragraph at lines 6599--6607
\T1/ptm/m/n/10 fer-ent pur-poses. For cloud, the data is un-struc-tured, and \T
1/pcr/m/n/10 x\T1/ptm/m/n/10 , \T1/pcr/m/n/10 y \T1/ptm/m/n/10 and \T1/pcr/m/n/
10 z \T1/ptm/m/n/10 are all passed to
Underfull \hbox (badness 1571) in paragraph at lines 6599--6607
\T1/ptm/m/n/10 the \T1/pcr/m/n/10 panel.3d.cloud \T1/ptm/m/n/10 func-tion. For
wire-frame, on the other hand, \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/
10 y \T1/ptm/m/n/10 are in-
[2657] [2658] [2659] [2660] [2661]
Underfull \hbox (badness 1320) in paragraph at lines 6955--6962
[]\T1/pcr/m/n/10 panel.levelplot.raster \T1/ptm/m/n/10 is an al-ter-na-tive pan
el func-tion that uses the raster draw-
Underfull \hbox (badness 1715) in paragraph at lines 6955--6962
\T1/ptm/m/n/10 can only ren-der data on an eq-ui-s-paced grid), but can be more
ef-fi-cient. When us-ing
[2662]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 7025--7025
[] \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels =
NULL,[]
[2663]
Underfull \hbox (badness 10000) in paragraph at lines 7055--7059
[]\T1/ptm/m/n/10 The panel func-tion used for the di-ag-o-nals. See ar-gu-ments
to
Underfull \hbox (badness 1584) in paragraph at lines 7055--7059
\T1/pcr/m/n/10 diag.panel.splom \T1/ptm/m/n/10 to know what ar-gu-ments this fu
nc-tion is passed
[2664]
Underfull \hbox (badness 10000) in paragraph at lines 7160--7163
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 diag.panel \T1/ptm/m/n/10 from \T1/pcr/m/n/10
panel.pairs\T1/ptm/m/n/10 . Cur-rently ig-nored by
[2665] [2666]
Underfull \hbox (badness 2012) in paragraph at lines 7326--7329
[]\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu
-ally passed on to
[2667]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7372--7372
[] \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta
ils.n = 50))[]
[2668] [2669]
Underfull \hbox (badness 2644) in paragraph at lines 7513--7517
\T1/ptm/m/n/10 ig-nores these. For types "r" and "smooth", these are passed on
to
Underfull \hbox (badness 2772) in paragraph at lines 7526--7529
[]\T1/ptm/m/n/10 Most gen-er-ally, \T1/pcr/m/n/10 grid \T1/ptm/m/n/10 can be a
list of ar-gu-ments to be sup-plied to
Underfull \hbox (badness 4242) in paragraph at lines 7540--7548
\T1/ptm/m/n/10 which is called with those ar-gu-ments. If spec-i-fied as a (pos
-si-bly
Underfull \hbox (badness 1147) in paragraph at lines 7540--7548
\T1/ptm/m/n/10 named) nu-meric vec-tor, \T1/pcr/m/n/10 abline \T1/ptm/m/n/10 is
co-erced to a list. This al-lows ar-
Underfull \hbox (badness 2351) in paragraph at lines 7540--7548
\T1/ptm/m/n/10 gu-ments of the form \T1/pcr/m/n/10 abline = c(0, 1)\T1/ptm/
m/n/10 , which adds the di-
Underfull \hbox (badness 1675) in paragraph at lines 7540--7548
\T1/ptm/m/n/10 ag-o-nal line, or \T1/pcr/m/n/10 abline = c(h = 0, v = 0)\T1
/ptm/m/n/10 , which adds the
Underfull \hbox (badness 1769) in paragraph at lines 7540--7548
\T1/ptm/m/n/10 x- and y-axes to the plot. Use the list form for finer con-trol;
e.g.,
[2670]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 7596--7596
[] \T1/pcr/m/n/9 ylab = list(c("horizontal=TRUE", "horizontal=FALSE"), y
= c(1/6, 4/6)),[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7606--7606
[] \T1/pcr/m/n/9 scales = list(alternating = c(0, 2), tck = c(0, 0.7), d
raw = FALSE),[]
[2671]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 7667--7667
[] \T1/pcr/m/n/10 font, fontfamily, fontface, cex, ..., identifier, nam
e.type)[]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 7672--7672
[] \T1/pcr/m/n/10 adj = c(0.5, 0.5), pos = NULL, offset = 0.5, ..., ident
ifier, name.type)[]
[2672] [2673] [2674]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 7857--7857
[]\T1/pcr/m/n/10 panel.grid(h=3, v=3, col, col.line, lty, lwd, x, y, ..., iden
tifier = "grid")[]
[2675]
Underfull \hbox (badness 1436) in paragraph at lines 7912--7918
[]\T1/ptm/m/n/10 A log-i-cal flag de-ter-min-ing whether the de-fault graph-i-c
al pa-ram-e-ters for
Underfull \hbox (badness 1231) in paragraph at lines 7912--7918
\T1/ptm/m/n/10 tings. The de-fault is to take them from the ``add.line'' set-ti
ngs. The
[2676] [2677] [2678] [2679] [2680] [2681] [2682] [2683]
Underfull \hbox (badness 10000) in paragraph at lines 8470--8473
[]\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to \T1/pcr/m/n/10 panel.superpo
se
Underfull \hbox (badness 10000) in paragraph at lines 8470--8473
\T1/ptm/m/n/10 from \T1/pcr/m/n/10 panel.superpose.2\T1/ptm/m/n/10 , and to \T1
/pcr/m/n/10 panel.groups \T1/ptm/m/n/10 from
[2684] [2685]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 8645--8645
[]\T1/pcr/m/n/10 prepanel.default.bwplot(x, y, horizontal, nlevels, origin, st
ack, ...)[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 8646--8646
[]\T1/pcr/m/n/10 prepanel.default.histogram(x, breaks, equal.widths, type, nin
t, ...)[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 8658--8658
[]\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr
ipts, ...)[]
[2686]
Underfull \hbox (badness 3118) in paragraph at lines 8677--8680
[]\T1/ptm/m/n/10 details of his-togram cal-cu-la-tions. \T1/pcr/m/n/10 type \T1
/ptm/m/n/10 has a dif-fer-ent mean-ing in
[2687]
Underfull \hbox (badness 1515) in paragraph at lines 8753--8757
[]\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti
es. If used with
[2688]
Underfull \hbox (badness 6316) in paragraph at lines 8859--8864
[]\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr
ibed in
[2689] [2690]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 8966--8966
[] \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b
ottom$labels$labels)[]
[2691] [2692]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9105--9105
[]\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su
nspot.year)),[]
[2693]
Overfull \hbox (84.94879pt too wide) in paragraph at lines 9164--9168
[]\T1/ptm/m/n/10 returns a list with sev-eral com-po-nents, in-clud-ing \T1/pcr
/m/n/10 left, right, left.name, right.name, condition
Overfull \hbox (104.63074pt too wide) in paragraph at lines 9164--9168
\T1/ptm/m/n/10 for 2-D, and \T1/pcr/m/n/10 left, right.x, right.y, left.name
, right.x.name, right.y.name, condition
[2694] [2695] [2696] [2697] [2698] [2699] [2700]
Underfull \hbox (badness 4205) in paragraph at lines 9622--9626
[]\T1/ptm/m/n/10 Factor with lev-els \T1/pcr/m/n/10 "Svansota"\T1/ptm/m/n/10 ,
\T1/pcr/m/n/10 "No. 462"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Manchuria"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "No. 475"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 4518) in paragraph at lines 9622--9626
\T1/pcr/m/n/10 "Velvet"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Peatland"\T1/ptm/m/n/10
, \T1/pcr/m/n/10 "Glabron"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "No. 457"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "Wisconsin No. 38"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 6300) in paragraph at lines 9627--9630
[]\T1/ptm/m/n/10 Factor with 6 lev-els: \T1/pcr/m/n/10 "Grand Rapids"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "Duluth"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "University Farm"
\T1/ptm/m/n/10 ,
[2701] [2702] [2703]pdfTeX warning (ext4): destination with the same identifier
(name{Rfn.melanoma}) has been already used, duplicate ignored
<to be read again>
\relax
l.9853 \aliasA{melanoma}{H\_melanoma}{melanoma}
[2704] [2705] [2706]
Underfull \hbox (badness 10000) in paragraph at lines 10015--10020
[]\T1/ptm/m/n/10 Cause of death. A fac-tor with lev-els \T1/pcr/m/n/10 Alzheime
rs\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Cancer\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 10015--10020
\T1/pcr/m/n/10 Cerebrovascular diseases\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Diabetes
\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Flu and pneumonia\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 10015--10020
\T1/pcr/m/n/10 Heart disease\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Lower respiratory\T
1/ptm/m/n/10 , \T1/pcr/m/n/10 Nephritis\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Suicide\
T1/ptm/m/n/10 , and
[2707]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10088--10088
[] \T1/pcr/m/n/9 par.settings = simpleTheme(pch = 16), auto.key = list(
columns = 2),[]
[2708]) (./mgcv-pkg.tex
Chapter 24.
[2709] [2710]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 147--147
[]\T1/pcr/m/n/10 bam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL,
Overfull \hbox (18.78088pt too wide) in paragraph at lines 150--150
[] \T1/pcr/m/n/10 paraPen=NULL,chunk.size=10000,rho=0,AR.start=NULL,discret
e=FALSE,[]
[2711]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 152--152
[] \T1/pcr/m/n/10 coef=NULL,drop.unused.levels=TRUE,G=NULL,fit=TRUE,drop.in
tercept=NULL,...)[]
Underfull \hbox (badness 1142) in paragraph at lines 171--175
\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
Underfull \hbox (badness 1043) in paragraph at lines 196--201
\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known
scale.
[2712] [2713] [2714] [2715]
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[][][]\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 ,
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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 ,
[2716]
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[]\T1/pcr/m/n/9 system.time(b2 <- bam(y ~ s(x0,bs=bs,k=k)+s(x1,bs=bs,k=k)+s(x2
,bs=bs,k=k)+[]
[2717] [2718] [2719]
Underfull \hbox (badness 2922) in paragraph at lines 603--604
[]\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
[2720] [2721]
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[]\T1/ptm/m/n/10 First con-sider \T1/pcr/m/n/10 choldrop\T1/ptm/m/n/10 . If \T1
/pcr/m/n/10 R \T1/ptm/m/n/10 is up-per tri-an-gu-lar then
[2722]
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[]\T1/ptm/m/n/10 Choosing the ba-sis di-men-sion, and check-ing the choice, whe
n us-ing pe-nal-ized re-gres-sion
[2723]
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[]\T1/ptm/m/n/10 Wood, S.N. (2017) Gen-er-al-ized Ad-di-tive Mod-els: An In-tro
-duc-tion with R (2nd edi-tion).
[2724]
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[2726] [2727] [2728] [2729]
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[]\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h + 2*b$family$data$
q^.5),col=2)[]
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[]\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$
q^.5),col=2)[]
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[]\T1/pcr/m/n/9 bs <- gam(cbind(time,strata)~s(age,by=sex)+sex+s(nodes)+perfor
+rx+obstruct+adhere,[]
[2730]
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[]\T1/pcr/m/n/9 ## create index picking out elements of stored hazard info for
this stratum...[]
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[]\T1/pcr/m/n/9 if (i==1) plot(bs$family$data$tr[ind],exp(-bs$family$data$h[in
d]),type="l",ylim=c(0,1),[]
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[] \T1/pcr/m/n/9 lines(bs$family$data$tr[ind],exp(-bs$family$data$h[ind])
,lwd=2,col=i)[]
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[]\T1/pcr/m/n/9 b <- gam(t~s(x0)+s(x1)+s(x2,k=15)+s(x3),family=cox.ph,weights=
d,data=surv)[]
[2731]
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[] \T1/pcr/m/n/9 if (inter) prg <- txtProgressBar(min = 0, max = length(sid),
initial = 0,[]
[2732]
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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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[2734] [2735] [2736] [2737] [2738] [2739] [2740] [2741]
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[]\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str
ict=FALSE)
[2742] [2743] [2744] [2745] [2746] [2747]
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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 2222--2225
[]\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 2235--2239
\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2748]
Underfull \hbox (badness 1043) in paragraph at lines 2261--2266
\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known
scale.
[2749] [2750]
Underfull \hbox (badness 1043) in paragraph at lines 2424--2430
\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
[2751] [2752]
Underfull \hbox (badness 10000) in paragraph at lines 2560--2566
[][][]\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 2560--2566
[][]\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 2560--2566
[][]\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 ,
[2753]
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[2757] [2758] [2759] [2760] [2761] [2762] [2763]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3216--3216
[] \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)),[]
[2764] [2765] [2766] [2767] [2768] [2769]
Underfull \hbox (badness 5189) in paragraph at lines 3580--3584
[]\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
[2770] [2771]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3697--3697
[]\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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[2773] [2774]
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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
[2775] [2776] [2777] [2778] [2779] [2780] [2781]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 4312--4312
[] \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)+[]
[2782] [2783] [2784]
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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,
[2785]
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[]\T1/pcr/m/n/10 niterPQL=20,verbosePQL=TRUE,method="ML",drop.unused.levels=TR
UE,...)[]
[2786]
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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
[2787]
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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
[2788] [2789]
Underfull \hbox (badness 5970) in paragraph at lines 4773--4779
[][][]\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 .
[2790]
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[2792] [2793]
Underfull \hbox (badness 1577) in paragraph at lines 5053--5056
[]\T1/ptm/m/n/10 If `outer' it-er-a-tion has been used to fit the model (see []
[]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 ar-gu-ment
Underfull \hbox (badness 2181) in paragraph at lines 5060--5061
[]\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic-
tion, used by
[2794] [2795] [2796] [2797] [2798] [2799] [2800]
Underfull \hbox (badness 6708) in paragraph at lines 5449--5450
[]\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
[2801]
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[] \T1/pcr/m/n/9 ## example using a scale location model for the motorcycle d
ata. A simple plotting[]
[2802]
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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[]
[2804] [2805] [2806] [2807] [2808] [2809]
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[]\T1/pcr/m/n/10 jagam(formula,family=gaussian,data=list(),file,weights=NULL,n
a.action,
Overfull \hbox (36.78088pt too wide) in paragraph at lines 5931--5931
[]\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
[2810] [2811] [2812] [2813] [2814] [2815]
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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)
[2816] [2817] [2818] [2819]
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[2822] [2823]
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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)[]
[2824] [2825] [2826] [2827] [2828] [2829] [2830] [2831] [2832]
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[]\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra
nts EP/K005251/1 and
[2833] [2834]
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[]\T1/pcr/m/n/9 ## Alternative, better scaling example, using the discrete opt
ion with bam...[]
[2835] [2836]
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[]\T1/pcr/m/n/9 for (sim in c(1,7)) { ## cycle over uncorrelated and correlate
d covariates[]
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[] \T1/pcr/m/n/9 dat1[[dname[i]]][dat1[[by.name]]] <- mean(dat1[[dname[i]]]
,na.rm=TRUE)[]
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[2849] [2850] [2851] [2852] [2853] [2854]
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[2856]
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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 8655--8658
\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 8655--8658
\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 .
[2857]
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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 8711--8714
\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
[2858] [2859] [2860]
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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,[]
[2861] [2862] [2863]
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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
[2864] [2865] [2866] [2867]
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[] \T1/pcr/m/n/10 na.action=na.pass,cluster=NULL,discrete=TRUE,n.thread
s=1,...)[]
[2868] [2869]
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[] \T1/pcr/m/n/10 na.action=na.pass,unconditional=FALSE,iterms.type=NUL
L,...)[]
[2870] [2871] [2872] [2873]
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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[]
[2875]
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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
[2876]
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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
[2877]
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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,
[2878] [2879]
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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,
[2880] [2881] [2882] [2883]
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[]\T1/ptm/m/n/10 The sec-ond method rep-re-sents the con-ven-tional ran-dom ef-
fects in a GAM in the same
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\T1/ptm/m/n/10 way that the smooths are rep-re-sented --- as pe-nal-ized re-gre
s-sion terms. This method
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\T1/ptm/m/n/10 can be used with [][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 by
mak-ing use of \T1/pcr/m/n/10 s(...,bs="re") \T1/ptm/m/n/10 terms in a model: 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:
Underfull \hbox (badness 5862) in paragraph at lines 10249--10252
\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.
[2884]
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[]\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat
,method="ML")[]
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[]\T1/ptm/m/n/10 the type of resid-u-als wanted. Usu-ally one of \T1/pcr/m/n/10
"deviance"\T1/ptm/m/n/10 ,
[2885] [2886] [2887] [2888] [2889]
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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)
[2890] [2891] [2892] [2893] [2894] [2895]
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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-
[2896]
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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-
[2897] [2898] [2899]
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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
[2900]
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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 .
Underfull \hbox (badness 1502) in paragraph at lines 11273--11285
\T1/pcr/m/n/10 cs.smooth.spec \T1/ptm/m/n/10 (cu-bic re-gres-sion splines with
shrinkage-to-zero); \T1/pcr/m/n/10 cc.smooth.spec
Underfull \hbox (badness 2401) in paragraph at lines 11290--11294
\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 11290--11294
\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 ,
[2901] [2902] [2903]
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Underfull \hbox (badness 6876) in paragraph at lines 11485--11491
[][][]\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
Underfull \hbox (badness 10000) in paragraph at lines 11526--11527
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[2905] [2906]
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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
[2907] [2908]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 11697--11697
[] \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 (25.98041pt too wide) in paragraph at lines 11720--11720
[] \T1/pcr/m/n/9 "1st order penalties: red tps; blue bs over (0,1); black bs
over (-.5,1.5)")[]
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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[]
[2909]
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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:[]
[2910]
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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
Underfull \hbox (badness 10000) in paragraph at lines 11802--11804
\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
[2911] [2912]
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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
[2913]
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[]\T1/pcr/m/n/9 b <- gam(y~s(x,z,bs="ds",m=c(1,.5),k=50),data=data) ## first
deriv penalty[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 12012--12012
[]\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[]
[2914] [2915] [2916]
Underfull \hbox (badness 10000) in paragraph at lines 12162--12163
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[2917] [2918] [2919] [2920]
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[]\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m
ethod="REML")[]
[2921]
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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
[2922] [2923]
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Underfull \hbox (badness 10000) in paragraph at lines 12621--12624
[]\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 12621--12624
\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 12621--12624
\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"
[2925] [2926]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 12703--12703
[]\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with
2 variances[]
Underfull \hbox (badness 10000) in paragraph at lines 12748--12754
[]\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a
Underfull \hbox (badness 2698) in paragraph at lines 12748--12754
\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-
[2927] [2928] [2929]
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[]\T1/pcr/m/n/9 ## notice NULL element in \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 xt\TS1
/pcr/m/n/9 ' \T1/pcr/m/n/9 list - to indicate no xt object for "cr" basis...[]
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[2932]
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[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths on the
sphere, via terms like
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[2933] [2934] [2935] [2936]
Underfull \hbox (badness 3396) in paragraph at lines 13352--13355
[][][]\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
[2937]
Underfull \hbox (badness 10000) in paragraph at lines 13397--13399
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[2938] [2939] [2940] [2941]
Underfull \hbox (badness 10000) in paragraph at lines 13621--13624
[]\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 13621--13624
\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
[2942]
Underfull \hbox (badness 10000) in paragraph at lines 13654--13658
[][][]\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 13654--13658
[][]\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 13654--13658
[][]\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 ,
[2943] [2944] [2945] [2946] [2947]
Underfull \hbox (badness 2158) in paragraph at lines 13944--13944
[]\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma-
trix from
[2948]
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[]\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0,
centre=FALSE)[]
[2949] [2950]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 14157--14157
[] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars
"),...)[]
[2951] [2952] [2953]
Underfull \hbox (badness 4846) in paragraph at lines 14288--14291
[]\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
[2954] [2955] [2956] [2957] [2958]
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[2960] [2961] [2962] [2963] [2964] [2965] [2966]
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[]\T1/ptm/m/n/10 Suppose that \T1/pcr/m/n/10 m=1 \T1/ptm/m/n/10 and you fill an
ar-ray us-ing code like
Underfull \hbox (badness 10000) in paragraph at lines 15113--15121
\T1/pcr/m/n/10 for(i in 1:K) for(j in i:K) for(k in j:K) for(l in k:K)
[2967] [2968] [2969] [2970] [2971] [2972]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 15477--15477
[]\T1/pcr/m/n/10 vcov(object, freq = FALSE, dispersion = NULL,unconditional=FA
LSE, ...)[]
[2973] [2974] [2975] [2976] [2977]
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[]\T1/pcr/m/n/9 ## 1. If the zero inflation rate becomes decoupled from the li
near predictor,[]
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[]\T1/pcr/m/n/9 ## it is possible for the linear predictor to be almost unboun
ded in regions[]
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[]\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val
ues, to check we[]
[2978] [2979] [2980]) (./nlme-pkg.tex
Chapter 25.
[2981]
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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
[2982]
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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
[2983] [2984] [2985] [2986] [2987]
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[] \T1/pcr/m/n/9 lme(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[]
[2988] [2989]
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[]\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 251-254 ---------------------------
---------------[]
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[]\T1/pcr/m/n/9 # Compare an "lme" object with a "gls" object (test would be n
on-sensical!)[]
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[]\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 222-225 ---------------------------
---------------[]
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[]\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 352-365 ---------------------------
---------------[]
[2990] [2991] [2992] [2993] [2994] [2995] [2996] [2997]
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[] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxil
lary fissure"),[]
[2998]
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[]\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
[2999] [3000] [3001] [3002] [3003] [3004] [3005]
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[][][]\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 ,
[3006]
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[]\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
[3007] [3008] [3009] [3010] [3011]
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\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 ,
[3012]
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[]\T1/pcr/m/n/9 collapse(Pixel, collapse = 1) # same as collapse(Pixel, colla
pse = "Dog")[]
[3013]
Underfull \hbox (badness 1132) in paragraph at lines 2144--2146
[]\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac
ted us-ing the
[3014] [3015]
Underfull \hbox (badness 4168) in paragraph at lines 2255--2261
[][][]\T1/pcr/m/n/10 ACF.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corARMA[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T
1/pcr/m/n/10 Dim.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize
.corStruct[][][]\T1/ptm/m/n/10 ,
[3016]
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[] \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[]
[3017] [3018] [3019] [3020] [3021] [3022] [3023] [3024]
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[][][]\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 ,
[3025] [3026] [3027] [3028] [3029] [3030] [3031] [3032] [3033] [3034] [3035]
[3036]
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[][][]\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 ,
[3037] [3038] [3039] [3040] [3041] [3042] [3043] [3044] [3045] [3046] [3047]
[3048] [3049] [3050] [3051] [3052] [3053] [3054] [3055] [3056] [3057] [3058]
[3059] [3060]
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[][][]\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 ,
[3061] [3062] [3063] [3064] [3065]
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[]\T1/ptm/m/n/10 Note that as from ver-sion 3.1-102, this only omits rows omit-
ted in the fit if
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\T1/pcr/m/n/10 na.action = na.omit\T1/ptm/m/n/10 , and does not omit at all if
\T1/pcr/m/n/10 na.action = na.exclude\T1/ptm/m/n/10 .
[3066] [3067]
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[][][]\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 ,
[3068] [3069] [3070] [3071] [3072] [3073] [3074] [3075] [3076]
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\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
[3077]
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[]\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in \
T1/pcr/m/n/10 model\T1/ptm/m/n/10 ,
[3078]
Underfull \hbox (badness 2057) in paragraph at lines 6242--6253
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsCon
trol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsObject[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gls[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gls[][][]\T1/ptm/m/n/10 ,
[3079]
Underfull \hbox (badness 10000) in paragraph at lines 6306--6308
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6338--6338
[]\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[]
[3080] [3081] [3082] [3083]
Underfull \hbox (badness 7133) in paragraph at lines 6556--6560
[]\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in \
T1/pcr/m/n/10 model\T1/ptm/m/n/10 ,
[3084]
Underfull \hbox (badness 10000) in paragraph at lines 6655--6661
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsCo
ntrol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsObject[][][]\T1/ptm/m/n/10 ,
[][]\T1/pcr/m/n/10 gnlsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict
.gnls[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (54.78088pt too wide) in paragraph at lines 6682--6682
[]\T1/pcr/m/n/10 gnlsControl(maxIter = 50, nlsMaxIter = 7, msMaxIter = 50, min
Scale = 0.001,
[3085]
Underfull \hbox (badness 10000) in paragraph at lines 6720--6722
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3086]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6750--6750
[]\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[]
[3087] [3088] [3089]
Underfull \hbox (badness 10000) in paragraph at lines 6993--7000
[][][]\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 ,
[3090]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7010--7010
[] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla
ry fissure" ),[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7018--7018
[]\T1/pcr/m/n/9 fm1 <- lme( Orth.new ) # fixed and groups formulae extracted
from object[]
Underfull \hbox (badness 2875) in paragraph at lines 7040--7042
[]\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
[3091] [3092] [3093]
Underfull \hbox (badness 10000) in paragraph at lines 7255--7260
[][][]\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 ,
[3094] [3095] [3096]
Underfull \hbox (badness 10000) in paragraph at lines 7407--7415
[]\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 7407--7415
\T1/ptm/m/n/10 tion and op-ti-miza-tion al-go-rithms used in \T1/pcr/m/n/10 lme
\T1/ptm/m/n/10 . De-faults to
Underfull \hbox (badness 1817) in paragraph at lines 7407--7415
\T1/pcr/m/n/10 list(niterEM=20, gradHess=TRUE)\T1/ptm/m/n/10 , im-ply-ing that
20 EM it-er-a-
Underfull \hbox (badness 3118) in paragraph at lines 7430--7433
[][][]\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 ,
[3097] [3098] [3099]
Underfull \hbox (badness 3354) in paragraph at lines 7645--7647
[]\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
[3100] [3101] [3102] [3103] [3104] [3105]
Underfull \hbox (badness 1642) in paragraph at lines 8037--8059
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o
f the form
[3106] [3107]
Underfull \hbox (badness 10000) in paragraph at lines 8157--8174
[][][]\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 8157--8174
[][]\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 8200--8200
[] \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data
= TRUE)[]
Underfull \hbox (badness 1642) in paragraph at lines 8209--8231
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o
f the form
[3108] [3109] [3110] [3111] [3112]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 8474--8474
[]\T1/pcr/m/n/10 lmeControl(maxIter = 50, msMaxIter = 50, tolerance = 1e-6, ni
terEM = 25,
Underfull \hbox (badness 10000) in paragraph at lines 8520--8522
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3113]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8558--8558
[]\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.8565 \aliasA{sigma}{lmeObject}{sigma}
[3114] [3115] [3116]
Underfull \hbox (badness 10000) in paragraph at lines 8726--8738
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 lmList\T1/ptm/m/n/10 , ei-ther a lin-ear fo
r-mula ob-ject of the form
[3117] [3118] [3119] [3120] [3121] [3122] [3123] [3124] [3125]
Underfull \hbox (badness 10000) in paragraph at lines 9317--9324
[][][]\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 9328--9328
[]\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me
thod = "ML")
[3126]
Underfull \hbox (badness 6300) in paragraph at lines 9410--9413
[]\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
[3127] [3128] [3129] [3130]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.Matrix}) has been already used, duplicate ignored
<to be read again>
\relax
l.9679 ...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.9679 ...rA{Matrix}{Assign Matrix Values}{Matrix}
[3131]
Underfull \hbox (badness 10000) in paragraph at lines 9699--9702
[]\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 9743--9746
[]\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 9743--9746
\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
[3132] [3133] [3134]
Underfull \hbox (badness 2435) in paragraph at lines 9917--9922
[]\T1/ptm/m/n/10 The model ma-tri-ces for each el-e-ment of \T1/pcr/m/n/10 form
ula(object)\T1/ptm/m/n/10 , cal-cu-lated us-ing \T1/pcr/m/n/10 data\T1/ptm/m/n/
10 ,
[3135] [3136] [3137] [3138] [3139]
Underfull \hbox (badness 7291) in paragraph at lines 10207--10209
[]\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
[3140] [3141] [3142]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10423--10423
[]\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation,
weights,
[3143]
Underfull \hbox (badness 1596) in paragraph at lines 10452--10478
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o
f the form
[3144] [3145] [3146]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10628--10628
[]\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation,
weights,[]
[3147] [3148]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 10779--10779
[] \T1/pcr/m/n/10 opt = c("nlminb", "nlm"), natural = TRUE, sigma =
NULL, ...)[]
Underfull \hbox (badness 2213) in paragraph at lines 10790--10795
[]\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[][][]
[3149]
Underfull \hbox (badness 10000) in paragraph at lines 10812--10816
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 10831--10833
[]\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 10867--10867
[]\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[]
[3150] [3151] [3152] [3153]
Overfull \hbox (96.18033pt too wide) in paragraph at lines 11123--11123
[]\T1/pcr/m/n/9 cfm1 <- confint(fm1) # via profiling each % FIXME: only *one*
message instead of one *each*[]
[3154] [3155] [3156] [3157] [3158] [3159] [3160] [3161] [3162] [3163] [3164]
[3165]
Underfull \hbox (badness 6268) in paragraph at lines 11902--11912
[][][]\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 ,
[3166] [3167] [3168] [3169]
Underfull \hbox (badness 10000) in paragraph at lines 12163--12169
[][][]\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 ,
[3170] [3171] [3172] [3173] [3174]
Underfull \hbox (badness 6876) in paragraph at lines 12485--12487
[]\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
[3175] [3176]
Underfull \hbox (badness 2452) in paragraph at lines 12641--12648
[][][]\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 ,
[3177]
Underfull \hbox (badness 10000) in paragraph at lines 12706--12712
[][][]\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 ,
[3178] [3179] [3180] [3181] [3182] [3183] [3184] [3185] [3186] [3187] [3188]
[3189] [3190] [3191]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13658--13658
[]\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline =
0, id = 0.05)[]
[3192]
Underfull \hbox (badness 10000) in paragraph at lines 13685--13688
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nffGroupedD
ata\T1/ptm/m/n/10 , rep-re-sent-ing a
Underfull \hbox (badness 6016) in paragraph at lines 13713--13716
[]\T1/ptm/m/n/10 an op-tional char-ac-ter string with the la-bel for the hor-i-
zon-tal axis.
Underfull \hbox (badness 2653) in paragraph at lines 13713--13716
\T1/ptm/m/n/10 De-fault is the \T1/pcr/m/n/10 y \T1/ptm/m/n/10 el-e-ments of \T
1/pcr/m/n/10 attr(object, "labels") \T1/ptm/m/n/10 and
Underfull \hbox (badness 1975) in paragraph at lines 13720--13723
[]\T1/ptm/m/n/10 an op-tional func-tion passed as the \T1/pcr/m/n/10 strip \T1/
ptm/m/n/10 ar-gu-ment to the \T1/pcr/m/n/10 dotplot
Underfull \hbox (badness 1838) in paragraph at lines 13728--13735
[]\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 13728--13735
\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
[3193]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 13785--13785
[]\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect,
panel,[]
Underfull \hbox (badness 10000) in paragraph at lines 13792--13795
[]\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 13792--13795
\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
[3194]
Underfull \hbox (badness 4582) in paragraph at lines 13820--13823
[]\T1/ptm/m/n/10 optional char-ac-ter strings with the la-bels for the plot. De
-fault is
Underfull \hbox (badness 2418) in paragraph at lines 13820--13823
\T1/ptm/m/n/10 the cor-re-spond-ing el-e-ments of \T1/pcr/m/n/10 attr(object,
"labels") \T1/ptm/m/n/10 and
Underfull \hbox (badness 2990) in paragraph at lines 13824--13827
[]\T1/ptm/m/n/10 an op-tional func-tion passed as the \T1/pcr/m/n/10 strip \T1/
ptm/m/n/10 ar-gu-ment to the \T1/pcr/m/n/10 xyplot
[3195]
Underfull \hbox (badness 10000) in paragraph at lines 13900--13903
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nmGroupedDa
ta\T1/ptm/m/n/10 , rep-re-sent-ing a
Underfull \hbox (badness 1472) in paragraph at lines 13925--13932
\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 ,
[3196]
Underfull \hbox (badness 10000) in paragraph at lines 13994--13996
[][][]\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 ,
[3197] [3198] [3199] [3200]
Underfull \hbox (badness 1540) in paragraph at lines 14209--14214
\T1/ptm/m/n/10 a \T1/pcr/m/n/10 loess \T1/ptm/m/n/10 smoother is added to the p
lot. If \T1/pcr/m/n/10 showModel = TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n/10 x \T1
/ptm/m/n/10 in-cludes an
Underfull \hbox (badness 1215) in paragraph at lines 14256--14258
[]\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis.
De-faults to
[3201] [3202] [3203] [3204] [3205]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 14500--14500
[]\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female",
"Male","Male"),[]
[3206] [3207] [3208] [3209] [3210] [3211] [3212] [3213] [3214]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.15153 ...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.15153 ...Extract Random Effects}{random.effects}
[3215] [3216] [3217]
[3218] [3219] [3220] [3221] [3222] [3223] [3224]
Underfull \hbox (badness 1009) in paragraph at lines 15810--15819
\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
[3225] [3226] [3227]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 15957--15957
[] \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi
st = FALSE, ...)[]
[3228] [3229] [3230] [3231]
Underfull \hbox (badness 10000) in paragraph at lines 16235--16253
[]\T1/ptm/m/n/10 any of the fol-low-ing: (i) a one-sided for-mula of the form
Underfull \hbox (badness 1708) in paragraph at lines 16235--16253
\T1/pcr/m/n/10 ~x1+...+xn | g1/.../gm\T1/ptm/m/n/10 , with \T1/pcr/m/n/10 x1+..
.+xn \T1/ptm/m/n/10 spec-i-fy-ing the model
[3232]
Underfull \hbox (badness 10000) in paragraph at lines 16292--16298
[][][]\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 ,
[3233]
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[] \T1/pcr/m/n/10 method = c("REML", "ML"), niterEM = c(40, 200), useG
en, ...)[]
[3234] [3235] [3236] [3237] [3238] [3239] [3240]
Underfull \hbox (badness 1728) in paragraph at lines 16812--16815
[]\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou
t-put in the
[3241] [3242] [3243] [3244] [3245]
Underfull \hbox (badness 1867) in paragraph at lines 17147--17156
\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 17147--17156
\T1/pcr/m/n/10 "Compound Symmetry" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdCompSymm
\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Diagonal"
Underfull \hbox (badness 10000) in paragraph at lines 17147--17156
\T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdDiag\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Multip
le of an Identity" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdIdent\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17147--17156
\T1/pcr/m/n/10 "General Positive-Definite, Natural Parametrization"
[3246]
Underfull \hbox (badness 10000) in paragraph at lines 17211--17219
[]\T1/ptm/m/n/10 an op-tional char-ac-ter string with a de-scrip-tion of the
Underfull \hbox (badness 10000) in paragraph at lines 17211--17219
\T1/pcr/m/n/10 varFunc \T1/ptm/m/n/10 class. De-fault de-pends on the method fu
nc-tion:
Underfull \hbox (badness 10000) in paragraph at lines 17211--17219
\T1/pcr/m/n/10 "Combination of variance functions" \T1/ptm/m/n/10 for \T1/pcr/m
/n/10 varComb\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17211--17219
\T1/pcr/m/n/10 "Constant plus power of covariate" \T1/ptm/m/n/10 for \T1/pcr/m/
n/10 varConstPower\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17211--17219
\T1/pcr/m/n/10 "Exponential of variance covariate" \T1/ptm/m/n/10 for \T1/pcr/m
/n/10 varExp\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17211--17219
\T1/pcr/m/n/10 "Different standard deviations per stratum" \T1/ptm/m/n/10 for
Underfull \hbox (badness 10000) in paragraph at lines 17211--17219
\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 ,
[3247] [3248] [3249] [3250]
Underfull \hbox (badness 10000) in paragraph at lines 17458--17465
[][][]\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 ,
[3251] [3252] [3253] [3254] [3255] [3256] [3257] [3258]
Underfull \hbox (badness 10000) in paragraph at lines 17993--18003
[][][]\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 17993--18003
[][]\T1/pcr/m/n/10 Variogram.corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10
Variogram.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corSphe
r[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 3579) in paragraph at lines 18031--18036
\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
[3259]
Underfull \hbox (badness 3579) in paragraph at lines 18095--18100
\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
[3260]
Underfull \hbox (badness 3579) in paragraph at lines 18158--18163
\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
[3261]
Underfull \hbox (badness 1577) in paragraph at lines 18219--18221
[]\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 18221--18226
\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
[3262]
Underfull \hbox (badness 3579) in paragraph at lines 18284--18289
\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
[3263]
Underfull \hbox (badness 10000) in paragraph at lines 18317--18326
[][][]\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 18317--18326
[][]\T1/pcr/m/n/10 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 V
ariogram.corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corRatio[][]
[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 3579) in paragraph at lines 18356--18361
\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
[3264] [3265] [3266]
Underfull \hbox (badness 1009) in paragraph at lines 18505--18514
\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
[3267] [3268]
Underfull \hbox (badness 1009) in paragraph at lines 18639--18648
\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
[3269] [3270] [3271] [3272] [3273] [3274] [3275] [3276]) (./nnet-pkg.tex
Chapter 26.
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.multinom}
) has been already used, duplicate ignored
<to be read again>
\relax
l.47 ...t Multinomial Log-linear Models}{multinom}
pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.multinom.1}) has been already used, du
plicate ignored
<to be read again>
\relax
l.47 ...t Multinomial Log-linear Models}{multinom}
[3277]
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[] \T1/pcr/m/n/10 contrasts = NULL, Hess = FALSE, summ = 0, censored =
FALSE,[]
Underfull \hbox (badness 10000) in paragraph at lines 78--87
[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[3278] [3279] [3280]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 369--369
[]\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size =
2, rang = 0.1,[]
[3281]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 426--426
[]\T1/pcr/m/n/9 targets <- matrix(c(rep(c(1,0,0),50), rep(c(0,1,0),50), rep(c(
0,0,1),50)),[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 429--429
[]\T1/pcr/m/n/9 ir1 <- nnet(ir[samp,], targets[samp,], size=2, rang=0.1, decay
=5e-4, maxit=200)[]
[3282]
Underfull \hbox (badness 4013) in paragraph at lines 474--477
\T1/ptm/m/n/10 the cor-re-spond-ing class (which is prob-a-bly only use-ful if
the net was gen-er-ated by
[3283]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 509--509
[]\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size =
2, rang = 0.1,[]
[3284]) (./rpart-pkg.tex
Chapter 27.
[3285] [3286] [3287] [3288]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 324--324
[]\T1/pcr/m/n/10 labels(object, digits = 4, minlength = 1L, pretty, collapse =
TRUE, ...)[]
[3289]
Underfull \hbox (badness 10000) in paragraph at lines 373--377
[]\T1/ptm/m/n/10 Vector of split la-bels (\T1/pcr/m/n/10 collapse = TRUE\T1/ptm
/m/n/10 ) or ma-trix of left and right splits
[3290] [3291] [3292]
Underfull \hbox (badness 1442) in paragraph at lines 591--597
[]\T1/ptm/m/n/10 if \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 , the leaf nodes will be
at the hor-i-zon-tal plot co-or-di-nates of
[3293] [3294]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 728--728
[] \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep =
""),[]
[3295]
Underfull \hbox (badness 2941) in paragraph at lines 785--787
[]\T1/ptm/m/n/10 a plot of \T1/pcr/m/n/10 rpart \T1/ptm/m/n/10 is cre-ated us-i
ng the \T1/pcr/m/n/10 postscript \T1/ptm/m/n/10 driver, or the cur-rent de-vice
if
[3296]
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[]\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie
s, probabilities[]
[3297]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 921--921
[]\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d
igits"), ...)[]
[3298] [3299] [3300]
Underfull \hbox (badness 2310) in paragraph at lines 1113--1116
[]\T1/ptm/m/n/10 For re-gres-sion or \T1/pcr/m/n/10 anova \T1/ptm/m/n/10 trees
all three resid-ual def-i-ni-tions re-duce to
Overfull \hbox (6.78088pt too wide) in paragraph at lines 1163--1163
[]\T1/pcr/m/n/10 rpart(formula, data, weights, subset, na.action = na.rpart, m
ethod,
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1164--1164
[] \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos
t, ...)[]
Underfull \hbox (badness 2837) in paragraph at lines 1187--1196
[]\T1/ptm/m/n/10 one of \T1/pcr/m/n/10 "anova"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "
poisson"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "class" \T1/ptm/m/n/10 or \T1/pcr/m/n/1
0 "exp"\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 method
Underfull \hbox (badness 2088) in paragraph at lines 1187--1196
\T1/ptm/m/n/10 is miss-ing then the rou-tine tries to make an in-tel-li-gent gu
ess. If \T1/pcr/m/n/10 y
Underfull \hbox (badness 1817) in paragraph at lines 1187--1196
\T1/ptm/m/n/10 is a sur-vival ob-ject, then \T1/pcr/m/n/10 method = "exp" \T1/p
tm/m/n/10 is as-sumed, if \T1/pcr/m/n/10 y \T1/ptm/m/n/10 has 2
[3301]
Underfull \hbox (badness 2846) in paragraph at lines 1226--1228
[]\T1/ptm/m/n/10 a list of op-tions that con-trol de-tails of the \T1/pcr/m/n/1
0 rpart \T1/ptm/m/n/10 al-go-rithm. See
[3302]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1270--1270
[]\T1/pcr/m/n/9 par(mfrow = c(1,2), xpd = NA) # otherwise on some devices the
text is clipped[]
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[]\T1/pcr/m/n/10 rpart.control(minsplit = 20, minbucket = round(minsplit/3), c
p = 0.01,
Overfull \hbox (60.78088pt too wide) in paragraph at lines 1287--1287
[] \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate
= 2, xval = 10,[]
[3303] [3304] [3305] [3306] [3307] [3308]
Underfull \hbox (badness 1565) in paragraph at lines 1739--1742
[]\T1/ptm/m/n/10 the ploidy sta-tus of the tu-mor, from flow cy-tom-e-try. Val-
ues are `\T1/pcr/m/n/10 diploid\T1/ptm/m/n/10 ',
[3309] [3310]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1833--1833
[] \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n =
FALSE,[]
[3311] [3312] [3313]) (./spatial-pkg.tex [3314]
Chapter 28.
[3315] [3316] [3317] [3318] [3319] [3320]
Underfull \hbox (badness 10000) in paragraph at lines 423--427
[3321] [3322] [3323] [3324] [3325] [3326] [3327] [3328] [3329] [3330] [3331]
[3332] [3333]) (./survival-pkg.tex [3334]
Chapter 29.
[3335] [3336]
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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.[]
[3337] [3338]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}
[3339] [3340]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 423--423
[]\T1/pcr/m/n/9 fit <- coxph(Surv(futime, fustat) ~ resid.ds *rx + ecog.ps, da
ta = ovarian)
Overfull \hbox (4.38043pt too wide) in paragraph at lines 425--425
[]\T1/pcr/m/n/9 fit2 <- coxph(Surv(futime, fustat) ~ resid.ds +rx + ecog.ps, d
ata=ovarian)[]
[3341]
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[] \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog),
lung)[]
[3342] [3343]
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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"),[]
[3345] [3346]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 805--805
[] \T1/pcr/m/n/9 subcoh = ~subcohort, id=~seqno, stratum=~instit, cohort.siz
e=stratsizes,[]
[3347] [3348] [3349]
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.
Overfull \hbox (4.38043pt too wide) in paragraph at lines 995--995
[]\T1/pcr/m/n/9 ppois(4, 10.24153) #chance of seeing 4 or fewer events wit
h large rate[]
[3350] [3351]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1110--1110
[]\T1/pcr/m/n/9 ## Not run: clogit(case ~ spontaneous + induced + strata(strat
um), data=infert)
[3352]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col
on}) has been already used, duplicate ignored
<to be read again>
\relax
l.1178 ...erapy for Stage B/C colon cancer}{colon}
[3353]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 1271--1271
[] \T1/pcr/m/n/10 cluster, ymin, ymax, timewt= c("n", "S", "S/G", "n/G", "n/G
2", "I"),[]
[3354] [3355] [3356] [3357] [3358] [3359]
Underfull \hbox (badness 1337) in paragraph at lines 1753--1757
[][][]\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 ,
[3360]
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[]\T1/pcr/m/n/10 iter.max = 20, toler.inf = sqrt(eps), outer.max = 10, timefix
=TRUE)[]
[3361] [3362] [3363] [3364] [3365] [3366]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2246--2246
[] \T1/pcr/m/n/9 [1] "extreme" "logistic" "gaussian" "weibull" "
exponential"[]
[3367] [3368] [3369] [3370]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 2495--2495
[]\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t
df = 5,[]
[3371] [3372] [3373] [3374] [3375]
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[]\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt
y(id), kidney)
Overfull \hbox (36.7804pt too wide) in paragraph at lines 2848--2848
[] \T1/pcr/m/n/9 factor(c(0, 1, 2,1,0,2), 0:2, c("censored", "progre
ssion", "death")))[]
Underfull \hbox (badness 1389) in paragraph at lines 2862--2864
[]\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
[3377]
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[]\T1/ptm/m/n/10 this pa-ram-e-ter is no longer nec-es-sary and is ig-nored. Se
e the note in
[3378]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 2995--2995
[] \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 )))[]
[3379] [3380] [3381] [3382] [3383]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3241--3241
[]\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential
ly the same.[]
[3384] [3385] [3386] [3387]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3507--3507
[] \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 )))[]
[3388]
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[3390] [3391] [3392] [3393] [3394]
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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,[]
[3395] [3396]
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[]\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign),
collapse,[]
[3397]
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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[]
[3398]
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[] \T1/pcr/m/n/9 predict(fit, reference="sample") + sum(coef(fit) * fit$means
, na.rm=TRUE)[]
[3399]
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[]\T1/pcr/m/n/9 pct <- 1:98/100 # The 100th percentile of predicted survival
is at +infinity[]
[3400] [3401]
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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
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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, ...)[]
[3404] [3405] [3406]
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[] \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year=
entry.dt),[]
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[]\T1/ptm/m/n/10 an ar-ray con-tain-ing the ex-pected num-ber of events (or per
-son years if
[3407]
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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)) +[]
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[3414]
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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
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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)[]
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l.5705 ...ata from a soldering experiment}{solder}
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[3420]
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[]\T1/pcr/m/n/10 statefig(layout, connect, margin = 0.03, box = TRUE, cex = 1,
col = 1,
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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,[]
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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 ),[]
[3431] [3432]
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 length \T1/ptm/m/n/10 of a \T1/pcr/m/n/10 S
urv \T1/ptm/m/n/10 ob-ject is the num-ber of sur-vival times
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\T1/ptm/m/n/10 it con-tains, not the num-ber of items re-quired to en-code it,
e.g.,
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\T1/pcr/m/n/10 x <- Surv(1:4, 5:9, c(1,0,1,0)); length(x) \T1/ptm/m/n/10 has a
value of 4. Like-
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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
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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
[3436]
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[] \T1/pcr/m/n/9 rmap= list(age=(accept.dt - birth.dt), sex=1
, year=accept.dt),[]
[3437]
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[] \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv
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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
[3438]
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[]\T1/ptm/m/n/10 numeric value to scale the re-sults. If \T1/pcr/m/n/10 ratetab
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[] \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d
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[3439]
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[]\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival
by 1/2 years[]
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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 ,
[3443]
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[] \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit",
"arcsin"),[]
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[]\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored
(status=3),[]
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[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the er-ror. Pos-si-ble val-
ues are
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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,
[3454]
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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
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 ,
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\T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 ,\T1/pcr/m/n/10 "lognormal" \T1/ptm/m/n
/10 and \T1/pcr/m/n/10 "loglogistic"\T1/ptm/m/n/10 . Oth-er-wise, it is
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[]\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi
on. The survreg[]
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^2*temp -1))[]
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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
inear",[]
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(/usr/share/texmf-dist/tex/latex/psnfss/t1pcr.fd) [1] [2] [3] [4] [5] [6]
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Chapter 1.
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[]\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h
igh-est, for
[3]
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[]\T1/pcr/m/n/10 .Devices \T1/ptm/m/n/10 is a [][]pairlist[][][] of length-one
char-ac-ter vec-tors. The first en-try is al-ways
[4]
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[]\T1/ptm/m/n/10 the small-est pos-i-tive floating-point num-ber \T1/pcr/m/n/10
x \T1/ptm/m/n/10 such that
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\T1/pcr/m/n/10 1 + x != 1\T1/ptm/m/n/10 . It equals \T1/pcr/m/n/10 double.base
^ ulp.digits \T1/ptm/m/n/10 if ei-
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\T1/ptm/m/n/10 ther \T1/pcr/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/pcr/m
/n/10 double.rounding \T1/ptm/m/n/10 is 0; oth-er-wise,
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\T1/ptm/m/n/10 it is \T1/pcr/m/n/10 (double.base ^ double.ulp.digits) / 2\T1/pt
m/m/n/10 . Nor-mally
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[]\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/pcr/m/n/10 x \T1
/ptm/m/n/10 such that \T1/pcr/m/n/10 1 - x != 1\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 It equals \T1/pcr/m/n/10 double.base ^ double.neg.ulp.digits \T1
/ptm/m/n/10 if
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\T1/pcr/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/pcr/m/n/10 double.roundin
g \T1/ptm/m/n/10 is 0; oth-er-wise, it is
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\T1/pcr/m/n/10 (double.base ^ double.neg.ulp.digits) / 2\T1/ptm/m/n/10 . Nor-ma
lly
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[]\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-
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\T1/ptm/m/n/10 i-cally, it is equal to \T1/pcr/m/n/10 (1 - double.neg.eps) *
[5] [6] [7]
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[][][]\T1/pcr/m/n/10 R.version[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 Sys.
info[][][] \T1/ptm/m/n/10 give more de-tails about the OS. In par-tic-u-lar,
[8]
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[]\T1/ptm/m/n/10 logical: should \T1/pcr/m/n/10 minlength \T1/ptm/m/n/10 be ob-
served strictly? Note that set-ting
[9] [10]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T
1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ',
[11] [12] (/usr/share/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [13] [14] [15]
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[]\T1/pcr/m/n/10 all.names(expr, functions = TRUE, max.names = -1L, unique = F
ALSE)
[16] [17] [18] [19]
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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
[20] [21] [22] [23]
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[]\T1/pcr/m/n/10 %% \T1/ptm/m/n/10 in-di-cates \T1/pcr/m/n/10 x mod y \T1/ptm/m
/n/10 and \T1/pcr/m/n/10 %/% \T1/ptm/m/n/10 in-di-cates in-te-ger di-vi-sion. I
t is guar-an-teed that
[24] [25] [26]
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[] \T1/pcr/m/n/10 cut.names = FALSE, col.names = names(x), fix.em
pty.names = TRUE,[]
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[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , set-ting row n
ames and con-vert-ing col-umn names
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\T1/ptm/m/n/10 (to syn-tac-tic names: see [][]\T1/pcr/m/n/10 make.names[][][]\T
1/ptm/m/n/10 ) is op-tional. Note that all
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\T1/ptm/m/n/10 of \T1/phv/m/n/10 R\T1/ptm/m/n/10 's \T1/ptm/b/n/10 base \T1/ptm
/m/n/10 pack-age \T1/pcr/m/n/10 as.data.frame() \T1/ptm/m/n/10 meth-ods use \T1
/pcr/m/n/10 optional
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\T1/ptm/m/n/10 only for col-umn names treat-ment, ba-si-cally with the mean-ing
of
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[][]\T1/pcr/m/n/10 data.frame[][][](*, check.names = !optional)\T1/ptm/m/n/10 .
See also the
[27]
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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
[28]
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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
[29] [30]
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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)[]
[31]
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[]\T1/ptm/m/n/10 If it is a list, the equiv-a-lent of [][]\T1/pcr/m/n/10 list2e
nv[][][](x, parent = emptyenv())
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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]
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[]\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by
[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]
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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
[38] [39]
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[]\T1/pcr/m/n/10 attach(what, pos = 2L, name = deparse(substitute(what), backt
ick=FALSE),
[40] [41] [42]
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[]\T1/ptm/m/n/10 The ex-trac-tion func-tion first looks for an ex-act match to
\T1/pcr/m/n/10 which \T1/ptm/m/n/10 amongst the at-
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\T1/ptm/m/n/10 tributes of \T1/pcr/m/n/10 x\T1/ptm/m/n/10 , then (un-less \T1/p
cr/m/n/10 exact = TRUE\T1/ptm/m/n/10 ) a unique par-tial match. (Set-ting
[43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56]
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[]\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim
-ited by set-ting
[57] [58] [59]
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[] \T1/pcr/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...)
, recursive=recursive)
[60] [61] [62] [63]
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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
[64] [65]
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[]\T1/ptm/m/n/10 is ICU avail-able for col-la-tion? See the help on [][]Com-par
-i-son[][][] and
[66] [67]
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[]\T1/pcr/m/n/9 cat(paste(letters, 100* 1:26), fill = TRUE, labels = paste0("{
", 1:10, "}:"))[]
[68]
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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
[69]
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 cbind \T1/ptm/m/n/10 data frame method is j
ust a wrap-per for
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[][]\T1/pcr/m/n/10 data.frame[][][](..., check.names = FALSE)\T1/ptm/m/n/10 . T
his means that it will split ma-
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\T1/ptm/m/n/10 trix columns in data frame ar-gu-ments, and con-vert char-ac-ter
columns to fac-tors un-less
[70]
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[]\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna
mes (default)[]
[71] [72] [73] [74]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c
har-ac-ter by
[75] [76] [77] [78] [79] [80]
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[]\T1/ptm/m/n/10 When a generic func-tion \T1/pcr/m/n/10 fun \T1/ptm/m/n/10 is
ap-plied to an ob-ject with class at-tribute
[81] [82] [83] [84] [85] [86] [87] [88]
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[]\T1/ptm/m/n/10 Collation of char-ac-ter strings is a com-plex topic. For an i
n-tro-duc-tion see [][]$\T1/pcr/m/n/10 https : / /
[89] [90]
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[]\T1/pcr/m/n/9 ## The exact result of this *depends* on the platform, compile
r, math-library:[]
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[]\T1/pcr/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex
_)), is.na(Im(NA_complex_)))[]
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[]\T1/pcr/m/n/9 showC(NpNA)# but not always is {shows \TS1/pcr/m/n/9 '\T1/pcr
/m/n/9 (R = NaN, I = NA)\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 on some platforms}[]
[91] [92] [93]
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[]\T1/ptm/m/n/10 User in-ter-rupts sig-nal a con-di-tion of class \T1/pcr/m/n/1
0 interrupt \T1/ptm/m/n/10 that in-her-its di-rectly from class
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[]\T1/ptm/m/n/10 Restarts are used for es-tab-lish-ing re-cov-ery pro-to-cols.
They can be es-tab-lished us-ing
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[]\T1/ptm/m/n/10 New restarts for \T1/pcr/m/n/10 withRestarts \T1/ptm/m/n/10 ca
n be spec-i-fied in sev-eral ways. The sim-plest is in
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[]\T1/ptm/m/n/10 One ad-di-tional field that can be spec-i-fied for a restart i
s \T1/pcr/m/n/10 interactive\T1/ptm/m/n/10 . This should
[94] [95]
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[]\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e
ncoding"))[]
[96]
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[]\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 :
[97] [98]
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[]\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
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\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
[99] [100]
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\T1/ptm/m/n/10 Byte Or-der Mark if present (which it of-ten is for files and we
b-pages gen-er-ated by Mi-
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\T1/ptm/m/n/10 crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not rec-o
m-mended) when writ-ing it
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[]\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in
g from
[101]
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\T1/ptm/m/n/10 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http : / / standar
ds . freedesktop . org / clipboards-[]spec /
[102] [103]
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[]\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE"))
; close(con)[]
[105]
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\T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the
first el-e-
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[]\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th
e call to
[110] [111]
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[]\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org") ## this redirect
s to https://[]
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[]\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h
igh-est, for
[112] [113] [114]
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[]\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng
th.out = 24)[]
[115] [116]
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[]\T1/ptm/m/n/10 logical: should char-ac-ter vec-tors be con-verted to fac-tors
? The
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\T1/ptm/m/n/10 `factory-fresh' de-fault is \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ,
but this can be changed by set-ting
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[]\T1/pcr/m/n/10 data.frame \T1/ptm/m/n/10 con-verts each of its ar-gu-ments to
a data frame by call-ing
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[][]\T1/pcr/m/n/10 as.data.frame[][][](optional = TRUE)\T1/ptm/m/n/10 . As that
is a generic func-tion, meth-ods can be
[117]
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[]\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")
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[][][]\T1/pcr/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.data.frame
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10
, [][]\T1/pcr/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 names[]
[][] \T1/ptm/m/n/10 (for the col-
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\T1/ptm/m/n/10 umn names), [][]\T1/pcr/m/n/10 [.data.frame[][][] \T1/ptm/m/n/10
for sub-set-ting meth-ods and \T1/pcr/m/n/10 I(matrix(..)) \T1/ptm/m/n/10 ex-a
m-
[118] [119] [120] [121] [122] [123]
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\T1/pcr/m/n/10 23:59:59", format = "%Y-%m-%d %H:%M:%S", tz = "UTC") \T1/ptm/m/n
/10 may give \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 8358--8370
\T1/ptm/m/n/10 and hence \T1/pcr/m/n/10 as.POSIXct("1969-12-31 23:59:59", tz =
"UTC") \T1/ptm/m/n/10 will give
[124] [125] [126]
Underfull \hbox (badness 5802) in paragraph at lines 8585--8589
[]\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 read.dcf(all = FALSE) \T1/ptm/m/n/10
reads the file byte-by-byte. This al-lows a
Underfull \hbox (badness 10000) in paragraph at lines 8620--8621
[][][]$\T1/pcr/m/n/10 https : / / www . debian . org / doc / debian-[]policy /
index . html #
[127] [128] [129]
Underfull \hbox (badness 10000) in paragraph at lines 8805--8809
[]\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
[130]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8893--8893
[]\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})[]
[131]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 8920--8920
[] \T1/pcr/m/n/10 backtick = mode(expr) %in% c("call", "expression", "(
", "function"),[]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 8921--8921
[] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "sh
owAttributes"),[]
[132] [133]
Underfull \hbox (badness 5403) in paragraph at lines 9039--9041
[]\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 9058--9060
[]\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
[134]
Underfull \hbox (badness 1132) in paragraph at lines 9130--9137
\T1/ptm/m/n/10 at-tributes as well, but not to use any of the other op-tions to
make the re-sult parseable.
[135]
Underfull \hbox (badness 1603) in paragraph at lines 9266--9269
[]\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
[136] [137] [138] [139] [140] [141] [142] [143] [144]
Underfull \hbox (badness 1917) in paragraph at lines 9872--9877
[]\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
[145]
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[]\T1/pcr/m/n/9 strd(provideDimnames(N, base= list(letters[-(1:9)], tail(LETTE
RS)))) # recycling[]
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[]\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling
on both levels[]
[146] [147]
Underfull \hbox (badness 1168) in paragraph at lines 10030--10035
\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 10069--10075
[]\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 10076--10079
[]\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
[148] [149]
Underfull \hbox (badness 2828) in paragraph at lines 10235--10239
[][][]$\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 10235--10239
\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 _
[150]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 10268--10268
[] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "showA
ttributes"))[]
[151] [152] [153]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10483--10483
[]\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon
th.abb[5:9]))
[154]
Underfull \hbox (badness 1629) in paragraph at lines 10557--10561
[]\T1/ptm/m/n/10 Promises will nor-mally only be en-coun-tered by users as a re
-sult of lazy-loading (when
[155] [156]
Underfull \hbox (badness 2150) in paragraph at lines 10658--10661
[]\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered
from the re-verse
Underfull \hbox (badness 3690) in paragraph at lines 10672--10680
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 anyDuplicated\T1/ptm/m/n/10 , \T1/pcr/m/n/10
anyDuplicated(x, ...) \T1/ptm/m/n/10 is a ``gen-er-al-ized'' short-cut for
Underfull \hbox (badness 10000) in paragraph at lines 10681--10683
[]\T1/pcr/m/n/10 duplicated(x, fromLast = TRUE) \T1/ptm/m/n/10 is equiv-a-lent
to but faster than
[157]
Underfull \hbox (badness 3735) in paragraph at lines 10701--10708
[]\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \
T1/pcr/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to
[158] [159]
Underfull \hbox (badness 10000) in paragraph at lines 10897--10900
[]\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
[160] [161] [162] [163] [164] [165] [166] [167] [168] [169]
Underfull \hbox (badness 5288) in paragraph at lines 11594--11596
[]\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val
ue of
Underfull \hbox (badness 3039) in paragraph at lines 11604--11609
[]\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
[170]
Underfull \hbox (badness 10000) in paragraph at lines 11664--11666
[]\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for
[171]
Underfull \hbox (badness 4569) in paragraph at lines 11781--11785
[]\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 11781--11785
\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
[172] [173]
Underfull \hbox (badness 10000) in paragraph at lines 11896--11898
[]\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
[174]
Underfull \hbox (badness 2790) in paragraph at lines 11939--11941
[]\T1/pcr/m/n/10 get0(): \T1/ptm/m/n/10 The object---as from [][]\T1/pcr/m/n/10
get[][][](x, *)\T1/ptm/m/n/10 --- if \T1/pcr/m/n/10 exists(x, *) \T1/ptm/m/n/1
0 is true, oth-er-wise
[175] [176]
Underfull \hbox (badness 4048) in paragraph at lines 12110--12120
[]\T1/pcr/m/n/10 as.expression \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-me
nt into an ex-pres-sion ob-ject. It is
Underfull \hbox (badness 3657) in paragraph at lines 12110--12120
\T1/ptm/m/n/10 generic, and only the de-fault method is de-scribed here. (The d
e-fault method calls
[177] [178] [179]
Underfull \hbox (badness 5460) in paragraph at lines 12358--12367
[]\T1/ptm/m/n/10 Both \T1/pcr/m/n/10 $ \T1/ptm/m/n/10 and \T1/pcr/m/n/10 [[ \T1
/ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a
l-
Underfull \hbox (badness 2221) in paragraph at lines 12358--12367
\T1/ptm/m/n/10 lowed and no par-tial match-ing is done. The se-man-tics of thes
e op-er-a-tions are those
Underfull \hbox (badness 2707) in paragraph at lines 12358--12367
\T1/ptm/m/n/10 of \T1/pcr/m/n/10 get(i, env = x, inherits = FALSE)\T1/ptm/m/
n/10 . If no match is found then \T1/pcr/m/n/10 NULL
Underfull \hbox (badness 2818) in paragraph at lines 12358--12367
\T1/ptm/m/n/10 is re-turned. The re-place-ment ver-sions, \T1/pcr/m/n/10 $<- \T
1/ptm/m/n/10 and \T1/pcr/m/n/10 [[<-\T1/ptm/m/n/10 , can also be used. Again,
Underfull \hbox (badness 6978) in paragraph at lines 12358--12367
\T1/ptm/m/n/10 only char-ac-ter ar-gu-ments are al-lowed. The se-man-tics in th
is case are those of
[180] [181] [182] [183] [184] [185]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12732--12732
[]\T1/pcr/m/n/9 ## "avector" := vector that keeps attributes. Could provide
a constructor[]
[186] [187] [188] [189]
Underfull \hbox (badness 5119) in paragraph at lines 13017--13020
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 iconv \T1/ptm/m/n/10 this will give the im-
ple-men-ta-tion as well as the ver-sion, for ex-am-ple
[190] [191]
Underfull \hbox (badness 2221) in paragraph at lines 13178--13187
\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
[192] [193] [194] [195]
Underfull \hbox (badness 2253) in paragraph at lines 13439--13441
[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
done: see
[196] [197]
Underfull \hbox (badness 10000) in paragraph at lines 13554--13556
[]\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
[198] [199]
Underfull \hbox (badness 10000) in paragraph at lines 13704--13706
[]\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See
[200]
Underfull \hbox (badness 10000) in paragraph at lines 13813--13817
[][][]\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 ,
[201]
Underfull \hbox (badness 10000) in paragraph at lines 13824--13827
[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][
] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / en . wikipedia .
Overfull \hbox (47.58038pt too wide) in paragraph at lines 13845--13845
[] \T1/pcr/m/n/9 # |--> (TRUE,FALSE) : ok for A but not B
as it exists already[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 13868--13868
[]\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode
= "0777")[]
[202]
Underfull \hbox (badness 10000) in paragraph at lines 13960--13963
[][][]\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 ,
[203]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13970--13970
[]\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu
rsive = TRUE)[]
[204]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 14045--14045
[]\T1/pcr/m/n/9 ## will not give an error, maybe a warning about *all* locatio
ns it is found:[]
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[]\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F
ALSE,
Underfull \hbox (badness 7238) in paragraph at lines 14098--14105
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 findInterval \T1/ptm/m/n/10 finds
the in-dex of one vec-tor \T1/pcr/m/n/10 x \T1/ptm/m/n/10 in an-other, \T1/pcr
/m/n/10 vec\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 14098--14105
\T1/ptm/m/n/10 where the lat-ter must be non-decreasing. Where this is triv-ial
, equiv-a-lent to
Underfull \hbox (badness 2126) in paragraph at lines 14098--14105
\T1/pcr/m/n/10 apply( outer(x, vec, ">="), 1, sum)\T1/ptm/m/n/10 , as a mat-ter
of fact, the in-ter-nal al-go-
[205]
Underfull \hbox (badness 3965) in paragraph at lines 14106--14110
[]\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,
[206] [207]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 14269--14269
[] \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING)
Overfull \hbox (0.78088pt too wide) in paragraph at lines 14270--14270
[] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING)[]
[208] [209]
Underfull \hbox (badness 10000) in paragraph at lines 14349--14353
[]\T1/ptm/m/n/10 The C type \T1/pcr/m/n/10 Rcomplex \T1/ptm/m/n/10 is de-fined
in `\T1/pcr/m/n/10 Complex.h\T1/ptm/m/n/10 ' as a
Underfull \hbox (badness 1389) in paragraph at lines 14349--14353
\T1/pcr/m/n/10 typedef struct {double r; double i;}\T1/ptm/m/n/10 . It may or m
ay not be equiv-a-lent to
[210] [211]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 14497--14497
[]\T1/pcr/m/n/9 ## formals returns a pairlist. Arguments with no default have
type symbol (aka name).[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 14500--14500
[]\T1/pcr/m/n/9 ## formals returns NULL for primitive functions. Use it in co
mbination with[]
[212]
Underfull \hbox (badness 1168) in paragraph at lines 14584--14588
[]\T1/ptm/m/n/10 Either a log-i-cal spec-i-fy-ing whether el-e-ments of a real
or com-plex vec-
Underfull \hbox (badness 2012) in paragraph at lines 14584--14588
\T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger
penalty (see
[213]
Underfull \hbox (badness 6944) in paragraph at lines 14679--14682
[][][]\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 ,
[214]
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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),[]
[215] [216]
Underfull \hbox (badness 10000) in paragraph at lines 14838--14840
[]\T1/pcr/m/n/10 prettyNum() \T1/ptm/m/n/10 is used for ``pret-ti-fy-ing'' (pos
-si-bly for-mat-ted) num-bers, also in
Overfull \hbox (48.78088pt too wide) in paragraph at lines 14857--14857
[] \T1/pcr/m/n/10 decimal.mark = getOption("OutDec"), input.d.mark =
decimal.mark,[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 14859--14859
[] \T1/pcr/m/n/10 zero.print = NULL, drop0trailing = FALSE, is.cmplx
= NA,[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 14862--14862
[]\T1/pcr/m/n/10 .format.zeros(x, zero.print, nx = suppressWarnings(as.numeric
(x)))[]
Underfull \hbox (badness 2790) in paragraph at lines 14868--14871
[]\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][]
\T1/pcr/m/n/10 complex[][][] \T1/ptm/m/n/10 only for
Underfull \hbox (badness 4254) in paragraph at lines 14884--14892
[]\T1/ptm/m/n/10 the to-tal field width; if both \T1/pcr/m/n/10 digits \T1/ptm/
m/n/10 and \T1/pcr/m/n/10 width \T1/ptm/m/n/10 are un-spec-i-fied,
Underfull \hbox (badness 1024) in paragraph at lines 14899--14903
[]\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
[217]
Underfull \hbox (badness 10000) in paragraph at lines 14968--14970
[]\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
[218]
Underfull \hbox (badness 10000) in paragraph at lines 14974--14978
[]\T1/pcr/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b
ers on the dec-i-mal point,
Underfull \hbox (badness 10000) in paragraph at lines 14974--14978
\T1/ptm/m/n/10 so \T1/pcr/m/n/10 formatC(c(6.11, 13.1), digits = 2, format = "f
g") \T1/ptm/m/n/10 gives
Underfull \hbox (badness 10000) in paragraph at lines 14979--14987
[]\T1/pcr/m/n/10 prettyNum \T1/ptm/m/n/10 is the util-ity func-tion for pret-ti
-fy-ing \T1/pcr/m/n/10 x\T1/ptm/m/n/10 . \T1/pcr/m/n/10 x \T1/ptm/m/n/10 can be
com-plex (or
Underfull \hbox (badness 3601) in paragraph at lines 15013--15017
[]\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 decimal.mark \T1/ptm/m/n/10 in
\T1/pcr/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt
m/m/n/10 3.2.0: for use
Underfull \hbox (badness 3302) in paragraph at lines 15013--15017
\T1/ptm/m/n/10 within [][]\T1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in
pack-ages which might be used with ear-lier ver-sions: use
[219]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 15080--15080
[]\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 [220]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 15102--15102
[]\T1/pcr/m/n/9 doLC <- FALSE # R warns, so change to TRUE manually if you wan
t see the effect[]
[221] [222] [223] [224] [225] [226] [227] [228] [229] [230] [231]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 15920--15920
[]\T1/pcr/m/n/9 utils::tail(getLoadedDLLs(), 2) # the last 2 loaded ones, stil
l a DLLInfoList[]
[232] [233]
Underfull \hbox (badness 2418) in paragraph at lines 16029--16033
\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 16036--16039
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 name \T1/ptm/m/n/10 con-tains only one sym-b
ol name and \T1/pcr/m/n/10 unlist \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\T1/ptm/
m/n/10 , then the sin-gle
Underfull \hbox (badness 2326) in paragraph at lines 16064--16071
[][][]\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 ,
[234] [235] [236] [237]
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[]\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F
ALSE,
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[]\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][]
[] (or char-ac-ter string for
[238] [239] [240] [241]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 16603--16603
[] \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:]]+)"[]
Underfull \vbox (badness 10000) has occurred while \output is active [242]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 16683--16683
[] \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F
ALSE)[]
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[]\T1/ptm/m/n/10 raw vec-tor con-tain-ing a [][]reg-u-lar ex-pres-sion[][][] (o
r fixed pat-tern for
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\T1/pcr/m/n/10 fixed = TRUE\T1/ptm/m/n/10 ) to be matched in the given raw vec-
tor. Co-erced by
[243] [244] [245] [246] [247]
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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)))
[248] [249] [250] [251]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 17302--17302
[]\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F
ALSE)
[252] [253] [254]
Underfull \hbox (badness 2435) in paragraph at lines 17563--17565
[]\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/pcr/m/n/10 http : / / www
. unicode . org / reports / tr35 /
[255]
Underfull \hbox (badness 1867) in paragraph at lines 17605--17612
[]\T1/ptm/m/n/10 It is op-tional on Win-dows: if \T1/phv/m/n/10 R \T1/ptm/m/n/1
0 has been built against ICU, it will only be used if
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\T1/ptm/m/n/10 en-vi-ron-ment vari-able \T1/pcr/m/n/10 R_ICU_LOCALE \T1/ptm/m/n
/10 is set or once \T1/pcr/m/n/10 icuSetCollate \T1/ptm/m/n/10 is called to se-
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\T1/ptm/m/n/10 lect the lo-cale (as ICU and Win-dows dif-fer in their idea of l
o-cale names). Note that
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[]\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))[]
[256]
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[]\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se
t = TRUE,
[257] [258]
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[]\T1/pcr/m/n/9 ### For functions ("closure"s): ------------------------------
----------------[]
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[]\T1/pcr/m/n/9 identical(f, g) # TRUE, as bytecode is
ignored by default[]
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[]\T1/pcr/m/n/9 ## GLM families contain several functions, some of which share
an environment:[]
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[]\T1/pcr/m/n/9 op <- options(keep.source = TRUE) # and so, these have differi
ng "srcref" :[]
[259] [260]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 17934--17934
[]\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):[]
[261] [262] [263]
Underfull \hbox (badness 10000) in paragraph at lines 18147--18149
[]\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
[264]
Underfull \hbox (badness 4217) in paragraph at lines 18231--18240
[][][]\T1/pcr/m/n/10 length[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 length<-[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 dimnames<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dim[][][]\T1/ptm
/m/n/10 , [][]\T1/pcr/m/n/10 dim<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 nam
es[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 names<-[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 2057) in paragraph at lines 18246--18262
[][][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.c
omplex[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.double[][][]\T1/ptm/m/n/10 ,
[][]\T1/pcr/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.logi
cal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.raw[][][]\T1/ptm/m/n/10 ,
[265] [266] [267] [268] [269] [270]
Underfull \hbox (badness 4699) in paragraph at lines 18660--18663
[]\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 ,
[271] [272]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 18783--18783
[]\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = "
GMT")[]
[273] [274]
Underfull \hbox (badness 4739) in paragraph at lines 18918--18920
[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
[275] [276] [277] [278] [279] [280] [281]
Underfull \hbox (badness 1430) in paragraph at lines 19331--19336
\T1/ptm/m/n/10 if \T1/pcr/m/n/10 simplify = "array"\T1/ptm/m/n/10 , an ar-ray i
f ap-pro-pri-ate, by ap-ply-ing \T1/pcr/m/n/10 simplify2array()\T1/ptm/m/n/10 .
Underfull \hbox (badness 10000) in paragraph at lines 19331--19336
\T1/pcr/m/n/10 sapply(x, f, simplify = FALSE, USE.NAMES = FALSE) \T1/ptm/m/n/10
is the same as
[282]
Underfull \hbox (badness 10000) in paragraph at lines 19392--19397
[]\T1/ptm/m/n/10 logical; if true, \T1/pcr/m/n/10 simplify2array() \T1/ptm/m/n/
10 will pro-duce a (``higher
Underfull \hbox (badness 10000) in paragraph at lines 19392--19397
\T1/ptm/m/n/10 rank'') ar-ray when ap-pro-pri-ate, whereas \T1/pcr/m/n/10 highe
r = FALSE \T1/ptm/m/n/10 would
Underfull \hbox (badness 5008) in paragraph at lines 19392--19397
\T1/ptm/m/n/10 re-turn a ma-trix (or vec-tor) only. These two cases cor-re-spon
d to
Underfull \hbox (badness 10000) in paragraph at lines 19392--19397
\T1/pcr/m/n/10 sapply(*, simplify = "array") \T1/ptm/m/n/10 or \T1/pcr/m/n/10 s
implify = TRUE\T1/ptm/m/n/10 , re-
[283]
Underfull \hbox (badness 10000) in paragraph at lines 19452--19459
[]\T1/pcr/m/n/10 vapply \T1/ptm/m/n/10 re-turns a vec-tor or ar-ray of type mat
ch-ing the \T1/pcr/m/n/10 FUN.VALUE\T1/ptm/m/n/10 . If
Underfull \hbox (badness 6364) in paragraph at lines 19452--19459
\T1/pcr/m/n/10 length(FUN.VALUE) == 1 \T1/ptm/m/n/10 a vec-tor of the same leng
th as \T1/pcr/m/n/10 X \T1/ptm/m/n/10 is re-turned, oth-
Underfull \hbox (badness 5064) in paragraph at lines 19452--19459
\T1/ptm/m/n/10 er-wise an ar-ray. If \T1/pcr/m/n/10 FUN.VALUE \T1/ptm/m/n/10 is
not an [][]\T1/pcr/m/n/10 array[][][]\T1/ptm/m/n/10 , the re-sult is a ma-trix
with
Underfull \hbox (badness 5908) in paragraph at lines 19452--19459
\T1/pcr/m/n/10 length(FUN.VALUE) \T1/ptm/m/n/10 rows and \T1/pcr/m/n/10 length(
X) \T1/ptm/m/n/10 columns, oth-er-wise an ar-ray \T1/pcr/m/n/10 a \T1/ptm/m/n/1
0 with
Underfull \hbox (badness 10000) in paragraph at lines 19468--19470
[]\T1/pcr/m/n/10 sapply(*, simplify = FALSE, USE.NAMES = FALSE) \T1/ptm/m/n/10
is equiv-a-lent to
[284]
Underfull \hbox (badness 1975) in paragraph at lines 19540--19543
[]\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
[285] [286] [287] [288] [289] [290]
Underfull \hbox (badness 1077) in paragraph at lines 19935--19940
[]\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
[291]
Underfull \hbox (badness 10000) in paragraph at lines 19949--19956
[][][]$\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 /
[292]
Underfull \hbox (badness 10000) in paragraph at lines 20023--20027
[]\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
[293]
Underfull \hbox (badness 10000) in paragraph at lines 20153--20157
[]\T1/ptm/m/n/10 To sup-press mes-sages dur-ing the load-ing of pack-ages use
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[][]\T1/pcr/m/n/10 suppressPackageStartupMessages[][][]\T1/ptm/m/n/10 : this wi
ll sup-press all mes-sages from \T1/phv/m/n/10 R \T1/ptm/m/n/10 it-self
[294] [295]
Underfull \hbox (badness 10000) in paragraph at lines 20251--20258
[][][]\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 ,
[296] [297]
Underfull \hbox (badness 10000) in paragraph at lines 20372--20376
[]\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
[298]
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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 20442--20447
\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 20442--20447
\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 20442--20447
\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
[299] [300]
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[] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. =
FALSE)[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 20613--20613
[] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. =
FALSE)[]
[301]
Underfull \hbox (badness 3343) in paragraph at lines 20669--20673
[][][]\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
[302]
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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))),[]
[303] [304]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 20877--20877
[]\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 20880--20880
[]\T1/pcr/m/n/9 attach("all.rda") # safer and will warn about masked objects w
/ same name in .GlobalEnv[]
[305]
Underfull \hbox (badness 6380) in paragraph at lines 20925--20930
[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways
be sup-
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[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 category = "LC_ALL" \T1/ptm/m/n/10 the de-t
ails of the string are system-specific: it might be
Underfull \hbox (badness 1960) in paragraph at lines 20983--20990
\T1/ptm/m/n/10 a sin-gle lo-cale name or a set of lo-cale names sep-a-rated by
\T1/pcr/m/n/10 "/" \T1/ptm/m/n/10 (So-laris, ma-cOS) or
Underfull \hbox (badness 1043) in paragraph at lines 20983--20990
\T1/ptm/m/n/10 not nec-es-sar-ily the case that the re-sult of \T1/pcr/m/n/10 f
oo <- Sys.getlocale() \T1/ptm/m/n/10 can be used in
[306]
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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
Overfull \hbox (4.38043pt too wide) in paragraph at lines 21046--21046
[]\T1/pcr/m/n/9 Sys.setlocale("LC_TIME", "de_DE.UTF-8") # Linux, macOS, other
Unix-alikes[]
[307]
Underfull \hbox (badness 1205) in paragraph at lines 21069--21074
\T1/ptm/m/n/10 10) log-a-rithms, and \T1/pcr/m/n/10 log2 \T1/ptm/m/n/10 com-put
es bi-nary (i.e., base 2) log-a-rithms. The gen-eral form
[308] [309]
Underfull \hbox (badness 1400) in paragraph at lines 21214--21218
[][][]\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
Overfull \hbox (36.83002pt too wide) in paragraph at lines 21234--21241
[]\T1/pcr/m/n/10 isTRUE(x) \T1/ptm/m/n/10 is the same as \T1/pcr/m/n/10 { is.lo
gical(x) && length(x) == 1 && !is.na(x) && x }\T1/ptm/m/n/10 ;
Underfull \hbox (badness 4886) in paragraph at lines 21234--21241
\T1/ptm/m/n/10 In ear-lier \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions, \T1/pcr/m
/n/10 isTRUE <- function(x) identical(x, TRUE)\T1/ptm/m/n/10 , had the
[310] [311]
Underfull \hbox (badness 2469) in paragraph at lines 21384--21390
[]\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 names.
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\T1/ptm/m/n/10 Char-ac-ter strings \T1/pcr/m/n/10 c("T", "TRUE", "True", "true"
) \T1/ptm/m/n/10 are re-garded as true,
[312] [313] [314] [315] [316]
Underfull \hbox (badness 10000) in paragraph at lines 21701--21703
[]\T1/ptm/m/n/10 The al-go-rithm used by \T1/pcr/m/n/10 make.unique \T1/ptm/m/n
/10 has the prop-erty that
[317] [318] [319] [320] [321]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 22005--22005
[]\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 22009--22009
[]\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)[]
[322] [323]
Underfull \hbox (badness 1655) in paragraph at lines 22133--22137
[]\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion
(also known as a `clo-sure'):
[324] [325] [326]
Underfull \hbox (badness 2277) in paragraph at lines 22382--22385
[]\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.
[327] [328] [329] [330] [331] [332] [333] [334]
Underfull \hbox (badness 10000) in paragraph at lines 22867--22873
[]\T1/ptm/m/n/10 There are also lim-its on in-di-vid-ual ob-jects. The stor-age
space can-not ex-ceed
Underfull \hbox (badness 6316) in paragraph at lines 22867--22873
\T1/ptm/m/n/10 the ad-dress limit, and if you try to ex-ceed that limit, the er
-ror mes-sage be-gins
Underfull \hbox (badness 1484) in paragraph at lines 22899--22907
[]\T1/ptm/m/n/10 The address-space limit is 2Gb un-der 32-bit Win-dows un-less
the OS's de-fault has been
Underfull \hbox (badness 2951) in paragraph at lines 22899--22907
\T1/ptm/m/n/10 changed to al-low more (up to 3Gb). See [][]$\T1/pcr/m/n/10 http
s : / / www . microsoft . com / whdc /
Underfull \hbox (badness 3460) in paragraph at lines 22899--22907
\T1/pcr/m/n/10 system / platform / server / PAE / PAEmem . mspx$[][] \T1/ptm/m/
n/10 and [][]$\T1/pcr/m/n/10 https : / / msdn . microsoft .
[335]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 22976--22976
[] \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y =
all,[]
[336]
Underfull \hbox (badness 10000) in paragraph at lines 23030--23034
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 by \T1/ptm/m/n/10 or both \T1/pcr/m/n/10 by.
x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 by.y \T1/ptm/m/n/10 are of length 0 (a leng
th zero vec-
Underfull \hbox (badness 10000) in paragraph at lines 23030--23034
\T1/ptm/m/n/10 tor or \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 ), the re-sult, \T1/pcr
/m/n/10 r\T1/ptm/m/n/10 , is the \T1/ptm/m/it/10 Carte-sian prod-uct \T1/ptm/m/
n/10 of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , i.
e.,
[337] [338] [339] [340] [341] [342]
Underfull \hbox (badness 10000) in paragraph at lines 23481--23489
\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 ;
[343] [344]
Underfull \hbox (badness 3849) in paragraph at lines 23595--23600
[]\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
[345]
Underfull \hbox (badness 7308) in paragraph at lines 23672--23678
[]\T1/ptm/m/n/10 For an [][]\T1/pcr/m/n/10 environment[][][] env\T1/ptm/m/n/10
, \T1/pcr/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond-
ing
Underfull \hbox (badness 5077) in paragraph at lines 23672--23678
\T1/ptm/m/n/10 list, i.e., \T1/pcr/m/n/10 names(as.list(env, all.names = TRUE))
\T1/ptm/m/n/10 which are also given by
Underfull \hbox (badness 10000) in paragraph at lines 23682--23685
[]\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute
via the gen-eral rules:
Underfull \hbox (badness 10000) in paragraph at lines 23682--23685
\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
[346] [347]
Underfull \hbox (badness 10000) in paragraph at lines 23834--23836
[]\T1/ptm/m/n/10 character string: par-tial match-ing to one of
[348] [349] [350] [351]
Underfull \hbox (badness 6188) in paragraph at lines 24053--24056
[]\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
[352] [353] [354] [355] [356] [357] [358]
Underfull \hbox (badness 2197) in paragraph at lines 24535--24539
[]\T1/ptm/m/n/10 Loading a names-pace should where pos-si-ble be silent, with s
tartup mes-sages given by
Underfull \hbox (badness 4048) in paragraph at lines 24535--24539
\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 24549--24553
[]\T1/ptm/m/n/10 Uses of \T1/pcr/m/n/10 library \T1/ptm/m/n/10 with ar-gu-ment
\T1/pcr/m/n/10 help \T1/ptm/m/n/10 to dis-play ba-sic in-for-ma-tion about the
pack-
Underfull \hbox (badness 1990) in paragraph at lines 24549--24553
\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
[359]
Underfull \hbox (badness 10000) in paragraph at lines 24642--24648
[]\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 24642--24648
\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
[360]
Underfull \hbox (badness 10000) in paragraph at lines 24655--24657
[]\T1/pcr/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m
ore ef-fi-cient than
Overfull \hbox (4.38043pt too wide) in paragraph at lines 24706--24706
[] \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:[]
[361] [362] [363]
Underfull \hbox (badness 10000) in paragraph at lines 24899--24905
[]\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 is.numeric \T1/ptm/m/n/
10 re-turns \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of
Underfull \hbox (badness 10000) in paragraph at lines 24899--24905
[][]\T1/ptm/m/n/10 mode[][][] \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/10 ([][]type
[][][] \T1/pcr/m/n/10 "double" \T1/ptm/m/n/10 or type \T1/pcr/m/n/10 "integer"\
T1/ptm/m/n/10 ) and not a fac-tor,
Underfull \hbox (badness 10000) in paragraph at lines 24899--24905
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 oth-er-wise. That is, \T
1/pcr/m/n/10 is.integer(x) || is.double(x)\T1/ptm/m/n/10 , or
[364]
Underfull \hbox (badness 4120) in paragraph at lines 24985--24992
[]\T1/ptm/m/n/10 Hexadecimal con-stants start with \T1/pcr/m/n/10 0x \T1/ptm/m/
n/10 or \T1/pcr/m/n/10 0X \T1/ptm/m/n/10 fol-lowed by a nonempty se-quence from
[365] [366]
Underfull \hbox (badness 1694) in paragraph at lines 25121--25124
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor with suit-able nu-meric ver-sion strings
(see `De-tails');
[367] [368] [369] [370]
Underfull \hbox (badness 1603) in paragraph at lines 25368--25370
[]\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a
re con-verted by
[371]
Overfull \hbox (73.28088pt too wide) in paragraph at lines 25491--25499
\T1/pcr/m/n/10 c("datasets", "utils", "grDevices", "graphics", "stats",
"methods")\T1/ptm/m/n/10 .
[372] [373]
Underfull \hbox (badness 5475) in paragraph at lines 25628--25638
[]\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/pcr/m
/n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to
Underfull \hbox (badness 3271) in paragraph at lines 25670--25673
[]\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men
t vari-able
Underfull \hbox (badness 10000) in paragraph at lines 25685--25687
[]\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v
alue
[374] [375] [376]
Underfull \hbox (badness 3138) in paragraph at lines 25948--25954
[]\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 25948--25954
\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 25948--25954
\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
[377]
Underfull \hbox (badness 1194) in paragraph at lines 25961--25964
[]\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/pcr/m/n/10 create.post[][
][] \T1/ptm/m/n/10 (and hence[][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/n/10
and
Underfull \hbox (badness 1389) in paragraph at lines 25987--25989
[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
l HTTP server, see
Underfull \hbox (badness 10000) in paragraph at lines 25999--26003
[]\T1/ptm/m/n/10 string used as the user agent in HTTP(S) re-quests. If
Underfull \hbox (badness 6592) in paragraph at lines 25999--26003
\T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 , re-quests will be made with-out a user agen
t header. The de-fault is
Underfull \hbox (badness 10000) in paragraph at lines 26004--26010
[]\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by
Underfull \hbox (badness 3826) in paragraph at lines 26019--26024
[]\T1/ptm/m/n/10 Used by [][]\T1/pcr/m/n/10 install.packages[][][] \T1/ptm/m/n/
10 (and in-di-rectly
Overfull \hbox (49.4607pt too wide) in paragraph at lines 26025--26036
[]\T1/ptm/m/n/10 Used by [][]\T1/pcr/m/n/10 install.packages[][][](type = "both
")
Underfull \hbox (badness 1009) in paragraph at lines 26037--26040
[]\T1/ptm/m/n/10 default email-ing method used by [][]\T1/pcr/m/n/10 create.pos
t[][][] \T1/ptm/m/n/10 and hence [][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/
n/10 and
Underfull \hbox (badness 10000) in paragraph at lines 26047--26059
[]\T1/ptm/m/n/10 The de-fault type of pack-ages to be down-loaded and in-stalle
d -- see
Underfull \hbox (badness 1072) in paragraph at lines 26047--26059
[][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 . Pos-si-ble val-ues ar
e \T1/pcr/m/n/10 "source" \T1/ptm/m/n/10 (the de-fault ex-cept un-der a
[378]
Underfull \hbox (badness 10000) in paragraph at lines 26061--26068
[]\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/pcr/m/n/10 upda
te.packages[][][]\T1/ptm/m/n/10 . De-faults to
Underfull \hbox (badness 10000) in paragraph at lines 26061--26068
\T1/pcr/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i
-ties to prompt for a
Underfull \hbox (badness 6380) in paragraph at lines 26061--26068
\T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi
ng like
Overfull \hbox (34.78088pt too wide) in paragraph at lines 26061--26068
\T1/pcr/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr
an";
[379] [380] [381] [382]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26392--26392
[]\T1/pcr/m/n/9 system.time(o <- sort.list(xx, method = "radix")) # 0.007 sec,
300X faster[]
Underfull \hbox (badness 10000) in paragraph at lines 26405--26409
[]\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/pcr/m/n/10 X \T1/ptm/m/n
/10 and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/pcr/m/n/10 A \T1/ptm/
m/n/10 with di-men-sion
Underfull \hbox (badness 10000) in paragraph at lines 26405--26409
\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)]
[383] [384] [385] [386] [387]
Underfull \hbox (badness 4341) in paragraph at lines 26729--26731
[]\T1/pcr/m/n/10 paste0(..., collapse) \T1/ptm/m/n/10 is equiv-a-lent to \T1/pc
r/m/n/10 paste(..., sep = "", collapse)\T1/ptm/m/n/10 ,
Underfull \hbox (badness 4518) in paragraph at lines 26765--26771
[][][]\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
[388]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 26787--26787
[]\T1/pcr/m/n/9 ## Notice that the recycling rules make every input as long as
the longest input.[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26799--26799
[]\T1/pcr/m/n/9 paste("1st", "2nd", "3rd", collapse = ", ") # probably not wha
t you wanted[]
[389] [390] [391] [392] [393] [394] [395]
Underfull \hbox (badness 10000) in paragraph at lines 27233--27237
[]\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,
[396]
Underfull \hbox (badness 1796) in paragraph at lines 27299--27302
[]\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
[397] [398] [399]
Underfull \hbox (badness 10000) in paragraph at lines 27499--27502
[]\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
[400] [401] [402] [403] [404] [405] [406] [407] [408]
Underfull \hbox (badness 1226) in paragraph at lines 28131--28136
\T1/pcr/m/n/10 ncol(X) <= nrow(X)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 complete \T
1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 or the ar-gu-ment \T1/pcr/m/
n/10 ncol \T1/ptm/m/n/10 is greater than
[409]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 28176--28176
[] \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))[]
[410] [411] [412] [413]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 28442--28442
[]\T1/pcr/m/n/9 (nn <- "\u0126\u0119\u1114\u022d\u2001\u03e2\u0954\u0f3f\u13d3
\u147b\u203c")[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 28453--28453
[]\T1/pcr/m/n/9 n2 <- "\U0126\U0119\U1114\U022d\U2001\U03e2\U0954\U0f3f\U13d3\
U147b\U203c"[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 28459--28459
[]\T1/pcr/m/n/9 ## https://cran.r-project.org/doc/manuals/r-release/R-lang.htm
l#Literal-constants[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 28460--28460
[]\T1/pcr/m/n/9 ## and bug 16098 https://bugs.r-project.org/bugzilla3/show_bug
.cgi?id=16098[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 28463--28463
[]\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow
ed (parse errors)[]
[414]
Underfull \hbox (badness 7415) in paragraph at lines 28538--28542
[]\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
[415]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 28559--28559
[]\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu
l bottom-right note[]
[416]
Underfull \hbox (badness 2418) in paragraph at lines 28718--28729
[]\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
[417] [418]
Underfull \hbox (badness 1248) in paragraph at lines 28852--28859
\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 28852--28859
\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 /
[419] [420]
Underfull \hbox (badness 1533) in paragraph at lines 28968--28971
[]\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
[421]
Underfull \hbox (badness 1337) in paragraph at lines 29065--29068
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 finite \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE
\T1/ptm/m/n/10 , the min-i-mum and max-i-mum of all fi-nite val-ues is com-pute
d, i.e.,
[422]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 29113--29113
[] \T1/pcr/m/n/10 ties.method = c("average", "first", "last", "random", "m
ax", "min"))[]
Underfull \hbox (badness 1038) in paragraph at lines 29131--29142
[]\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/pcr/m/n/10 NA\
T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in
Underfull \hbox (badness 10000) in paragraph at lines 29143--29146
[]\T1/pcr/m/n/10 NA \T1/ptm/m/n/10 val-ues are never con-sid-ered to be equal:
for \T1/pcr/m/n/10 na.last = TRUE \T1/ptm/m/n/10 and
[423] [424]
Underfull \hbox (badness 1117) in paragraph at lines 29238--29244
\T1/ptm/m/n/10 e-ments which have a class in-cluded in \T1/pcr/m/n/10 classes \
T1/ptm/m/n/10 are re-placed by the re-sult of ap-ply-ing
[425] [426] [427] [428] [429] [430]
Underfull \hbox (badness 4048) in paragraph at lines 29616--29621
[]\T1/ptm/m/n/10 Either an ob-ject whose mode will give the mode of the vec-tor
to
Underfull \hbox (badness 4582) in paragraph at lines 29616--29621
\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 29616--29621
\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 ,
[431] [432] [433] [434] [435] [436] [437] [438]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 30162--30162
[]\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene
d as needed.[]
[439] [440] [441] [442]
Overfull \hbox (13.9408pt too wide) in paragraph at lines 30448--30450
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 ! " # $ % & \TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 ( )
* + , - . / : ; < = > ? @ [ \ ] ^ _ \TS1/pcr/m/n/10 ` \T1/pcr/m/n/10 { | } ~\T
1/ptm/m/n/10 '.
[443] [444] [445]
Underfull \hbox (badness 7558) in paragraph at lines 30664--30668
[]\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 30674--30676
[]\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 30679--30682
[][][]\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 30683--30685
[]\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 30686--30688
[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 http : / / p
ubs . opengroup . org / onlinepubs /
[446] [447] [448] [449] [450] [451]
Underfull \hbox (badness 10000) in paragraph at lines 31091--31095
[][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] []
[]NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple
x_[][][]
[452] [453] [454] [455] [456]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 31422--31422
[] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"))[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 31425--31425
[] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"),[]
[457] [458] [459]
Underfull \hbox (badness 3375) in paragraph at lines 31653--31660
\T1/ptm/m/n/10 pen if the spec-i-fied row names, i.e., \T1/pcr/m/n/10 value\T1/
ptm/m/n/10 , are in-valid, e.g., du-
Underfull \hbox (badness 2359) in paragraph at lines 31653--31660
\T1/ptm/m/n/10 pli-cated or \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 . The de-fault (is
back com-pat-i-ble), \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 , will sig-nal
Underfull \hbox (badness 2582) in paragraph at lines 31653--31660
\T1/ptm/m/n/10 an er-ror, where \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 will ``au-to-m
atic'' row names and \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 will call
[460] [461] [462]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 31806--31806
[] \T1/pcr/m/n/10 useHash = (!replace && is.null(prob) && size <= n/
2 && n > 1e7))[]
[463] [464]
Underfull \hbox (badness 10000) in paragraph at lines 31937--31941
[]\T1/pcr/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c
ur-rent
Underfull \hbox (badness 10000) in paragraph at lines 31937--31941
\T1/ptm/m/n/10 workspace', i.e., \T1/pcr/m/n/10 save(list = ls(all.names = TRUE
), file =
[465] [466] [467]
Underfull \hbox (badness 2302) in paragraph at lines 32188--32195
[]\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d
e-fined as $[]$,
Underfull \hbox (badness 2837) in paragraph at lines 32188--32195
\T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no
n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non
-missing
Underfull \hbox (badness 3815) in paragraph at lines 32188--32195
\T1/ptm/m/n/10 val-ues. In the case \T1/pcr/m/n/10 center = TRUE\T1/ptm/m/n/10
, this is the same as the stan-dard de-vi-a-tion,
Underfull \hbox (badness 2181) in paragraph at lines 32188--32195
\T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti
ons with-out cen-ter-ing, use
[468]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 32240--32240
[] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul =
FALSE)[]
[469]
Underfull \hbox (badness 1158) in paragraph at lines 32344--32349
[]\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
[470]
Underfull \hbox (badness 10000) in paragraph at lines 32371--32377
[]\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac-
ters
Underfull \hbox (badness 1953) in paragraph at lines 32371--32377
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 \a, \b, \f, \n, \r, \t, \v\T1/ptm/m/n/10 ' and o
c-tal and hex-adec-i-mal rep-re-
[471]
Underfull \hbox (badness 10000) in paragraph at lines 32447--32452
[]\T1/ptm/m/n/10 Note that since \T1/pcr/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r
a-tor and not a ter-mi-na-tor, read-ing a file by
Underfull \hbox (badness 6725) in paragraph at lines 32447--32452
\T1/pcr/m/n/10 scan("foo", sep = "\n", blank.lines.skip = FALSE) \T1/ptm/m/n/10
will give an empty
[472]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 32529--32529
[]\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data
", sep = "\n")
[473] [474] [475]
Underfull \hbox (badness 2809) in paragraph at lines 32793--32799
[]\T1/ptm/m/n/10 The fifth form gen-er-ates the se-quence \T1/pcr/m/n/10 1, 2,
..., length(from) \T1/ptm/m/n/10 (as if ar-gu-ment
Underfull \hbox (badness 7759) in paragraph at lines 32800--32803
[]\T1/ptm/m/n/10 The fi-nal form gen-er-ates the in-te-ger se-quence \T1/pcr/m/
n/10 1, 2, ..., length.out \T1/ptm/m/n/10 un-less
[476] [477] [478] [479] [480] [481] [482] [483] [484] [485] [486] [487]
Underfull \hbox (badness 1735) in paragraph at lines 33605--33611
\T1/ptm/m/n/10 Only prompts and (most) mes-sages con-tinue to ap-pear on the co
n-sole. Mes-sages sent
[488]
Underfull \hbox (badness 4303) in paragraph at lines 33621--33624
[]\T1/pcr/m/n/10 split = TRUE \T1/ptm/m/n/10 only splits \T1/phv/m/n/10 R \T1/p
tm/m/n/10 out-put (via \T1/pcr/m/n/10 Rvprintf\T1/ptm/m/n/10 ) and the de-fault
out-put from
[489] [490] [491] [492]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 33939--33939
[] \T1/pcr/m/n/10 method = c("auto", "shell", "quick", "radix"), index
.return = FALSE)[]
[493] [494] [495] [496]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 34191--34191
[] \T1/pcr/m/n/10 print. = TRUE, echo = TRUE, max.deparse.length
= Inf,[]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 34193--34193
[] \T1/pcr/m/n/10 deparseCtrl = c("keepInteger", "showAttributes"
, "keepNA"),[]
[497]
Underfull \hbox (badness 10000) in paragraph at lines 34236--34242
[][][]\T1/pcr/m/n/10 character[][][] \T1/ptm/m/n/10 vec-tor, passed as \T1/pcr/
m/n/10 control \T1/ptm/m/n/10 to [][]\T1/pcr/m/n/10 deparse[][][]()\T1/ptm/m/n/
10 , see
Underfull \hbox (badness 10000) in paragraph at lines 34236--34242
\T1/ptm/m/n/10 also [][]\T1/pcr/m/n/10 .deparseOpts[][][]\T1/ptm/m/n/10 . In \T
1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion <= 3.3.x, this was hard-
Underfull \hbox (badness 10000) in paragraph at lines 34236--34242
\T1/ptm/m/n/10 coded to \T1/pcr/m/n/10 "showAttributes"\T1/ptm/m/n/10 , which i
s the de-fault cur-rently;
Underfull \hbox (badness 2512) in paragraph at lines 34251--34253
[]\T1/ptm/m/n/10 integer; how many com-ment lines at the start of the file to s
kip if
[498]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 34347--34347
[]\T1/pcr/m/n/9 ## (all should look "as if on top level", e.g. non-assignments
should print:)[]
[499] [500] [501] [502] [503]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 34675--34675
[]\T1/pcr/m/n/9 ### Calculate \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 z-scores\TS1/pcr/m
/n/9 ' \T1/pcr/m/n/9 by group (standardize to mean zero, variance one)[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 34690--34690
[]\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is
being added[]
[504] [505] [506] [507] [508] [509]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 35129--35129
[]\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un
known")
Overfull \hbox (12.78088pt too wide) in paragraph at lines 35130--35130
[]\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile =
FALSE)[]
[510] [511] [512] [513]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 35394--35394
[]\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS
E, nowadays often three
[514]
Underfull \hbox (badness 10000) in paragraph at lines 35478--35488
[]\T1/ptm/m/n/10 A func-tion \T1/pcr/m/n/10 .First \T1/ptm/m/n/10 (and [][]\T1/
pcr/m/n/10 .Last[][][]\T1/ptm/m/n/10 ) can be de-fined in ap-pro-pri-ate `\T1/p
cr/m/n/10 .Rprofile\T1/ptm/m/n/10 '
Underfull \hbox (badness 10000) in paragraph at lines 35478--35488
\T1/ptm/m/n/10 or `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' files or have b
een saved in `\T1/pcr/m/n/10 .RData\T1/ptm/m/n/10 '. If you want
Underfull \hbox (badness 8113) in paragraph at lines 35478--35488
\T1/ptm/m/n/10 a dif-fer-ent set of pack-ages than the de-fault ones when you s
tart, in-sert a call
Underfull \hbox (badness 10000) in paragraph at lines 35478--35488
\T1/ptm/m/n/10 to [][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 in the `\T1/p
cr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n
/10 ' file. For ex-am-ple,
Underfull \hbox (badness 6542) in paragraph at lines 35478--35488
\T1/pcr/m/n/10 options(defaultPackages = character()) \T1/ptm/m/n/10 will at-ta
ch no ex-tra pack-ages on
Underfull \hbox (badness 5189) in paragraph at lines 35478--35488
\T1/ptm/m/n/10 startup (only the \T1/ptm/b/n/10 base \T1/ptm/m/n/10 pack-age) (
or set \T1/pcr/m/n/10 R_DEFAULT_PACKAGES=NULL \T1/ptm/m/n/10 as an en-vi-
Underfull \hbox (badness 4193) in paragraph at lines 35478--35488
\T1/ptm/m/n/10 ron-ment vari-able be-fore run-ning \T1/phv/m/n/10 R\T1/ptm/m/n/
10 ). Us-ing \T1/pcr/m/n/10 options(defaultPackages = "") \T1/ptm/m/n/10 or
[515]
Underfull \hbox (badness 10000) in paragraph at lines 35522--35528
[]\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 35522--35528
\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 35522--35528
\T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/i386/R
environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/pcr/m/n/10 .Renviron.i386\T1/ptm/m/
n/10 ' will be
Underfull \hbox (badness 1728) in paragraph at lines 35534--35541
[]\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 here is a
lso a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/Renviron\T1/ptm
/m/n/10 ' which is read
Underfull \hbox (badness 1038) in paragraph at lines 35534--35541
\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 35534--35541
\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
[516] [517] [518] [519] [520]
Underfull \hbox (badness 10000) in paragraph at lines 35875--35881
[]\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/pcr/m/n/10 form
at \T1/ptm/m/n/10 meth-ods is
[521] [522] [523]
Underfull \hbox (badness 1163) in paragraph at lines 36064--36071
[]\T1/ptm/m/n/10 Specific to \T1/phv/m/n/10 R \T1/ptm/m/n/10 is \T1/pcr/m/n/10
%OSn\T1/ptm/m/n/10 , which for out-put gives the sec-onds trun-cated to \T1/pcr
/m/n/10 0 <= n <= 6
Underfull \hbox (badness 8132) in paragraph at lines 36064--36071
\T1/ptm/m/n/10 dec-i-mal places (and if \T1/pcr/m/n/10 %OS \T1/ptm/m/n/10 is no
t fol-lowed by a digit, it uses the set-ting of
[524] [525] [526] [527]
Underfull \hbox (badness 1142) in paragraph at lines 36346--36352
[]\T1/ptm/m/n/10 Note that split-ting into sin-gle char-ac-ters can be done \T1
/ptm/m/it/10 via \T1/pcr/m/n/10 split = character(0) \T1/ptm/m/n/10 or
Overfull \hbox (0.78088pt too wide) in paragraph at lines 36361--36361
[] \T1/pcr/m/n/10 add the string to the left of the match to the ou
tput.[]
[528] [529] [530] [531]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 36609--36609
[] \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p
refix)[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 36653--36653
[]\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll
apse = "\n")[]
[532] [533] [534] [535] [536] [537] [538]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 37087--37087
[]\T1/pcr/m/n/9 ## In fact, you can pass vectors into several arguments, and e
verything gets added.[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 37090--37090
[]\T1/pcr/m/n/9 ## If there are missing values, the sum is unknown, i.e., also
missing, ....[]
[539]
Underfull \hbox (badness 10000) in paragraph at lines 37141--37148
[]\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 37141--37148
\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 37192--37192
[]\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau
lt precision
[540] [541] [542] [543]
Underfull \hbox (badness 2762) in paragraph at lines 37431--37440
\T1/ptm/m/n/10 of the el-e-ments in \T1/pcr/m/n/10 ...\T1/ptm/m/n/10 . If there
is a match then that el-e-ment is eval-u-ated un-less
Underfull \hbox (badness 1466) in paragraph at lines 37431--37440
\T1/ptm/m/n/10 it is miss-ing, in which case the next non-missing el-e-ment is
eval-u-ated, so for ex-am-ple
[544]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 37493--37493
[] \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw
ise: last"),"\n")[]
[545] [546]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 37658--37658
[]\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.
[547]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 37696--37696
[]\T1/pcr/m/n/9 if(.Platform$OS.type == "unix") ## on Unix-alikes such Linux,
macOS, FreeBSD:[]
[548]
Underfull \hbox (badness 3219) in paragraph at lines 37745--37750
[]\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 37745--37750
\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
[549]
Underfull \hbox (badness 2452) in paragraph at lines 37835--37838
\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 37835--37838
\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
[550] [551] [552]
Underfull \hbox (badness 10000) in paragraph at lines 38022--38026
[]\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 38037--38040
[]\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
[553] [554]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 38169--38169
[]\T1/pcr/m/n/9 is.symlink <- function(paths) isTRUE(nzchar(Sys.readlink(paths
), keepNA=TRUE))[]
[555]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 38239--38239
[]\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
[556] [557] [558]
Underfull \hbox (badness 1082) in paragraph at lines 38377--38380
[]\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
[559] [560]
Underfull \hbox (badness 1038) in paragraph at lines 38564--38567
[]\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
[561] [562] [563] [564] [565] [566]
Underfull \hbox (badness 1515) in paragraph at lines 38928--38931
[]\T1/ptm/m/n/10 Because of the way it is im-ple-mented, on a Unix-alike \T1/pc
r/m/n/10 stderr = TRUE \T1/ptm/m/n/10 im-plies
[567] [568] [569]
Underfull \hbox (badness 4096) in paragraph at lines 39169--39172
[]\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 ,
[570] [571]
Underfull \hbox (badness 10000) in paragraph at lines 39283--39287
[]\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.,
[572] [573]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 39437--39437
[] \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 39439--39439
[] \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),[]
[574]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 39441--39441
[] \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 39454--39456
[]\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
[575]
Underfull \hbox (badness 10000) in paragraph at lines 39534--39537
[][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$https : / / developer .
[576] [577]
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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 getTaskCallbackNames
[][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 https : / /
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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 : / /
[578] [579] [580] [581] [582] [583] [584]
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\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 ',
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[]\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-
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\T1/ptm/m/n/10 lected Ol-son/IANA database. The system-specific lo-ca-tion in t
he file sys-tem varies,
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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-
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\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 '
[585]
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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
[586]
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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[]
[587] [588] [589]
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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
[590] [591]
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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:[]
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[593] [594] [595] [596]
Underfull \hbox (badness 6542) in paragraph at lines 41042--41044
[]\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
[597] [598] [599]
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[]\T1/ptm/m/n/10 a [][]con-nec-tion[][][], or a char-ac-ter string nam-ing the
file to print to (via
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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
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[]\T1/pcr/m/n/10 try \T1/ptm/m/n/10 is im-ple-mented us-ing [][]\T1/pcr/m/n/10
tryCatch[][][]\T1/ptm/m/n/10 ; for pro-gram-ming, in-
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\T1/ptm/m/n/10 stead of \T1/pcr/m/n/10 try(expr, silent = TRUE)\T1/ptm/m/n/10 ,
some-thing like
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\T1/pcr/m/n/10 tryCatch(expr, error = function(e) e) \T1/ptm/m/n/10 (or other s
im-ple er-ror han-dler func-
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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;
[600]
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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
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\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 ,
[601] [602] [603]
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[]\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an
d sock-ets.
[604] [605]
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[]\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp
ression(1+x))[]
[606] [607] [608] [609] [610] [611]
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[]\T1/pcr/m/n/9 (xx <- intToUtf8(x, , TRUE)) # will only display in some local
es and fonts[]
[612]
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[]\T1/pcr/m/n/9 system(paste("od -x", foo)) # 2-byte units, correct on little-
endian platform[]
[613]
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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
[614]
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[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 is.vector\T1/ptm/m/n/10 , \T1/pcr/m/n/10 TR
UE \T1/ptm/m/n/10 or \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 . \T1/pcr/m/n/10 is.vec
tor(x, mode = "numeric") \T1/ptm/m/n/10 can be
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\T1/ptm/m/n/10 true for vec-tors of types \T1/pcr/m/n/10 "integer" \T1/ptm/m/n/
10 or \T1/pcr/m/n/10 "double" \T1/ptm/m/n/10 whereas \T1/pcr/m/n/10 is.vector(x
, mode =
[615] [616]
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[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di-
ately, even if
[617] [618]
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[] \T1/pcr/m/n/10 header = ngettext(n, "Warning message:\n", "Warning mes
sages:\n"),[]
[619]
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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 ...[]
[620] [621]
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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/pcr/m/n/10 which(*, arr.ind=TRUE)\T1/ptm/m/n/10 ). If [][]\T1/pcr/m/n/10 na
mes[][][](.dimnames) \T1/ptm/m/n/10 is not empty,
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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
[622]
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[][][]\T1/pcr/m/n/10 Logic[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 which.min[]
[][] \T1/ptm/m/n/10 for the in-dex of the min-i-mum or max-i-mum, and [][]\T1/p
cr/m/n/10 match[][][] \T1/ptm/m/n/10 for the
[623]
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[]\T1/ptm/m/n/10 If this ex-tremum is unique (or empty), the re-sults are the s
ame as
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\T1/ptm/m/n/10 (but more ef-fi-cient than) \T1/pcr/m/n/10 which(x == min(x, na.
rm = TRUE)) \T1/ptm/m/n/10 or
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[]\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:[]
[624] [625]
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[]\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 .
[626] [627] [628] [629]
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[]\T1/ptm/m/n/10 This is a spe-cial case of rank-ing, but as a less gen-eral fu
nc-tion than [][]\T1/pcr/m/n/10 rank[][][]
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\T1/ptm/m/n/10 is more suit-able to be made generic. The de-fault method is sim
-i-lar to
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\T1/pcr/m/n/10 rank(x, ties.method = "min", na.last = "keep")\T1/ptm/m/n/10
, so \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 val-ues are
[630]
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[]\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
[631]
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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
[632]) (./compiler-pkg.tex
Chapter 2.
[633]
Underfull \hbox (badness 2884) in paragraph at lines 101--115
[]\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
[634] [635] [636]) (./datasets-pkg.tex
Chapter 3.
Underfull \hbox (badness 10000) in paragraph at lines 12--14
[]\T1/ptm/m/n/10 This pack-age con-tains a va-ri-ety of datasets. For a com-ple
te list, use
[637] [638] [639] [640] [641]
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[] \T1/pcr/m/n/9 plot(ff, data = anscombe, col = "red", pch = 21, bg = "orang
e", cex = 1.2,[]
[642]
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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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[644] [645] [646] [647]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[648] [649]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[650] [651]
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.
[652] [653]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[654] [655] [656] [657] [658]
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[]\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption
time (sec)")[]
[659] [660]
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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
[661] [662] [663]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[664]
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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)[]
[665] [666]
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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]]))))[]
[667] [668] [669] [670]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[671] [672] [673]
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[674] [675] [676] [677] [678]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[679]
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[680]
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[682]
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[683] [684]
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[685]
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[]\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main =
1.2, pch = ".")[]
[686] [687] [688] [689] [690] [691] [692]
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[] \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t
he monthly one:[]
[693] [694]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[695]
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[696]
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\T1/ptm/m/it/10 Ed-u-ca-tion\T1/ptm/m/n/10 , \T1/ptm/b/n/10 3\T1/ptm/m/n/10 . [
][]$\T1/pcr/m/n/10 https : / / www . amstat . org / publications / jse / v3n3 /
datasets .
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[697]
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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 /
[698] [699] [700] [701] [702] [703] [704] [705] [706] [707] [708] [709]
[710] [711]) (./grDevices-pkg.tex [712]
Chapter 4.
[713] [714] [715] [716] [717] [718]
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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/pcr/m/n/10 quantile[][][](x, c(1,3)/4)\T1/ptm/m/n/10 . The hinges equal
the quar-tiles for odd $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 (where
[719]
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[]\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d
.pdf",[]
[720] [721] [722] [723] [724] [725] [726] [727] [728]
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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
[729]
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\T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 make.rgb[][][]\T1/ptm/m/n/10 . Built-in co
lor spaces may be ref-er-enced by strings: \T1/pcr/m/n/10 "XYZ"\T1/ptm/m/n/10 ,
\T1/pcr/m/n/10 "sRGB"\T1/ptm/m/n/10 ,
[730]
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[]\T1/ptm/m/n/10 For the white points [][]$\T1/pcr/m/n/10 http : / / www . efg2
. com / Lab / Graphics / Colors /
[731]
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[]\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab",
scale.in = 255))[]
[732]
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[]\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
[733] [734] [735]
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[]\T1/ptm/m/n/10 character: Which events can be gen-er-ated on
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\T1/ptm/m/n/10 this de-vice? Cur-rently this will be a sub-set of
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\T1/pcr/m/n/10 c("MouseDown", "MouseMove", "MouseUp", "Keybd")\T1/ptm/m/n/10
,
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[]\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 if the de-vice does not sup-port cap-ture,
oth-er-wise a ma-trix of color names (for
[736]
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[]\T1/ptm/m/n/10 logical; if \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion
also re-turns \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 when
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[][]\T1/pcr/m/n/10 .Device[][][] == "null device" \T1/ptm/m/n/10 and [][]\T1/pc
r/m/n/10 getOption[][][]("device") \T1/ptm/m/n/10 is
[737] [738] [739]
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[]\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
[740]
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[]\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res
= 72,[]
[741]
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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 ,
[742]
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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
[743] [744]
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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
[745] [746]
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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
[747] [748]
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[]\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r"
, yaxs = "r") {[]
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[750] [751] [752] [753] [754]
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[756] [757] [758] [759] [760]
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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))[]
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[]\T1/ptm/m/n/10 A length two in-te-ger vec-tor \T1/pcr/m/n/10 nr, nc \T1/ptm/m
/n/10 giv-ing the num-ber of rows and columns, ful-fill-ing
[761]
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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
[762] [763] [764]
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[]\T1/pcr/m/n/10 rainbow(n, s = 1, v = 1, start = 0, end = max(1, n - 1)/n, al
pha = 1)
[765]
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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 C in-te-ger for-mat such as
[766]
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[]\T1/ptm/m/n/10 title string to em-bed as the `\T1/pcr/m/n/10 /Title\T1/ptm/m/
n/10 ' field in the file. De-faults to
[767] [768] [769] [770]
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[]\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 ,
[771] [772] [773] [774] [775]
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\T1/pcr/m/n/10 / / www . adobe . com / products / postscript / pdfs / PLRM . pd
f$[][] \T1/ptm/m/n/10 or PDF [][]$\T1/pcr/m/n/10 https : / /
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\T1/pcr/m/n/10 www . adobe . com / devnet / acrobat / pdfs / pdf _ reference _
1-[]7 . pdf$[][] \T1/ptm/m/n/10 and in dec-i-
[776]
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[] \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz
w+p", "zip+p"),[]
[778]
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[]\T1/ptm/m/n/10 for \T1/pcr/m/n/10 type = "cairo"\T1/ptm/m/n/10 , giv-ing the
type of anti-aliasing (if any) to be
[779] [780]
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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
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[][][]\T1/pcr/m/n/10 capabilities[][][] \T1/ptm/m/n/10 to see if these de-vices
are sup-ported by this build of \T1/phv/m/n/10 R\T1/ptm/m/n/10 , and if
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[]\T1/pcr/m/n/9 ## Not run: dev.print(png, file = "myplot.png", width = 1024,
height = 768)[]
[781]
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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
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[]\T1/ptm/m/n/10 title string to em-bed as the \T1/pcr/m/n/10 Title \T1/ptm/m/n
/10 com-ment in the file. De-faults to
[782]
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\T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/pcr/
m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as
[783]
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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
[784] [785]
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[]\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
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[][][]\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
[786] [787]
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\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
[788]
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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
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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 /
[789] [790]
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[]\T1/pcr/m/n/9 ## time ranges in diverse scales:% also in ../../../../tests/r
eg-tests-1c.R[]
[791]
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[]\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100
, ...)[]
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[]\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on
ly), de-fault
[792] [793]
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[]\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
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[]\T1/ptm/m/n/10 A fairly com-mon Mac prob-lem is no text ap-pear-ing on plots
due to cor-rupted or du-pli-
[794] [795] [796] [797] [798]
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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
[799] [800] [801] [802] [803] [804] [805]
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[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
[806]
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[]\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK
lan-guages and
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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
[807]
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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
[808]
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[] \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height
= 6, xpos = 0,[]
[809]
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[]\T1/ptm/m/n/10 These func-tions ap-ply only to an [][]\T1/pcr/m/n/10 X11[][][
] \T1/ptm/m/n/10 de-vice with \T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 --
[810]
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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 /
[811] [812] [813]
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\T1/ptm/m/n/10 ity of co-or-di-nates. These are com-pared af-ter round-ing them
via
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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
[814] [815] [816]) (./graphics-pkg.tex
Chapter 5.
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[]\T1/ptm/m/n/10 For a com-plete list of func-tions with in-di-vid-ual help pag
es, use
[817] [818] [819] [820]
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[]\T1/ptm/m/n/10 Friendly, M. (1992), Graph-i-cal meth-ods for cat-e-gor-i-cal
data. \T1/ptm/m/it/10 SAS User Group In-ter-na-
[821] [822] [823]
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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
[824] [825] [826]
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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
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[]\T1/pcr/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p
tm/m/n/10 in-ter-face to the C func-tion \T1/pcr/m/n/10 CreateAtVector() \T1/pt
m/m/n/10 in
[827]
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[] \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n
intLog = 5))[]
[828] [829]
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[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , the lines whic
h di-vide ad-ja-cent (non-stacked!) bars
[830] [831] [832] [833] [834] [835] [836]
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[] \T1/pcr/m/n/10 horizontal = FALSE, add = FALSE, at = NULL, show.names =
NULL,[]
[837]
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\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 width, point char-ac-ter, point size ex-pan-sion, color, and bac
k-ground
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\T1/ptm/m/n/10 color. The de-fault \T1/pcr/m/n/10 medpch = NA \T1/ptm/m/n/10 su
p-presses the point, and
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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 ),
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[]\T1/ptm/m/n/10 When \T1/pcr/m/n/10 add = FALSE\T1/ptm/m/n/10 , \T1/pcr/m/n/10
xlim \T1/ptm/m/n/10 now de-faults to \T1/pcr/m/n/10 xlim = range(at, *) +
c(-0.5, 0.5)\T1/ptm/m/n/10 .
[838]
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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",[]
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[] \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl
ty = 1, outpch = NA)[]
[839] [840] [841] [842] [843]
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[][][]\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
[844]
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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 = "")[]
[845]
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[]\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col
umns,
[846] [847]
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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))[]
[848] [849] [850] [851]
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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
[852] [853] [854] [855] [856] [857]
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[]\T1/pcr/m/n/9 ## maybe change the desired number of tick marks: par(lab = c
(mx, my, 7))[]
[858] [859]
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\T1/ptm/m/n/10 they are the rel-a-tive fre-quen-cies \T1/pcr/m/n/10 counts/n \T
1/ptm/m/n/10 and in gen-eral sat-isfy
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[]\T1/ptm/m/n/10 Typical plots with ver-ti-cal bars are \T1/ptm/m/it/10 not \T1
/ptm/m/n/10 his-tograms. Con-sider [][]\T1/pcr/m/n/10 barplot[][][] \T1/ptm/m/n
/10 or
[860]
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[]\T1/pcr/m/n/9 ## Extreme outliers; the "FD" rule would take very large numbe
r of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 breaks\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[]
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[]\T1/pcr/m/n/9 length(hh$breaks) ## typically 1 million -- though 1e6 was "a
suggestion only"[]
[861]
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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
[862] [863] [864]
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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, ...)[]
[865]
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[]\T1/ptm/m/n/10 a list of col-ors such as that gen-er-ated by [][]\T1/pcr/m/n/
10 rainbow[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 heat.colors[][][]\T1/ptm/m/
n/10 ,
[866]
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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
[867] [868] [869]
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[]\T1/pcr/m/n/9 barplot(yhist$counts, axes = FALSE, xlim = c(0, top), space =
0, horiz = TRUE)[]
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[] \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col =
par("fg"),[]
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[] \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace =
FALSE,[]
[870] [871] [872]
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[] \T1/pcr/m/n/9 text (1, y.leg[i] - 0.1, paste("cex=", formatC(cexv[i])), c
ex = 0.8, adj = 0)[]
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[] \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce
x = cexv[i])[]
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[] \T1/pcr/m/n/9 "text(c(3,3),2:3,\"c(rect(...)\")"), adj
= c(0, 0.3))[]
Underfull \vbox (badness 10000) has occurred while \output is active [873]
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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)[]
Underfull \vbox (badness 10000) has occurred while \output is active [874]
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[] \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste
("text.font =",i))[]
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[][][]\T1/pcr/m/n/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
[875] [876]
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[] \T1/pcr/m/n/10 log = "", ..., add = FALSE, verbose = getOption("verb
ose"))[]
[877]
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[]\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol
s given by
[878] [879]
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[]\T1/ptm/m/n/10 The mag-ni-fi-ca-tion to be used for axis an-no-ta-tion, as a
mul-ti-ple of
[880] [881] [882] [883]
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[]\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat
a con-tain
[884]
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\T1/ptm/m/n/10 which draws the ti-tle. You may want to spec-ify \T1/pcr/m/n/10
oma \T1/ptm/m/n/10 when chang-ing
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[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are
to be used, see
[885] [886]
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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))[]
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[]\T1/pcr/m/n/9 pairs(swiss, panel = panel.smooth, lwd = 2, cex = 1.5, col = "
blue") # hmm...[]
[887]
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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 ,
[888] [889]
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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.
[890] [891]
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[892 </usr/src/RPM/BUILD/R-3.5.3/library/graphics/help/figures/mai.pdf>]
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[893 </usr/src/RPM/BUILD/R-3.5.3/library/graphics/help/figures/oma.pdf>]
[894]
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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
[895]
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[]\T1/pcr/m/n/9 c(prof.pilots = 16, lawyers = 11, farmers = 10, salesmen = 9,
physicians = 9,[]
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[] \T1/pcr/m/n/9 mechanics = 6, policemen = 6, managers = 6, engineers = 5, t
eachers = 4,[]
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[897]
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[]\T1/ptm/m/n/10 a ex-pan-sion fac-tor ap-plied to the \T1/pcr/m/n/10 z \T1/ptm
/m/n/10 co-or-di-nates. Of-ten used with
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\T1/ptm/m/n/10 are con-trolled by graph-ics pa-ram-e-ters \T1/pcr/m/n/10 "cex.l
ab"\T1/ptm/m/n/10 /\T1/pcr/m/n/10 "font.lab" \T1/ptm/m/n/10 and
[898] [899] [900] [901]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5589--5589
[]\T1/pcr/m/n/9 pie(c(Sky = 78, "Sunny side of pyramid" = 17, "Shady side of p
yramid" = 5),[]
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[] \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow
3"), border = FALSE)[]
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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.,
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\T1/pcr/m/n/10 type = "punkte" \T1/ptm/m/n/10 be-ing equiv-a-lent to \T1/pcr/m/
n/10 type = "p" \T1/ptm/m/n/10 for S com-
[902] [903] [904] [905] [906] [907] [908]
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[]\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth) # numeric v
ector ~ factor[]
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[]\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes") # ext
remely silly[]
[909] [910] [911] [912] [913] [914]
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[]\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see
[915] [916]
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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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[][]
[917 </usr/src/RPM/BUILD/R-3.5.3/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,[]
[918]
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[] \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes = FALSE, xlab = "", ylab =
"", main = main)[]
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[920]
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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)))))[]
[921]
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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
[922] [923] [924]
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[]\T1/ptm/m/n/10 color for rect-an-gle bor-der(s). The de-fault means \T1/pcr/m
/n/10 par("fg")\T1/ptm/m/n/10 . Use
[925]
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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))[]
[926] [927] [928] [929] [930] [931]
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[]\T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), sp
ace = "Lab")[]
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[]\T1/pcr/m/n/9 ## label the 20 very lowest-density points,the "outliers" (wit
h obs.number):[]
[932]
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[]\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0
, add = TRUE),[]
[933] [934] [935] [936] [937]
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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,[]
[938]
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[] \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10
, key.loc = 0:1,[]
[939] [940]
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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, ...)[]
[941] [942]
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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
[943] [944]
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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),[]
[945] [946]
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[]\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll
apse = ","),[]
[947] [948] [949]
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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...")[]
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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
[950]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit
s}) has been already used, duplicate ignored
<to be read again>
\relax
l.8805 \HeaderA{units}{Graphical Units}{units}
[951]
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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
[952] [953]
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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)[]
[954]) (./grid-pkg.tex
Chapter 6.
[955] [956] [957] [958] [959] [960]
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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-
[971] [972] [973] [974]
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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
[975] [976] [977] [978] [979] [980]
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[] \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75)
, list(...)))[]
[981] [982] [983]
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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")[]
[984]
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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 ,
[985]
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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
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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-
[992] [993] [994]
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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)[]
[995] [996] [997] [998]
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[] \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1
, "inches"),[]
[999] [1000] [1001] [1002]
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[] \T1/pcr/m/n/9 children=vpList(viewpor
t(name="vp2"))))[]
[1003] [1004]
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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")))[]
[1005]
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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
[1006]
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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,[]
[1007] [1008] [1009]
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[] \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant
i-clockwise")[]
[1010]
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[] \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other
anti-clockwise")[]
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[1022]
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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
[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-
[1024] [1025] [1026]
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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
[1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035]
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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
[1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045]
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\T1/ptm/m/n/10 to add and sub-tract unit ob-jects (e.g., \T1/pcr/m/n/10 unit(1,
"npc") - unit(1, "inches")\T1/ptm/m/n/10 ),
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\T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob-
jects (e.g.,
[1046] [1047] [1048] [1049] [1050]
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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
[1051]
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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 ,
[1052] [1053]
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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
[1054] [1055] [1056]
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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"))))[]
[1057]) (./methods-pkg.tex [1058]
Chapter 7.
[1059] [1060]
Underfull \hbox (badness 1688) in paragraph at lines 166--171
\T1/ptm/m/n/10 func-tion. See that doc-u-men-ta-tion also for de-tails of how c
o-erce meth-ods work. Use
[1061] [1062] [1063]
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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-
[1064] [1065]
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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[]
[1066]
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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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[1069]
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[]\T1/ptm/m/n/10 A ma-trix (or ma-trix like ob-ject) com-bin-ing the columns (o
r rows) of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y\T1/ptm/m/n/10 .
Note
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\T1/ptm/m/n/10 that meth-ods must con-struct [][]\T1/pcr/m/n/10 colnames[][][]
\T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 rownames[][][] \T1/ptm/m/n/10 from the co
r-re-spond-ing col-
Underfull \hbox (badness 1789) in paragraph at lines 791--797
\T1/ptm/m/n/10 umn and row names of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr
/m/n/10 y \T1/ptm/m/n/10 (but not from de-pars-ing ar-gu-ment names such as in
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[1081] [1082]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1794--1794
[]\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[]
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[]\T1/pcr/m/n/10 signature(from = "ANY", to = "environment")\T1/ptm/m/n/10 : ca
lls
[1083] [1084]
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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
[1085] [1086] [1087]
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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 =
[1088] [1089]
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[]\T1/ptm/m/n/10 To see the ac-tual ta-ble (an en-vi-ron-ment) used for meth-od
s dis-patch, call
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[]\T1/pcr/m/n/10 ## Deprecated in 2010 and defunct in 2015 for \code{table = F
ALSE}:[]
[1090] [1091] [1092]
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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
[1093]
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[]\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin
g(where))[]
[1094] [1095] [1096]
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[]\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers
ions visible:[]
[1097] [1098] [1099] [1100] [1101] [1102] [1103]
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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
[1104] [1105]
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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
[1106]
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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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[]
[1107] [1108]
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[] \T1/pcr/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric",
longitude = "numeric", altitude = "numeric"))
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[]\T1/pcr/m/n/10 setMethod("plot", c("Pos", "missing"), function(x, y, ...) {
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[]\T1/pcr/m/n/10 GPS <- setClass("GPS", slots = c(time = "POSIXt"), contains =
"Pos")
[1109]
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[]\T1/pcr/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character")
, contains = "numeric")
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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
[1110] [1111] [1112]
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[]\T1/pcr/m/n/10 signature(from = "ANY", to = "call")\T1/ptm/m/n/10 . A method
ex-ists for
[1113] [1114]
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\T1/pcr/m/n/10 x$ensureLocal() \T1/ptm/m/n/10 on the ob-ject. The other way is
to mod-ify a field ex-plic-itly by
[1115]
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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,[]
[1116]
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[]\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w
here)
[1117] [1118]
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\T1/ptm/m/n/10 se-lect-ing class \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/10 for \T
1/pcr/m/n/10 y \T1/ptm/m/n/10 would pro-duce a method as-so-ci-ated with the si
g-na-ture
[1119]
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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 ,
[1120] [1121] [1122]
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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
[1123] [1124] [1125] [1126]
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[]\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate
inheritance[]
[1127]
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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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[1129]
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[]\T1/pcr/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...)
[1130]
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[]\T1/pcr/m/n/10 signature(method = "MethodWithNext")\T1/ptm/m/n/10 : used in-t
er-nally by
[1131]
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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
[1132] [1133] [1134]
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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
[1135]
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
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\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1136]
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
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\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1137] [1138] [1139] [1140]
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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
[1141] [1142]
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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
[1143]
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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
[1144]
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[]\T1/ptm/m/n/10 Establish a traced ver-sion of method
[1145]
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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
[1146]
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[1148] [1149]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}
[1150]
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[]\T1/pcr/m/n/10 ## Create a new object from the class or use the replacement
version of as().[]
Underfull \hbox (badness 2042) in paragraph at lines 7065--7072
\T1/ptm/m/n/10 i-nat-ing all the for-mally de-fined slots and turn-ing off the
S4 bit of the ob-ject. With
[1151] [1152]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 7200--7200
[]\T1/pcr/m/n/9 fit <- lm(sepal ~ Petal.Length + Petal.Width + Species, data =
datasets::iris)[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7204--7204
[]\T1/pcr/m/n/9 myReg <- setClass("myReg", slots = c(title = "character"), con
tains = "mlm")[]
[1153]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}
pdfTeX warning (ext4): destination wi
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}
Underfull \hbox (badness 2050) in paragraph at lines 7296--7300
[]\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
[1154]
Underfull \hbox (badness 6708) in paragraph at lines 7309--7321
[]\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 ,
[1155] [1156]
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
[1157] [1158]
Underfull \hbox (badness 10000) in paragraph at lines 7663--7670
[]\T1/ptm/m/n/10 If no sub-class/superclass re-la-tion-ship pro-vides a method,
\T1/pcr/m/n/10 as \T1/ptm/m/n/10 looks for an in-her-
Underfull \hbox (badness 7704) in paragraph at lines 7663--7670
\T1/ptm/m/n/10 ited method, but ap-ply-ing, in-her-i-tance for the ar-gu-ment \
T1/pcr/m/n/10 from \T1/ptm/m/n/10 only, not for the
Underfull \hbox (badness 10000) in paragraph at lines 7663--7670
\T1/ptm/m/n/10 ar-gu-ment \T1/pcr/m/n/10 to \T1/ptm/m/n/10 (if you think about
it, you'll prob-a-bly agree that you wouldn't
Underfull \hbox (badness 5817) in paragraph at lines 7663--7670
\T1/ptm/m/n/10 want the re-sult to be from some class other than the \T1/pcr/m/
n/10 Class \T1/ptm/m/n/10 spec-i-fied). Thus,
Overfull \hbox (0.78088pt too wide) in paragraph at lines 7663--7670
\T1/pcr/m/n/10 selectMethod("coerce", sig, useInherited= c(from=TRUE, to= FALSE
))
[1159] [1160] [1161] [1162] [1163] [1164] [1165] [1166] [1167] [1168] [1169]
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
[1170]
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(),
[1171]
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[] \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class
Def =,[]
[1172] [1173] [1174] [1175]
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[]\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col
umn matrices[]
[1176] [1177] [1178]
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")[]
[1179] [1180]
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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[]
[1182] [1183] [1184] [1185]
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[]\T1/pcr/m/n/9 ## Define a new generic function to compute the residual degre
es of freedom[]
[1186]
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[]\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][]
[1187]
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][]
[1188] [1189] [1190] [1191] [1192] [1193] [1194] [1195] [1196]
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
[1197] [1198] [1199] [1200]) (./parallel-pkg.tex
Chapter 8.
Underfull \hbox (badness 2418) in paragraph at lines 14--16
[]\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/pcr
/m/n/10 "L\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[
][][]: see
[1201]
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
[1202] [1203]
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
[1204]
Underfull \hbox (badness 10000) in paragraph at lines 318--326
[]\T1/ptm/m/n/10 On Sparc So-laris \T1/pcr/m/n/10 logical = FALSE \T1/ptm/m/n/1
0 re-turns the num-ber of phys-i-cal cores and
[1205] [1206]
Underfull \hbox (badness 10000) in paragraph at lines 443--445
[]\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
[1207] [1208] [1209] [1210]
Underfull \hbox (badness 1917) in paragraph at lines 742--751
[]\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 742--751
\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
[1211] [1212]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 824--824
[] \T1/pcr/m/n/10 mc.cleanup = TRUE, mc.allow.recursive = TRUE, affini
ty.list = NULL)[]
[1213]
Underfull \hbox (badness 10000) in paragraph at lines 884--887
[]\T1/pcr/m/n/10 mclapply \T1/ptm/m/n/10 is a par-al-lelized ver-sion of [][]\T
1/pcr/m/n/10 lapply[][][]\T1/ptm/m/n/10 , pro-vided \T1/pcr/m/n/10 mc.cores > 1
\T1/ptm/m/n/10 : for
[1214]
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[]\T1/pcr/m/n/9 mclapply(list(A, A, A), first, mc.preschedule = FALSE, affinit
y.list = affL)[]
[1215]
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[]\T1/pcr/m/n/9 # To optimize the overall execution time elements of X are sch
eduled to suitable CPUs[]
[1216]
Underfull \hbox (badness 5388) in paragraph at lines 1119--1124
[]\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 1143--1151
[]\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
[1217]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1180--1180
[]\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)[]
[1218] [1219]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1296--1296
[] \T1/pcr/m/n/9 as.integer(runif(N, 1, 12)), as.integer(runif
(N, 1, 28)))[]
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[]\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct, format =
"%Y-%m-%d")))[]
Underfull \hbox (badness 1577) in paragraph at lines 1339--1342
[]\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
[1220]
Underfull \hbox (badness 3375) in paragraph at lines 1385--1387
[]\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
[1221] [1222]) (./splines-pkg.tex
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
[1223] [1224] [1225] [1226] [1227] [1228] [1229]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 492--492
[]\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height, women, bSpl
ine = TRUE))[]
[1230] [1231] [1232] [1233]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 706--706
[]\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37,
sparse = TRUE)))[]
[1234] [1235] [1236]) (./stats-pkg.tex
Chapter 10.
[1237]
Underfull \hbox (badness 2781) in paragraph at lines 65--68
[]\T1/pcr/m/n/10 .MFclass \T1/ptm/m/n/10 re-turns a char-ac-ter string, one of
\T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ordered"\T1/ptm/m/n/10
, \T1/pcr/m/n/10 "factor"\T1/ptm/m/n/10 ,
[1238] [1239] [1240] [1241] [1242]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 417--417
[]\T1/pcr/m/n/9 add1(glm.D93, scope = ~outcome*treatment, test = "Rao") ## Pea
rson Chi-square[]
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[]\T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet =
FALSE)
[1243] [1244] [1245] [1246] [1247] [1248] [1249]
Underfull \hbox (badness 1024) in paragraph at lines 847--849
[]\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
[1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257]
Underfull \hbox (badness 10000) in paragraph at lines 1391--1393
[]\T1/ptm/m/n/10 an es-ti-mate of the ra-tio of scales. (Only present if ar-gu-
ment
[1258]
Underfull \hbox (badness 10000) in paragraph at lines 1508--1512
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("aov", "lm") \T1/ptm/m/n/
10 or for mul-ti-ple re-sponses of class
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\T1/pcr/m/n/10 c("maov", "aov", "mlm", "lm") \T1/ptm/m/n/10 or for mul-ti-ple e
r-ror strata of class
Underfull \hbox (badness 1490) in paragraph at lines 1508--1512
\T1/pcr/m/n/10 c("aovlist", "[][]listof[][][]")\T1/ptm/m/n/10 . There are [][]\
T1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 summary[][][] \
T1/ptm/m/n/10 meth-ods avail-able for
[1259] [1260] [1261] [1262]
Underfull \hbox (badness 10000) in paragraph at lines 1773--1777
[]\T1/ptm/m/n/10 function to be called to han-dle miss-ing val-ues. Cur-rently,
via
Underfull \hbox (badness 2197) in paragraph at lines 1773--1777
\T1/pcr/m/n/10 na.action = na.pass\T1/ptm/m/n/10 , only Yule-Walker method can
han-dle miss-
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 x \T1/ptm/m/n/10 con-tains miss-ing val-ues,
see [][]\T1/pcr/m/n/10 NA[][][]\T1/ptm/m/n/10 , also con-sider us-ing [][]\T1/
pcr/m/n/10 arima[][][]()\T1/ptm/m/n/10 , pos-si-bly with
[1265] [1266] [1267]
Underfull \hbox (badness 10000) in paragraph at lines 2096--2101
[]\T1/ptm/m/n/10 logical; if true, the AR pa-ram-e-ters are trans-formed to en-
sure
Underfull \hbox (badness 10000) in paragraph at lines 2096--2101
\T1/ptm/m/n/10 that they re-main in the re-gion of sta-tion-ar-ity. Not used fo
r
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\T1/pcr/m/n/10 method = "CSS"\T1/ptm/m/n/10 . For \T1/pcr/m/n/10 method = "ML"\
T1/ptm/m/n/10 , it has been ad-van-ta-geous
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[]\T1/ptm/m/n/10 optional nu-meric vec-tor of the same length as the to-tal num
-ber of pa-
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\T1/ptm/m/n/10 ram-e-ters. If sup-plied, only \T1/pcr/m/n/10 NA \T1/ptm/m/n/10
en-tries in \T1/pcr/m/n/10 fixed \T1/ptm/m/n/10 will be var-ied.
[1268] [1269]
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[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
[1270] [1271] [1272]
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[]\T1/ptm/m/n/10 optional nu-meric vec-tor of the same length as the to-tal num
-ber of pa-
Underfull \hbox (badness 4608) in paragraph at lines 2457--2462
\T1/ptm/m/n/10 ram-e-ters. If sup-plied, only \T1/pcr/m/n/10 NA \T1/ptm/m/n/10
en-tries in \T1/pcr/m/n/10 fixed \T1/ptm/m/n/10 will be var-ied.
[1273]
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[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
[1274] [1275]
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[]\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F
ALSE)
[1276] [1277] [1278] [1279]
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[]\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co
l = "green")[]
[1280] [1281] [1282]
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[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Bartlett test of homoge
neity of variances"\T1/ptm/m/n/10 .
[1283]
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[]\T1/pcr/m/n/10 pbeta(q, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p =
FALSE)[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3177--3177
[]\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p =
FALSE)[]
[1284]
Underfull \hbox (badness 2726) in paragraph at lines 3260--3276
\T1/ptm/m/n/10 We have slightly tweaked the orig-i-nal ``TOMS 708'' al-go-rithm
, and en-hanced for
[1285] [1286] [1287] [1288] [1289]
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[]\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = "
log density",[]
[1290] [1291] [1292] [1293]
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[]\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit
df = 0)
[1294] [1295] [1296] [1297] [1298]
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[]\T1/pcr/m/n/10 pcauchy(q, location = 0, scale = 1, lower.tail = TRUE, log.p
= FALSE)[]
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[]\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p
= FALSE)[]
[1299] [1300] [1301]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4374--4374
[]\T1/pcr/m/n/9 chisq.test(x, p = p) # maybe doubtful
, but is ok![]
[1302] [1303] [1304]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4542--4542
[] \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df =
df, ncp = L)),[]
[1305]
Underfull \hbox (badness 3989) in paragraph at lines 4634--4641
[]\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 =
[1306] [1307]
Underfull \hbox (badness 2080) in paragraph at lines 4754--4756
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 "aov" \T1/ptm/m/n/10 method does not re-por
t aliased co-ef-fi-cients (see [][]\T1/pcr/m/n/10 alias[][][]\T1/ptm/m/n/10 ) b
y de-fault where
Underfull \hbox (badness 2050) in paragraph at lines 4757--4763
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 complete \T1/ptm/m/n/10 ar-gu-ment also ex-
ists for com-pat-i-bil-ity with [][]\T1/pcr/m/n/10 vcov[][][] \T1/ptm/m/n/10 me
th-ods, and \T1/pcr/m/n/10 coef
Underfull \hbox (badness 4954) in paragraph at lines 4757--4763
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 aov \T1/ptm/m/n/10 meth-ods for other classes
should typ-i-cally also keep the \T1/pcr/m/n/10 complete = *
Underfull \hbox (badness 4726) in paragraph at lines 4757--4763
\T1/ptm/m/n/10 be-hav-ior in sync. By that, with \T1/pcr/m/n/10 p <- length(coe
f(obj, complete = TF))\T1/ptm/m/n/10 ,
[1308] [1309] [1310] [1311]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5019--5019
[]\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 5021--5021
[]\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))[]
[1312]
Underfull \hbox (badness 7397) in paragraph at lines 5108--5112
[]\T1/ptm/m/n/10 For con-sis-tency, \T1/pcr/m/n/10 sparse \T1/ptm/m/n/10 is an
ar-gu-ment to all these con-trast func-tions, how-ever
Underfull \hbox (badness 7326) in paragraph at lines 5108--5112
\T1/pcr/m/n/10 sparse = TRUE \T1/ptm/m/n/10 for \T1/pcr/m/n/10 contr.poly \T1/p
tm/m/n/10 is typ-i-cally point-less and is rarely use-ful for
[1313] [1314]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5242--5242
[]\T1/pcr/m/n/9 ## using sparse contrasts: % useful, once model.matrix() works
with these :[]
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[]\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil
ter"))
Underfull \hbox (badness 2680) in paragraph at lines 5287--5289
[]\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
[1315]
Underfull \hbox (badness 10000) in paragraph at lines 5292--5294
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 r <- convolve(x, y, type = "open") \T1/ptm/m
/n/10 and \T1/pcr/m/n/10 n <- length(x)\T1/ptm/m/n/10 ,
[1316] [1317]
Underfull \hbox (badness 1436) in paragraph at lines 5470--5475
[]\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 5470--5475
\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 5470--5475
\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 ,
[1318] [1319] [1320]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5668--5668
[] \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE,
...)[]
[1321]
Underfull \hbox (badness 1168) in paragraph at lines 5740--5745
[]\T1/ptm/m/n/10 For Spear-man's test, p-values are com-puted us-ing al-go-rith
m AS 89 for $\OML/cmm/m/it/10 n < \OT1/cmr/m/n/10 1290$ \T1/ptm/m/n/10 and
[1322] [1323]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5835--5835
[]\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center =
TRUE,
[1324] [1325] [1326]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 6020--6020
[]\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter =
NULL)
[1327] [1328]
Underfull \hbox (badness 10000) in paragraph at lines 6183--6188
[]\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
[1329] [1330] [1331]
Underfull \hbox (badness 5954) in paragraph at lines 6379--6381
[]\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn
, see
[1332]
Underfull \hbox (badness 2503) in paragraph at lines 6461--6464
[]\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 6465--6467
[]\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 6468--6473
\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,
[1333]
Underfull \hbox (badness 7238) in paragraph at lines 6504--6507
[][][]\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
[1334]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6539--6539
[]\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 6554--6554
[]\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 6569--6569
[]\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h
oriz = TRUE)[]
[1335] [1336] [1337] [1338]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6813--6813
[] \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker
n = TRUE))))[]
[1339] [1340]
Underfull \vbox (badness 10000) has occurred while \output is active [1341]
[1342] [1343] [1344]
Underfull \hbox (badness 10000) in paragraph at lines 7211--7215
\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
[1345]
Underfull \hbox (badness 6493) in paragraph at lines 7310--7313
[]\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
[1346] [1347]
Underfull \hbox (badness 10000) in paragraph at lines 7447--7450
[]\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 =
[1348] [1349] [1350] [1351] [1352] [1353]
Underfull \hbox (badness 10000) in paragraph at lines 7857--7862
[]\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 , ...,
[1354] [1355]
Overfull \hbox (33.6622pt too wide) in paragraph at lines 7995--7997
[]\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 (
\OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1
\OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1
/cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/pcr/m/n/10 -pexp(t, r, lower = FALSE, log
= TRUE)\T1/ptm/m/n/10 .
[1356] [1357] [1358]
Underfull \hbox (badness 1210) in paragraph at lines 8212--8214
[]\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
[1359] [1360] [1361] [1362] [1363] [1364] [1365]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 8687--8687
[]\T1/pcr/m/n/9 ## Not run: glm(y ~ x, family = quasi(variance = "mu^3", link
= "log")) # fails[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 8690--8690
[]\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit
"), start = c(0,1))[]
[1366] [1367]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 8828--8828
[]\T1/pcr/m/n/9 quantile(rel.err(qf(2*p - 1, df1 = 1, df2 = df), qt(p, df)^2),
.90) # ~= 7e-9[]
[1368]
Underfull \hbox (badness 1859) in paragraph at lines 8867--8872
\T1/ptm/m/n/10 If \T1/pcr/m/n/10 inverse \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\
T1/ptm/m/n/10 , the (un-nor-mal-ized) in-verse Fourier trans-form is re-turned,
i.e., if
[1369] [1370] [1371]
Underfull \hbox (badness 2865) in paragraph at lines 9113--9122
[]\T1/ptm/m/n/10 For larger than $\OT1/cmr/m/n/10 2 \OMS/cmsy/m/n/10 ^^B \OT1/c
mr/m/n/10 2$ \T1/ptm/m/n/10 ta-bles and \T1/pcr/m/n/10 hybrid = TRUE\T1/ptm/m/n
/10 , asymp-totic chi-squared prob-a-bil-i-
Underfull \hbox (badness 1331) in paragraph at lines 9113--9122
\T1/ptm/m/n/10 ties are only used if the `Cochran con-di-tions' (or mod-i-fied
ver-sion thereof) spec-i-fied by
[1372] [1373]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 9255--9255
[] \T1/pcr/m/n/9 dimnames = list(income = c("< 15k", "15-25k", "25-4
0k", "> 40k"),[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 9256--9256
[] \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Mod
erateS", "VeryS")))[]
[1374] [1375] [1376]
Overfull \hbox (61.88992pt too wide) in paragraph at lines 9435--9437
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Fligner-Killeen test of
homogeneity of variances"\T1/ptm/m/n/10 .
[1377] [1378] [1379] [1380] [1381] [1382] [1383]
Underfull \hbox (badness 2443) in paragraph at lines 9888--9894
[][][]\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);
[1384] [1385] [1386]
Underfull \hbox (badness 3758) in paragraph at lines 10101--10104
[]\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
[1387] [1388] [1389] [1390]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 10337--10337
[] \T1/pcr/m/n/10 x = FALSE, y = TRUE, singular.ok = TRUE, contrasts = NULL
, ...)[]
Underfull \hbox (badness 4518) in paragraph at lines 10363--10368
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1391]
Underfull \hbox (badness 4132) in paragraph at lines 10402--10406
[]\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth
od
[1392]
Underfull \hbox (badness 10000) in paragraph at lines 10507--10510
[]\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
[1393] [1394] [1395]
Underfull \hbox (badness 2142) in paragraph at lines 10711--10714
[]\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 ^^@
[1396]
Underfull \hbox (badness 1708) in paragraph at lines 10792--10796
[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
[1397]
Underfull \hbox (badness 10000) in paragraph at lines 10834--10840
[][][]\T1/pcr/m/n/10 glm[][][] \T1/ptm/m/n/10 for com-put-ing \T1/pcr/m/n/10 gl
m.obj\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 anova.glm[][][]\T1/ptm/m/n/10 ; the co
r-re-spond-ing \T1/ptm/m/it/10 generic \T1/ptm/m/n/10 func-tions,
Underfull \hbox (badness 1418) in paragraph at lines 10872--10877
\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 (=
[1398] [1399]
Underfull \hbox (badness 2635) in paragraph at lines 11005--11008
\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
[1400] [1401] [1402]
Underfull \hbox (badness 1694) in paragraph at lines 11190--11193
[]\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these
de-fault to
Underfull \hbox (badness 1337) in paragraph at lines 11209--11218
[]\T1/ptm/m/n/10 If ei-ther is a vec-tor (of `weights') then the ap-pro-pri-ate
den-dro-gram is re-ordered ac-cord-
Underfull \hbox (badness 3049) in paragraph at lines 11209--11218
\T1/ptm/m/n/10 ing to the sup-plied val-ues sub-ject to the con-straints im-pos
ed by the den-dro-gram, by
[1403]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 11291--11291
[]\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col
SideColors = cc,[]
[1404]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11324--11324
[] \T1/pcr/m/n/10 optim.start = c(alpha = 0.3, beta = 0.1, gamma =
0.1),[]
Underfull \hbox (badness 10000) in paragraph at lines 11337--11341
[]\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
[1405] [1406] [1407]
Underfull \hbox (badness 7379) in paragraph at lines 11517--11520
[]\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds
[][]\T1/pcr/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq
uiv-a-lent of
[1408] [1409]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11656--11656
[]\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.11671 \aliasA{hat}{influence.measures}{hat}
[1410]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11724--11724
[]\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA
LSE),[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11736--11736
[]\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE),
...)[]
[1411]
Underfull \hbox (badness 1062) in paragraph at lines 11785--11790
[]\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 11802--11804
[]\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
[1412] [1413]
Underfull \hbox (badness 3623) in paragraph at lines 11956--11958
[]\T1/pcr/m/n/10 rel.tol \T1/ptm/m/n/10 can-not be less than \T1/pcr/m/n/10 max
(50*.Machine$double.eps, 0.5e-28) \T1/ptm/m/n/10 if
[1414] [1415]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12052--12052
[] \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend =
TRUE,[]
[1416]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12145--12145
[] \T1/pcr/m/n/9 interaction.plot(agegp, tobgp, ncases/ncontrols, trace.label
= "tobacco",[]
[1417]
Underfull \hbox (badness 10000) in paragraph at lines 12193--12196
[]\T1/ptm/m/n/10 For nor-mally $\OML/cmm/m/it/10 N\OT1/cmr/m/n/10 (\OML/cmm/m/i
t/10 m; \OT1/cmr/m/n/10 1)$ \T1/ptm/m/n/10 dis-tributed $\OML/cmm/m/it/10 X$\T1
/ptm/m/n/10 , the ex-pected value of \T1/pcr/m/n/10 IQR(X) \T1/ptm/m/n/10 is
[1418] [1419] [1420]
Underfull \hbox (badness 4441) in paragraph at lines 12388--12390
[]\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is
fit-ted to
Underfull \hbox (badness 10000) in paragraph at lines 12395--12397
[]\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
[1421]
Underfull \hbox (badness 4739) in paragraph at lines 12418--12420
[]\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
[1422]
Underfull \hbox (badness 2753) in paragraph at lines 12487--12489
[]\T1/ptm/m/n/10 R bug re-port PR#14682 (2011-2013) [][]$\T1/pcr/m/n/10 https :
/ / bugs . r-[]project . org / bugzilla3 /
[1423] [1424]
Underfull \hbox (badness 1292) in paragraph at lines 12612--12616
\T1/ptm/m/n/10 than one, it means the con-vo-lu-tion of ker-nels of di-men-sion
\T1/pcr/m/n/10 m[j]\T1/ptm/m/n/10 , for
[1425]
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[]\T1/ptm/m/n/10 an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of class \T1/pcr/m/
n/10 "kmeans"\T1/ptm/m/n/10 , typ-i-cally the re-sult \T1/pcr/m/n/10 ob \T1/ptm
/m/n/10 of
Underfull \hbox (badness 2894) in paragraph at lines 12731--12735
[]\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 13438--13438
[]\T1/pcr/m/n/9 dimnames(cAS) <- list(paste("it =", format(1:10)), c("intercep
t", "slope"))[]
[1437]
Underfull \hbox (badness 4518) in paragraph at lines 13481--13486
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
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Underfull \hbox (badness 10000) in paragraph at lines 13680--13684
[]\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
,
[1440] [1441] [1442]
Underfull \hbox (badness 6995) in paragraph at lines 13865--13867
[][][]\T1/pcr/m/n/10 naresid[][][] \T1/ptm/m/n/10 is ap-plied to the re-sults a
nd so will fill in with \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 s it the fit had
[1443] [1444]
Underfull \hbox (badness 1163) in paragraph at lines 14013--14021
\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 ,
[1445] [1446]
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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
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Underfull \hbox (badness 10000) in paragraph at lines 14271--14275
[]\T1/ptm/m/n/10 Only for the (de-fault) case \T1/pcr/m/n/10 (surface =
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\T1/pcr/m/n/10 "interpolate", statistics = "approximate")\T1/ptm/m/n/10 : shoul
d the
[1449]
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[]\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)[]
[1450]
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[]\T1/ptm/m/n/10 The dis-tri-bu-tion func-tion is a rescaled hy-per-bolic tan-g
ent,
Underfull \hbox (badness 1715) in paragraph at lines 14375--14378
\T1/pcr/m/n/10 plogis(x) == (1+ [][]tanh[][][](x/2))/2\T1/ptm/m/n/10 , and it i
s called a \T1/ptm/m/it/10 sig-moid func-tion \T1/ptm/m/n/10 in con-texts
[1451] [1452] [1453] [1454]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 14663--14663
[]\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)[]
[1455]
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[]\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 (
\OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1
\OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1
/cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/pcr/m/n/10 -plnorm(t, r, lower = FALSE, l
og = TRUE)\T1/ptm/m/n/10 .
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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)))
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Underfull \hbox (badness 2726) in paragraph at lines 15164--15167
[]\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 ,
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[]\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc
gp, data = esoph)
[1474] [1475]
Underfull \hbox (badness 1014) in paragraph at lines 16017--16022
\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
[1476]
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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,
Underfull \hbox (badness 2591) in paragraph at lines 16097--16106
\T1/ptm/m/n/10 us-ing the data in \T1/pcr/m/n/10 data \T1/ptm/m/n/10 which must
sup-ply vari-ables with the same names as would
Underfull \hbox (badness 3930) in paragraph at lines 16097--16106
\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
[1477]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 16165--16165
[]\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 16719--16719
[]\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[]
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Overfull \hbox (25.98041pt too wide) in paragraph at lines 16947--16947
[]\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x,
s, prob = 0.4)),[]
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Underfull \hbox (badness 2359) in paragraph at lines 17533--17535
[]\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For-
tran code used by
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[] \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21
), th = b[1]))[]
[1501]
Underfull \hbox (badness 10000) in paragraph at lines 17785--17789
[]\T1/ptm/m/n/10 Fits the asymp-totic re-gres-sion model, in the form \T1/pcr/m
/n/10 b0 +
[1502] [1503]
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[]\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 )[]
[1504]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 17959--17959
[]\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 18450--18453
[]\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma
-tion to the gra-di-ent, on
Underfull \hbox (badness 1127) in paragraph at lines 18463--18467
\T1/ptm/m/n/10 value by a fac-tor of \T1/pcr/m/n/10 reltol * (abs(val) + reltol
) \T1/ptm/m/n/10 at a step. De-faults to
[1513]
Underfull \hbox (badness 1478) in paragraph at lines 18471--18475
\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 18529--18531
[]\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
[1514] [1515]
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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",[]
Overfull \hbox (96.18033pt too wide) in paragraph at lines 18698--18698
[]\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 18721--18721
[]\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max
(interval),[]
[1517]
Underfull \hbox (badness 2564) in paragraph at lines 18756--18767
[]\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 18756--18767
\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
[1518]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18819--18819
[]\T1/pcr/m/n/9 f <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x -
1)), 10), 10)[]
[1519] [1520] [1521]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 19044--19044
[]\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp =
1, lty = 1:6,[]
[1522]
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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
[1523] [1524] [1525] [1526] [1527] [1528]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19439--19439
[] \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd =
1.5),[]
[1529]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 19527--19527
[] \T1/pcr/m/n/10 expression("Cook\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s dist
vs Leverage " * h[ii] / (1 - h[ii]))),[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 19530--19530
[] \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact
ive(),[]
[1530]
Underfull \hbox (badness 3049) in paragraph at lines 19609--19613
[]\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
[1531] [1532] [1533] [1534]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19857--19857
[] \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3,
...)[]
Underfull \hbox (badness 4779) in paragraph at lines 19864--19866
[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read
y ex-ist-ing plot. Only valid for
Underfull \hbox (badness 1194) in paragraph at lines 19867--19870
[]\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting
of the con-fi-dence
[1535]
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[]\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
[1536]
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[]\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange
") # all colors[]
[1537]
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[]\T1/pcr/m/n/9 legend(2.5, 1.9, paste("f =", c(0, 0.2, 1)), col = 1:3, lty =
1, y.intersp = 1)[]
Underfull \hbox (badness 10000) in paragraph at lines 20037--20040
[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 function(x, col, bg, pch, type, ...) \T1/ptm/
m/n/10 which gives
Underfull \hbox (badness 10000) in paragraph at lines 20037--20040
\T1/ptm/m/n/10 the ac-tion to be car-ried out in each panel of the dis-play for
[1538]
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[]\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma
r..., oma...)")[]
[1539] [1540]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20206--20206
[] \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE) # no
cancellation[]
[1541]
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[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Exact Poisson test" \T1
/ptm/m/n/10 or
Overfull \hbox (6.78088pt too wide) in paragraph at lines 20317--20317
[]\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple =
FALSE)
[1542]
Underfull \hbox (badness 10000) in paragraph at lines 20372--20374
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 poly(*, simple=TRUE)\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 polym(*, coefs=<non-NULL>)\T1/ptm/m/n/10 , and
[1543]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20409--20409
[] \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 20414--20414
[]\T1/pcr/m/n/9 ## poly(<matrix>, df) --- used to fail till July 14 (vive la F
rance!), 2017:[]
[1544] [1545] [1546] [1547] [1548] [1549] [1550] [1551] [1552] [1553] [1554]
[1555] [1556]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 21264--21264
[] \T1/pcr/m/n/9 all.equal(pz3$sdev, pZ$sdev, tol = 1e-15)) # exactly
equal typically[]
[1557]
Underfull \hbox (badness 6859) in paragraph at lines 21331--21338
[][][]\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 21342--21348
[]\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 ,
[1558] [1559] [1560] [1561] [1562] [1563] [1564] [1565] [1566] [1567] [1568]
[1569]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 22080--22080
[] \T1/pcr/m/n/10 subset = rep_len(TRUE, nrow(as.matrix(x))), fix_sign
= TRUE, ...)[]
[1570] [1571] [1572] [1573] [1574]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 22364--22364
[] \T1/pcr/m/n/10 has.Pvalue = nc >= 4L && length(cn <- colnames(x
)) &&[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 22365--22365
[] \T1/pcr/m/n/10 substr(cn[nc], 1L, 3L) %in% c("Pr("
, "p-v"),[]
[1575] [1576] [1577] [1578] [1579]
Underfull \hbox (badness 1337) in paragraph at lines 22689--22695
[]\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
[1580] [1581] [1582] [1583] [1584] [1585] [1586] [1587]
Overfull \hbox (133.98029pt too wide) in paragraph at lines 23251--23251
[] \T1/pcr/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty
p, ...), quantile(x, prob, type=1)))[]
[1588] [1589]
Underfull \hbox (badness 1028) in paragraph at lines 23392--23395
[]\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
[1590] [1591]
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[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by
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\T1/pcr/m/n/10 cutree(hclust.obj, k = k)\T1/ptm/m/n/10 , can be spec-i-fied for
ef-fi-ciency if
[1592]
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[]\T1/ptm/m/n/10 This, as [][]\T1/pcr/m/n/10 reorder[][][]()\T1/ptm/m/n/10 , is
a spe-cial case of sim-ply call-ing
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[]\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
[1593] [1594]
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[]\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd,
10:1, mean)")[]
[1595] [1596] [1597]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 23941--23941
[]\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide
", v.names = "x")[]
[1598] [1599] [1600]
Underfull \hbox (badness 10000) in paragraph at lines 24087--24090
[]\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
Underfull \hbox (badness 2134) in paragraph at lines 24139--24143
[][][]\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
[1601]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 24152--24152
[]\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi
ans Example")[]
[1602] [1603] [1604] [1605] [1606] [1607] [1608]
Underfull \hbox (badness 6268) in paragraph at lines 24616--24621
[][]\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 ,
[1609]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 24644--24644
[] \T1/pcr/m/n/9 setNames(pars[c(".lin", "xmid", "scal")], nm = mCall[c("As
ym", "xmid", "scal")])[]
[1610] [1611]
Underfull \hbox (badness 1867) in paragraph at lines 24821--24823
[]\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 24834--24838
\T1/ptm/m/n/10 where \T1/pcr/m/n/10 NN <- [][]nobs[][][](object, use.fallback =
use.fallback) \T1/ptm/m/n/10 and
Underfull \hbox (badness 10000) in paragraph at lines 24834--24838
\T1/pcr/m/n/10 PP <- sum(!is.na([][]coef[][][](object))) \T1/ptm/m/n/10 -- wher
e in older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was
[1612]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 24870--24870
[]\T1/pcr/m/n/9 sigma(lm1) # ~= 7.165 = "Residual standard error" printed fr
om summary(lm1)[]
[1613] [1614] [1615]
Underfull \hbox (badness 2495) in paragraph at lines 25060--25069
[]\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 [][]$\T1/pcr/m/n/10 https : / / en .
[1616]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 25142--25142
[] \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends
= FALSE)[]
Underfull \hbox (badness 1412) in paragraph at lines 25149--25151
[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui
red; de-faults to
[1617]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 25236--25236
[]\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS
S"), smooth(x)))[]
[1618]
Overfull \hbox (84.78088pt too wide) in paragraph at lines 25261--25261
[]\T1/pcr/m/n/10 smooth.spline(x, y = NULL, w = NULL, df, spar = NULL, lambda
= NULL, cv = FALSE,
Overfull \hbox (66.78088pt too wide) in paragraph at lines 25264--25264
[] \T1/pcr/m/n/10 control.spar = list(), tol = 1e-6 * IQR(x), kee
p.stuff = FALSE)[]
[1619]
Underfull \hbox (badness 10000) in paragraph at lines 25306--25311
[]\T1/ptm/m/n/10 integer or [][]\T1/pcr/m/n/10 function[][][] \T1/ptm/m/n/10 gi
v-ing the num-ber of knots to use when
Underfull \hbox (badness 2435) in paragraph at lines 25306--25311
\T1/pcr/m/n/10 all.knots = FALSE\T1/ptm/m/n/10 . If a func-tion (as by de-fault
), the num-ber of
[1620]
Underfull \hbox (badness 2980) in paragraph at lines 25451--25453
[]\T1/ptm/m/n/10 the value of \T1/pcr/m/n/10 spar \T1/ptm/m/n/10 com-puted or g
iven, un-less it has been given as
[1621]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 25487--25487
[] \T1/pcr/m/n/10 nx <- length(x) - sum(duplicated( round((x - mean(x)) /
tol) ))[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 25536--25536
[]\T1/pcr/m/n/9 plot(dist ~ speed, data = cars, main = "data(cars) & smoothi
ng splines")[]
[1622]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 25557--25557
[]\T1/pcr/m/n/9 with(cars.spl$fit, min + range * knot[-c(1:3, nk+1 +1:3)]) # =
= unique(cars$speed)[]
Underfull \vbox (badness 10000) has occurred while \output is active [1623]
[1624]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 25661--25661
[]\T1/pcr/m/n/9 legend(1, 470, paste("endrule", c("keep","constant","median"),
sep = " = "),[]
[1625]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 25728--25728
[]\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na.
fail,
[1626] [1627] [1628] [1629] [1630] [1631]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 26107--26107
[] \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC"
, "hyman"),[]
Underfull \hbox (badness 6477) in paragraph at lines 26161--26164
[]\T1/ptm/m/n/10 Method \T1/pcr/m/n/10 "hyman" \T1/ptm/m/n/10 com-putes a \T1/p
tm/m/it/10 mono-tone \T1/ptm/m/n/10 cu-bic spline us-ing Hy-man fil-ter-ing of
an
[1632] [1633]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 26292--26292
[]\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 26293--26293
[]\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman") (x), add = TRUE, c
ol = 4, n = 1001)[]
Underfull \vbox (badness 10000) has occurred while \output is active [1634]
Underfull \hbox (badness 2922) in paragraph at lines 26362--26367
[]\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
[1635]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 26399--26399
[] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5.2), xlim
= c(-.3, 5),[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 26402--26402
[] \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 26411--26411
[] \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 26412--26412
[] \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 26416--26416
[] \T1/pcr/m/n/9 axis(2, at = c(1,AR2,5), labels= expression(phi[2], frac(phi
[1]+phi[2],2), phi[1]),[]
[1636]
Underfull \hbox (badness 2922) in paragraph at lines 26458--26463
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
Underfull \hbox (badness 3240) in paragraph at lines 26470--26473
[][][]\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 26491--26491
[] \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 26494--26494
[] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(-.5,6), xlim
= c(-1, 8),[]
[1637]
Underfull \hbox (badness 2922) in paragraph at lines 26544--26549
[]\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
[1638]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26577--26577
[] \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 26581--26581
[] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5), xlim =
c(-1/4, 5),[]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 26591--26591
[] \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 26596--26596
[] \T1/pcr/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5]
== frac(log(2), e^{phi[2]})}),[]
[1639]
Underfull \hbox (badness 2922) in paragraph at lines 26632--26638
[]\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 26654--26654
[]\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 26670--26670
[] \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 =
1.5 * exp(-x)"),[]
[1640] [1641]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 26784--26784
[]\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK
a)*input))
[1642]
Underfull \hbox (badness 2922) in paragraph at lines 26846--26851
[]\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
[1643]
Overfull \hbox (69.18036pt too wide) in paragraph at lines 26884--26884
[] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "A", phi[2] == "B", phi[3] == "xm
id", phi[4] == "scal")))[]
[1644]
Underfull \hbox (badness 2922) in paragraph at lines 26933--26938
[]\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 26964--26964
[]\T1/pcr/m/n/9 lines(x, do.call(SSgompertz, c(list(x=x), coef(fm1))), col = "
red", lwd=2)[]
[1645]
Underfull \hbox (badness 2922) in paragraph at lines 26998--27003
[]\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 (25.98041pt too wide) in paragraph at lines 27023--27023
[]\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 27027--27027
[]\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 27047--27047
[] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "Asym", phi[2] == "xmid", phi[3]
== "scal")))[]
[1646]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 27057--27057
[] \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[]
Underfull \hbox (badness 2922) in paragraph at lines 27092--27097
[]\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
[1647]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27114--27114
[]\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt),
digits = 3)[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 27132--27132
[] \T1/pcr/m/n/9 ann = FALSE, axes = FALSE, main = "Parameters in the SS
micmen model")[]
[1648]
Underfull \hbox (badness 6493) in paragraph at lines 27184--27189
[]\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
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27211--27211
[]\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 27213--27213
[]\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 27216--27216
[]\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 27219--27219
[]\T1/pcr/m/n/9 As <- coef(fm1)[["Asym"]]; abline(v = 0, h = c(As, As - coef(f
m1)[["Drop"]]), lty = 3)[]
[1649] [1650] [1651] [1652] [1653] [1654] [1655] [1656]
Underfull \hbox (badness 10000) in paragraph at lines 27714--27717
[]\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex-
Underfull \hbox (badness 10000) in paragraph at lines 27714--27717
\T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/pcr/m/n/10 NULL\T1/ptm/m/
n/10 , the de-fault,
[1657] [1658] [1659] [1660] [1661] [1662] [1663]
Underfull \hbox (badness 3396) in paragraph at lines 28143--28145
[]\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
[1664] [1665] [1666]
Underfull \hbox (badness 2237) in paragraph at lines 28320--28322
[]\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
[1667] [1668]
Underfull \hbox (badness 2591) in paragraph at lines 28484--28486
[]\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
[1669]
Underfull \hbox (badness 2237) in paragraph at lines 28530--28533
[]\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
[1670]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 28603--28603
[]\T1/pcr/m/n/10 supsmu(x, y, wt =, span = "cv", periodic = FALSE, bass = 0, t
race = FALSE)
[1671] [1672]
Underfull \hbox (badness 3407) in paragraph at lines 28711--28715
[]\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)
[1673] [1674]
Underfull \hbox (badness 1337) in paragraph at lines 28844--28848
[]\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
[1675] [1676]
Underfull \hbox (badness 10000) in paragraph at lines 28961--28964
[]\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/
10 ; cur-rently ex-cept for \T1/pcr/m/n/10 rt()\T1/ptm/m/n/10 , only for
[1677] [1678]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 29090--29090
[]\T1/pcr/m/n/9 persp(tt, ncp, ptn, zlim = 0:1, r = 2, phi = 20, theta = 200,
main = t.tit,[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 29118--29118
[] \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com
mon",[]
[1679]
Underfull \hbox (badness 1616) in paragraph at lines 29144--29147
[]\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial
resid-u-als, when
[1680]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 29223--29223
[]\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s
pan.smth = 1/4)[]
[1681]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 29300--29300
[]\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out =
TRUE,[]
[1682]
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[]\T1/ptm/m/n/10 A [][]\T1/pcr/m/n/10 terms.object[][][] \T1/ptm/m/n/10 ob-ject
is re-turned. The ob-ject it-self is the re-ordered (un-less
[1683]
Underfull \hbox (badness 2205) in paragraph at lines 29389--29394
[]\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
[1684] [1685] [1686] [1687] [1688] [1689] [1690] [1691]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 29984--29984
[]\T1/pcr/m/n/10 ptukey(q, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
FALSE)
[1692]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 29985--29985
[]\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
FALSE)[]
[1693] [1694] [1695] [1696]
Underfull \hbox (badness 10000) in paragraph at lines 30274--30278
[]\T1/ptm/m/n/10 Setting \T1/pcr/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/p
cr/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect
Underfull \hbox (badness 1596) in paragraph at lines 30274--30278
\T1/pcr/m/n/10 interval = c(lower,upper) \T1/ptm/m/n/10 if \T1/pcr/m/n/10 sign(
f(x)) \T1/ptm/m/n/10 does not sat-isfy the re-quire-ments at
Overfull \hbox (30.78088pt too wide) in paragraph at lines 30285--30285
[] \T1/pcr/m/n/10 extendInt = c("no", "yes", "downX", "upX"), check.con
v = FALSE,[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 30286--30286
[] \T1/pcr/m/n/10 tol = .Machine$double.eps^0.25, maxiter = 1000, trace
= 0)[]
[1697] [1698]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 30412--30412
[]\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:[]
[1699] [1700] [1701] [1702]
Underfull \hbox (badness 1337) in paragraph at lines 30638--30642
[]\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
[1703] [1704] [1705] [1706] [1707] [1708] [1709] [1710]
Underfull \hbox (badness 1337) in paragraph at lines 31165--31169
[]\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
[1711]
Underfull \hbox (badness 1946) in paragraph at lines 31242--31247
[]\T1/ptm/m/n/10 When \T1/pcr/m/n/10 x \T1/ptm/m/n/10 (and \T1/pcr/m/n/10 y \T1
/ptm/m/n/10 if ap-pli-ca-ble) are valid, the func-tion now al-ways re-turns, al
so in the
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[]\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if
ar-gu-ment
[1712] [1713] [1714] [1715] [1716]
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[]\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F
ALSE,
[1717]
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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
[1718]
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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 "")[]
[1719]) (./stats4-pkg.tex [1720]
Chapter 11.
[1721] [1722] [1723]
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[] \T1/pcr/m/n/9 -sum(stats::dpois(y, lambda = exp(lymax)/(1+x/exp(lxhalf))
, log = TRUE))[]
[1724] [1725] [1726]pdfTeX warning (ext4): destination with the same identifier
(name{Rfn.show.Rdash.methods}) has been already used, duplicate ignored
<to be read again>
\relax
l.407 ...Package \pkg{stats4}}{show.Rdash.methods}
[1727]
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[]\T1/ptm/m/n/10 Generate a sum-mary as an ob-ject of class
[1728] [1729]) (./tcltk-pkg.tex [1730]
Chapter 12.
[1731] [1732] [1733] [1734]
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[]\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all = TRUE) # .Tcl.args put a callback
ref in here[]
[1735] [1736] [1737]
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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/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
[1750]) (./tools-pkg.tex
Chapter 13.
[1751]
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[]\T1/pcr/m/n/9 ## is used for simple print methods in R, and as prototype for
new methods.[]
[1752]
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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
[1753]
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[]\T1/pcr/m/n/9 assertCondition(ff(), "error", "warning") # ok (quietly, catch
ing warning)[]
[1754]
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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 ,
[1755]
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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
[1756] [1757] [1758] [1759] [1760] [1761] [1762]
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[1763] [1764]
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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")[]
[1765] [1766]
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[]\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i
g-nored when
[1767]
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[]\T1/ptm/m/n/10 a named list of char-ac-ter vec-tors with ar-gu-ments to be pa
ssed to
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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-
[1768]
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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
[1769]
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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
[1770] [1771]
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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/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S
up-port func-tion for
[1772] [1773] [1774] [1775] [1776]
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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 .
[1777] [1778] [1779]pdfTeX warning (ext4): destination with the same identifier
(name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored
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l.1897 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD}
[1780] [1781] [1782]
[1783]
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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}",[]
[1784]
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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
[1785]
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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
[1786]
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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 .
[1787]
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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)[]
[1788] [1789] [1790] [1791]
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[] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macros", "system.
Rd"),[]
[1792]
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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
[1793] [1794] [1795] [1796] [1797]
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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
[1798] [1799] [1800] [1801] [1802]
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[] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macro
s", "system.Rd"))[]
[1803] [1804] [1805] [1806]
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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
[1807] [1808]
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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
[1811]
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[] \T1/pcr/m/n/10 depLevel = c("Depends", "Imports", "Sugg
ests"))[]
[1812]
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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
[1813] [1814] [1815]
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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
[1816]
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 reduce \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE
\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/pcr/m/n/10 De
pendsList
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\T1/ptm/m/n/10 ob-ject such that a min-i-mal set of de-pen-den-cies are spec-i-
fied (for in-stance if
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\T1/ptm/m/n/10 there was `\T1/pcr/m/n/10 foo, foo (>= 1.0.0), foo (>= 1.3.0)\T1
/ptm/m/n/10 ', it would only re-turn
[1817] [1818]
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[] \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F
ALSE,[]
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[] \T1/pcr/m/n/10 latestOnly = TRUE, addFiles = FALSE, rds_compr
ess = "xz")[]
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[]\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 ',
[1819]
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\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 ,
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[]\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
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\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 ',
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[]\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
[1820] [1821] [1822]) (./utils-pkg.tex
Chapter 14.
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[]\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 ',
[1823] [1824] [1825]
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[]\T1/pcr/m/n/10 find \T1/ptm/m/n/10 is a dif-fer-ent user in-ter-face for a si
m-i-lar task to \T1/pcr/m/n/10 apropos\T1/ptm/m/n/10 . By de-fault
[1826]
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[]\T1/pcr/m/n/9 find("cor", numeric = TRUE) # numbers with
these names[]
[1827]
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[] \T1/pcr/m/n/10 prompts = getOption("askYesNo", gettext(c("Yes", "No
", "Cancel"))),[]
[1828] [1829] [1830]
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\T1/ptm/m/n/10 28. [][]$\T1/pcr/m/n/10 https : / / journal . r-[]project . org
/ archive / 2011-[]2 / RJournal _ 2011-[]2 _
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[]\T1/pcr/m/n/10 aspell_package_Rd_files(dir, drop = c("\\author", "\\referenc
es"),
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[]\T1/pcr/m/n/10 aspell_package_R_files(dir, ignore = character(), control = l
ist(),[]
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[] \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[]
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[]\T1/pcr/m/n/10 aspell_package_C_files(dir, ignore = character(), control = l
ist(),[]
[1831]
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[] \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[]
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[]\T1/ptm/m/n/10 Functions \T1/pcr/m/n/10 aspell_package_Rd_files\T1/ptm/m/n/10
, \T1/pcr/m/n/10 aspell_package_vignettes\T1/ptm/m/n/10 ,
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\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-
[1832]
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[] \T1/pcr/m/n/10 ignore_repo_cache = FALSE, max_repo_cache
_age,[]
[1833]
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\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
[1834]
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\T1/ptm/m/n/10 ory avail-able and con-trol-ling the load/save pro-cess. If \T1/
pcr/m/n/10 infile \T1/ptm/m/n/10 starts
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\T1/ptm/m/n/10 with a `\T1/pcr/m/n/10 -\T1/ptm/m/n/10 ', use `\T1/pcr/m/n/10 --
\T1/ptm/m/n/10 ' as the fi-nal op-tion. The de-fault op-tions are
[1835]
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[]\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer =
NULL,
[1836]
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\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 1003--1005
[]\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing
[1837] [1838]
Underfull \hbox (badness 10000) in paragraph at lines 1111--1114
[]\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org
/ wiki / Digital _ Object _
[1839]
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[] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[]
[1840] [1841] [1842] [1843] [1844]
Underfull \hbox (badness 1859) in paragraph at lines 1565--1574
[]\T1/ptm/m/n/10 For ex-am-ple, sup-pose that on a data set which you know to b
e quite large the com-
[1845] [1846]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1666--1666
[] \T1/pcr/m/n/9 data = infert, family = b
inomial())))[]
[1847]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 1701--1701
[]\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b
efore$timestamp,[]
[1848]
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[]\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp"
), md5sum=TRUE)[]
[1849]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 1867--1867
[]\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind =
NULL,
Overfull \hbox (6.78088pt too wide) in paragraph at lines 1919--1919
[]\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind =
NULL,
[1850]
Underfull \hbox (badness 2213) in paragraph at lines 1953--1956
[]\T1/pcr/m/n/10 ind \T1/ptm/m/n/10 chooses a row in the list of cur-rent mir-r
ors, by num-ber. It is best used with
[1851] [1852]
Underfull \hbox (badness 10000) in paragraph at lines 2054--2056
[]\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the
`\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' file via
Overfull \hbox (36.7804pt too wide) in paragraph at lines 2088--2088
[] \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")[]
[1853]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2111--2111
[]\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after =
NULL,[]
Underfull \hbox (badness 5189) in paragraph at lines 2156--2158
[]\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w
hen
[1854]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2231--2231
[] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[]
[1855]
Underfull \hbox (badness 1082) in paragraph at lines 2305--2309
[][][]\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;
[1856]
Underfull \hbox (badness 10000) in paragraph at lines 2342--2344
[]\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
Underfull \hbox (badness 1057) in paragraph at lines 2374--2381
\T1/ptm/m/n/10 a [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 ); if FALSE, the
func-tion re-turns a [][]\T1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 . Note that w
hen
[1857] [1858] [1859]
Underfull \hbox (badness 10000) in paragraph at lines 2563--2565
[]\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see
[1860] [1861] [1862] [1863]
Underfull \hbox (badness 10000) in paragraph at lines 2800--2804
[]\T1/ptm/m/n/10 files end-ing `\T1/pcr/m/n/10 .tab\T1/ptm/m/n/10 ', `\T1/pcr/m
/n/10 .txt\T1/ptm/m/n/10 ' or `\T1/pcr/m/n/10 .TXT\T1/ptm/m/n/10 ' are read us-
ing
Underfull \hbox (badness 5203) in paragraph at lines 2800--2804
[][]\T1/pcr/m/n/10 read.table[][][](..., header = TRUE, as.is=FALSE)\T1/ptm/m/n
/10 , and hence re-sult in a
Overfull \hbox (133.10922pt too wide) in paragraph at lines 2805--2808
[]\T1/ptm/m/n/10 files end-ing `\T1/pcr/m/n/10 .csv\T1/ptm/m/n/10 ' or `\T1/pcr
/m/n/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/pcr/m/n/10 read.table[][][
](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 2854--2857
[]\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
[1864]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 2941--2941
[]\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 '[]
[1865]
Underfull \hbox (badness 2452) in paragraph at lines 3017--3020
[]\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
[1866] [1867] [1868] [1869] [1870] [1871] [1872]
Underfull \hbox (badness 1072) in paragraph at lines 3499--3507
[]\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
[1873]
Underfull \hbox (badness 1231) in paragraph at lines 3548--3554
[]\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 3555--3560
[]\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 3555--3560
\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 3555--3560
\T1/pcr/m/n/10 [user:password@]machine[:port] \T1/ptm/m/n/10 where the parts in
brack-ets are op-tional. See
[1874] [1875]
Underfull \hbox (badness 4660) in paragraph at lines 3677--3680
\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 3701--3703
[]\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
[1876] [1877] [1878]
Underfull \hbox (badness 1565) in paragraph at lines 3886--3890
[]\T1/ptm/m/n/10 Data frame columns are co-erced on in-put to \T1/ptm/m/it/10 c
har-ac-ter \T1/ptm/m/n/10 un-less nu-meric (in the sense of
Underfull \hbox (badness 10000) in paragraph at lines 3907--3913
[]\T1/ptm/m/n/10 For a data frame, the row names will be taken from the orig-i-
nal ob-ject if
[1879]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 3969--3969
[] \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F
ALSE,[]
Overfull \hbox (2.55087pt too wide) in paragraph at lines 3997--4004
\T1/pcr/m/n/10 setRNG = {RNGkind("default", "default"); set.seed(1)}\T1/ptm/m/n
/10 .
[1880] [1881] [1882] [1883] [1884]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4324--4324
[]\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o
ne is in the[]
[1885]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for
mat}) has been already used, duplicate ignored
<to be read again>
\relax
l.4395 ...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.4395 ...mat Unordered and Ordered Lists}{format}
[1886] [1887] [1888]
[1889] [1890] [1891] [1892] [1893] [1894] [1895] [1896] [1897] [1898] [1899]
[1900]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5348--5348
[] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h
elp(dgamma):[]
[1901]
Underfull \hbox (badness 10000) in paragraph at lines 5432--5434
[]\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
[1902]
Underfull \hbox (badness 1502) in paragraph at lines 5481--5486
[]\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 5481--5486
\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are
listed in file
[1903] [1904]
Underfull \hbox (badness 10000) in paragraph at lines 5654--5663
[]\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 5654--5663
\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
[1905]
Underfull \hbox (badness 2150) in paragraph at lines 5717--5720
[]\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 5733--5736
[]\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
[1906] [1907]
Underfull \hbox (badness 3118) in paragraph at lines 5854--5856
[]\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
[1908]
Underfull \hbox (badness 2409) in paragraph at lines 5887--5891
[]\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the
sub-architecture used by
[1909]
Underfull \hbox (badness 5091) in paragraph at lines 5991--5993
[]\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
Overfull \hbox (44.55087pt too wide) in paragraph at lines 6007--6012
\T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/
ptm/m/n/10 .
Overfull \hbox (48.30977pt too wide) in paragraph at lines 6020--6027
[]\T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 means to use \T1/pcr/m/n/10 c("Depends", "
Imports", "LinkingTo", "Suggests")
[1910]
Underfull \hbox (badness 10000) in paragraph at lines 6078--6081
[]\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to
be passed
Underfull \hbox (badness 10000) in paragraph at lines 6078--6081
\T1/ptm/m/n/10 to \T1/pcr/m/n/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pack
-age in-stall. E.g.,
[1911]
Underfull \hbox (badness 10000) in paragraph at lines 6137--6141
[]\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 ,
Underfull \hbox (badness 2376) in paragraph at lines 6151--6158
[]\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 6151--6158
\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 6151--6158
\T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com
-piled is con-trolled by
[1912]
Underfull \hbox (badness 1314) in paragraph at lines 6210--6217
[]\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 6251--6256
[][][]\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 ,
[1913]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 6274--6274
[] \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc
lude/udunits2"))[]
Underfull \hbox (badness 5133) in paragraph at lines 6310--6314
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to ex-tract from each
pack-age's
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[]\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
[1914]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6371--6371
[]\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields
= "License")[]
[1915] [1916]
Underfull \hbox (badness 4132) in paragraph at lines 6490--6492
[]\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
[1917] [1918] [1919]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6648--6648
[]\T1/pcr/m/n/9 ls.str(mode = "list") #- what are the structured objects I h
ave defined?[]
[1920] [1921]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 6791--6791
[]\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F
ALSE)
[1922]
Underfull \hbox (badness 10000) in paragraph at lines 6831--6833
[]\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
[1923] [1924]
Underfull \hbox (badness 10000) in paragraph at lines 6972--6974
[]\T1/ptm/m/n/10 a sym-bol or char-ac-ter string nam-ing a class: only used if
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[]\T1/ptm/m/n/10 typically the re-sult of \T1/pcr/m/n/10 methods(..)\T1/ptm/m/n
/10 , an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of class
[1925] [1926] [1927]
Underfull \hbox (badness 1859) in paragraph at lines 7200--7203
[]\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br
owser (by
[1928]
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[]\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 7293--7293
[]\T1/pcr/m/n/9 db3 <- news(Version == "3.0.1" & grepl("^BUG", Category) & gre
pl("PR#", Text),[]
[1929]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7297--7297
[]\T1/pcr/m/n/9 ## News from a date range (\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 Matri
x\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is there in a regular R installation):[]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 7305--7305
[]\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st
andardize a bit more[]
[1930]
Underfull \hbox (badness 10000) in paragraph at lines 7390--7394
[]\T1/ptm/m/n/10 For all stan-dards, \T1/pcr/m/n/10 unit = "auto" \T1/ptm/m/n/1
0 is also al-lowed. If
[1931] [1932] [1933] [1934]
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[] \T1/pcr/m/n/10 date.fields = c("Date", "Packaged", "Date/Publica
tion", "Built"),[]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 7655--7655
[] \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 7656--7656
[] \T1/pcr/m/n/10 desc = packageDescription(pkg, lib.loc=lib.loc, f
ields=date.fields))[]
[1935]
Underfull \hbox (badness 10000) in paragraph at lines 7684--7686
[]\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 7698--7700
[]\T1/pcr/m/n/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut,
al-low-ing things like
Underfull \hbox (badness 1259) in paragraph at lines 7706--7711
[]\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,
[1936]
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[] \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 7753--7753
[] \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[]
[1937] [1938]
Underfull \hbox (badness 10000) in paragraph at lines 7882--7887
[]\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 7882--7887
[][]\T1/pcr/m/n/10 installed.packages[][][] \T1/ptm/m/n/10 plus \T1/pcr/m/n/10
"Status"\T1/ptm/m/n/10 , a fac-tor with lev-els
Underfull \hbox (badness 10000) in paragraph at lines 7889--7892
[]\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 7889--7892
[][]\T1/pcr/m/n/10 available.packages[][][] \T1/ptm/m/n/10 plus \T1/pcr/m/n/10
"Status"\T1/ptm/m/n/10 , a fac-tor with lev-els
[1939]
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[] \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme
nt"),[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 8006--8006
[] \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<",
">"),[]
[1940] [1941] [1942]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8177--8177
[] \T1/pcr/m/n/9 "S original, <http://statwww.epfl.ch/davison/BMA/libr
ary.html>"),[]
[1943]
Underfull \hbox (badness 1789) in paragraph at lines 8300--8302
[]\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
[1944]
Underfull \hbox (badness 10000) in paragraph at lines 8358--8362
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
Underfull \hbox (badness 10000) in paragraph at lines 8358--8362
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1945] [1946]
Underfull \hbox (badness 10000) in paragraph at lines 8473--8477
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
Underfull \hbox (badness 10000) in paragraph at lines 8473--8477
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1947]
Underfull \hbox (badness 10000) in paragraph at lines 8538--8542
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
Underfull \hbox (badness 10000) in paragraph at lines 8538--8542
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1948] [1949] [1950] [1951]
Underfull \hbox (badness 5203) in paragraph at lines 8869--8872
[]\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
[1952] [1953] [1954]
Underfull \hbox (badness 1776) in paragraph at lines 9095--9102
[]\T1/ptm/m/n/10 If you are un-com-fort-able with un-so-licited eval-u-a-tion o
f pieces of code, you should set
[1955]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 9119--9119
[] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "
no.loss"),[]
[1956] [1957]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 9280--9280
[]\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr
anspose = TRUE)[]
[1958] [1959]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9461--9461
[]\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[]
[1960] [1961]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 9547--9547
[] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss",
"no.loss"),[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 9550--9550
[] \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines.
skip,[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 9555--9555
[] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski
pNul = FALSE)[]
[1962]
Underfull \hbox (badness 1077) in paragraph at lines 9627--9630
[]\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
[1963] [1964] [1965] [1966] [1967] [1968]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10067--10067
[] \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c
(1, 0)))
[1969]
Underfull \hbox (badness 10000) in paragraph at lines 10154--10156
[]\T1/ptm/m/n/10 To re-move from the li-brary tree \T1/ptm/m/sl/10 lib \T1/ptm/
m/n/10 in-stead of the de-fault one, use
[1970] [1971]
Underfull \hbox (badness 2181) in paragraph at lines 10277--10281
[]\T1/pcr/m/n/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/pcr/m/n
/10 "roman" \T1/ptm/m/n/10 which are in-ter-nally rep-re-sented as in-te-
Underfull \hbox (badness 2269) in paragraph at lines 10277--10281
\T1/ptm/m/n/10 gers, and have suit-able meth-ods for print-ing, for-mat-ting, s
ub-set-ting, co-er-cion, etc, see
Underfull \hbox (badness 10000) in paragraph at lines 10289--10293
\T1/pcr/m/n/10 en . wikipedia . org / w / index . php ? title = Roman _ numeral
s & oldid = 78252134$[][]\T1/ptm/m/n/10 .
[1972]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 10307--10307
[]\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 10311--10311
[]\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in
{1,2,..,3899} :[]
[1973] [1974]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 10443--10443
[]\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold
= 0)
[1975]
Underfull \hbox (badness 1917) in paragraph at lines 10566--10569
[]\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 10566--10569
\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
[1976]
Overfull \hbox (106.98032pt too wide) in paragraph at lines 10589--10589
[]\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 '[]
[1977]
Underfull \hbox (badness 8075) in paragraph at lines 10652--10654
[]\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
[1978]
Underfull \hbox (badness 6725) in paragraph at lines 10702--10711
\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 10702--10711
\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 10702--10711
\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
[1979]
Underfull \hbox (badness 3646) in paragraph at lines 10828--10830
[][][]$\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 /
[1980]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 10866--10866
[] \T1/pcr/m/n/10 split = FALSE, quiet = FALSE, drop.evalFALSE = F
ALSE, ...)[]
[1981] [1982] [1983]
Underfull \hbox (badness 10000) in paragraph at lines 11047--11051
[]\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 11078--11084
[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
[1984]
Underfull \hbox (badness 2012) in paragraph at lines 11173--11179
\T1/ptm/m/n/10 and `\T1/pcr/m/n/10 \includegraphics\T1/ptm/m/n/10 ' state-ments
for fig-ures should be auto-generated. Use
[1985]
Underfull \hbox (badness 2096) in paragraph at lines 11186--11188
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w
hether EPS fig-ures should be gen-er-ated. Ig-nored if
Underfull \hbox (badness 2698) in paragraph at lines 11189--11191
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ), in-di-cat-ing wh
ether PDF fig-ures should be gen-er-ated. Ig-nored if
Underfull \hbox (badness 1527) in paragraph at lines 11196--11199
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w
hether PNG fig-ures should be gen-er-ated. Ig-nored if
Underfull \hbox (badness 1067) in paragraph at lines 11200--11203
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w
hether JPEG fig-ures should be gen-er-ated. Ig-nored if
Overfull \hbox (6.78088pt too wide) in paragraph at lines 11254--11254
[] \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa
rent")[]
[1986]
Underfull \hbox (badness 1009) in paragraph at lines 11272--11283
[]\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
[1987]
Underfull \hbox (badness 2846) in paragraph at lines 11359--11369
\T1/ptm/m/n/10 con-trols the num-ber of lines that are saved (de-fault 512), an
d \T1/pcr/m/n/10 R_HISTFILE \T1/ptm/m/n/10 (de-fault
[1988] [1989]
Underfull \hbox (badness 10000) in paragraph at lines 11498--11501
[]\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the plat-form \T1/phv/m/n/10
R \T1/ptm/m/n/10 was built un-
Underfull \hbox (badness 10000) in paragraph at lines 11498--11501
\T1/ptm/m/n/10 der. Where sub-architectures are in use this is of the form
Underfull \hbox (badness 10000) in paragraph at lines 11515--11518
[]\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in
g
[1990]
Underfull \hbox (badness 2158) in paragraph at lines 11594--11597
[]\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
[1991] [1992] [1993]
Underfull \hbox (badness 3333) in paragraph at lines 11774--11776
[]\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-
[1994] [1995]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 11939--11939
[] \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing =
TRUE, ...))[]
[1996]
Underfull \hbox (badness 5970) in paragraph at lines 11972--11975
[]\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 11972--11975
[][]\T1/pcr/m/n/10 options[][][]("width")\T1/ptm/m/n/10 ; note that this has on
ly a weak ef-fect, un-less
Underfull \hbox (badness 1052) in paragraph at lines 11983--11992
\T1/ptm/m/n/10 (see [][]\T1/pcr/m/n/10 options[][][]\T1/ptm/m/n/10 ) which de-f
aults to \T1/pcr/m/n/10 "no" \T1/ptm/m/n/10 for back com-pat-i-bil-ity rea-sons
;
[1997]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 12027--12027
[]\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification
of binary numbers[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 12058--12058
[]\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 12065--12065
[]\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 12067--12067
[]\T1/pcr/m/n/9 invisible(lapply(60:66, function(N) str( ch , nchar.max = N)))
# "1 is 1" here[]
[1998] [1999] [2000]
Underfull \hbox (badness 10000) in paragraph at lines 12235--12237
[]\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
[2001] [2002]
Underfull \hbox (badness 4492) in paragraph at lines 12392--12399
[]\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 12392--12399
\T1/ptm/m/n/10 turn, and se-lected if their \T1/pcr/m/n/10 extension \T1/ptm/m/
n/10 com-po-nent matches (as a reg-exp) the file
Underfull \hbox (badness 2452) in paragraph at lines 12392--12399
\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$"\T1/ptm/m/n/10 ) and
[2003] [2004] [2005]
Underfull \hbox (badness 2020) in paragraph at lines 12555--12571
\T1/ptm/m/n/10 si-bly use-ful val-ues in-clude `\T1/pcr/m/n/10 -h\T1/ptm/m/n/10
' (fol-low sym-bolic links, also `\T1/pcr/m/n/10 -L\T1/ptm/m/n/10 ' on some pl
at-forms),
Underfull \hbox (badness 1194) in paragraph at lines 12555--12571
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 --acls\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclud
e-backups\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclude-vcs\T1/ptm/m/n/10 ' (and s
im-i-lar) and on Win-dows
[2006]
Underfull \hbox (badness 2809) in paragraph at lines 12675--12679
[]\T1/ptm/m/n/10 NetBSD prior to 8.0 used flag `\T1/pcr/m/n/10 --xz\T1/ptm/m/n/
10 ' rather than `\T1/pcr/m/n/10 -J\T1/ptm/m/n/10 ', so this should be used \T1
/ptm/m/it/10 via
Underfull \hbox (badness 1596) in paragraph at lines 12675--12679
\T1/pcr/m/n/10 extra_flags = "--xz" \T1/ptm/m/n/10 rather than \T1/pcr/m/n/10 c
ompression = "xz"\T1/ptm/m/n/10 . The com-mands from
Underfull \hbox (badness 5022) in paragraph at lines 12690--12694
[]\T1/ptm/m/n/10 When ar-gu-ment \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 is set to th
e com-mand \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-abl
e
Underfull \hbox (badness 10000) in paragraph at lines 12697--12700
[][][]$\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 12697--12700
\T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht
ml # tag _ 20 _
[2007] [2008] [2009]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 12862--12862
[] \T1/pcr/m/n/10 numerals = c("allow.loss", "warn.loss", "no.loss
"), ...)[]
[2010] [2011] [2012] [2013] [2014] [2015]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 13246--13246
[] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc,
...),[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 13252--13252
[] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc,
...),[]
Underfull \hbox (badness 4467) in paragraph at lines 13273--13275
[]\T1/ptm/m/n/10 Download method, see [][]\T1/pcr/m/n/10 download.file[][][]\T1
/ptm/m/n/10 . Un-used if a non-\T1/pcr/m/n/10 NULL
Underfull \hbox (badness 4660) in paragraph at lines 13286--13290
\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
Overfull \hbox (36.87935pt too wide) in paragraph at lines 13300--13304
[]\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][]\T1/pcr/m/n/10 insta
lled.packages[][][](lib.loc = lib.loc)\T1/ptm/m/n/10 .
Underfull \hbox (badness 10000) in paragraph at lines 13306--13311
[]\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 13306--13311
\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 13306--13311
\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[][][]
[2016]
Underfull \hbox (badness 1052) in paragraph at lines 13312--13314
[]\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and
in-stall. See
Underfull \hbox (badness 10000) in paragraph at lines 13342--13347
[]\T1/ptm/m/n/10 For how the list of suit-able avail-able pack-ages is de-ter-m
ined see
Underfull \hbox (badness 10000) in paragraph at lines 13342--13347
[][]\T1/pcr/m/n/10 available.packages[][][]\T1/ptm/m/n/10 . \T1/pcr/m/n/10 avai
lable = NULL \T1/ptm/m/n/10 make a call to
Underfull \hbox (badness 10000) in paragraph at lines 13342--13347
\T1/pcr/m/n/10 available.packages(contriburl = contriburl, method = method) \T1
/ptm/m/n/10 and
Underfull \hbox (badness 10000) in paragraph at lines 13363--13368
[]\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 13371--13374
[][][]\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 ,
[2017]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13425--13425
[]\T1/pcr/m/n/9 ## Not run: url.show("http://www.stats.ox.ac.uk/pub/datasets/c
sb/ch3a.txt")
[2018] [2019] [2020]
Underfull \hbox (badness 10000) in paragraph at lines 13613--13616
[][][]\T1/pcr/m/n/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi-
gnette browser;
Overfull \hbox (42.18039pt too wide) in paragraph at lines 13629--13629
[]\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:[]
[2021]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 13696--13696
[] \T1/pcr/m/n/9 lm(weight ~ (Time + I(Time^2)) * Diet, d
ata = DAT)))[]
[2022]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13718--13718
[] \T1/pcr/m/n/9 nls(weight ~ SSlogis(Time, Asym, xmid, scal),
data = DD)))[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 13737--13737
[]\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep =
" ",
[2023]
Underfull \hbox (badness 1454) in paragraph at lines 13764--13768
[]\T1/ptm/m/n/10 the char-ac-ter(s) to print at the end of each line (row). For
ex-am-ple,
Underfull \hbox (badness 1715) in paragraph at lines 13789--13792
[]\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 13834--13836
[]\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec-
tion
[2024]
Underfull \hbox (badness 3271) in paragraph at lines 13846--13850
\T1/ptm/m/n/10 set \T1/pcr/m/n/10 sep \T1/ptm/m/n/10 and \T1/pcr/m/n/10 dec \T1
/ptm/m/n/10 (see be-low), \T1/pcr/m/n/10 qmethod = "double"\T1/ptm/m/n/10 , and
\T1/pcr/m/n/10 col.names \T1/ptm/m/n/10 to \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 if
[2025] [2026]) [2027] [2028] (./KernSmooth-pkg.tex
Chapter 15.
[2029]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 124--124
[]\T1/pcr/m/n/10 bkde2D(x, bandwidth, gridsize = c(51L, 51L), range.x, truncat
e = TRUE)
[2030] [2031] [2032] [2033] [2034]
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[]\T1/pcr/m/n/10 dpill(x, y, blockmax = 5, divisor = 20, trim = 0.01, proptrun
= 0.05,
[2035] [2036] [2037] [2038]) (./MASS-pkg.tex
Chapter 16.
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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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[2061]
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[]\T1/ptm/m/n/10 logical. If true and the re-sult would be sparse (only true fo
r
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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"),[]
[2073] [2074] [2075] [2076]
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[]\T1/ptm/m/n/10 further ar-gu-ments for \T1/pcr/m/n/10 plot \T1/ptm/m/n/10 and
graph-i-cal pa-ram-e-ters. Note that
[2077] [2078] [2079]
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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 ,
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\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 ,
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[]\T1/ptm/m/n/10 For the fol-low-ing named dis-tri-bu-tions, rea-son-able start
-ing val-ues will be com-puted if
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\T1/pcr/m/n/10 start \T1/ptm/m/n/10 is omit-ted or only par-tially spec-i-fied:
\T1/pcr/m/n/10 "cauchy"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 ,
\T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 ,
[2080] [2081]
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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
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[]\T1/ptm/m/n/10 where \T1/pcr/m/n/10 p1\T1/ptm/m/n/10 , \T1/pcr/m/n/10 p2\T1/p
tm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/pcr/m/n
/10 cycles \T1/ptm/m/n/10 terms or when a
[2082] [2083] [2084]
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[] \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL
SE, ...)[]
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[]\T1/ptm/m/n/10 Fitted model ob-ject from a \T1/pcr/m/n/10 Gamma \T1/ptm/m/n/1
0 fam-ily or \T1/pcr/m/n/10 quasi \T1/ptm/m/n/10 fam-ily with
[2085]
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[]\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist =
"exponential")[]
[2086] [2087] [2088] [2089] [2090] [2091] [2092] [2093] [2094] [2095] [2096]
[2097]
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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
[2098] [2099] [2100] [2101] [2102] [2103] [2104]
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[] \T1/pcr/m/n/10 col = 5, xlab = deparse(substitute(data)), bty = "n",
...)[]
[2105] [2106]
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[2107]
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[]\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model
= FALSE,
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[2108] [2109] [2110] [2111] [2112]
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[]\T1/ptm/m/n/10 the quan-tile to be used: see \T1/pcr/m/n/10 Details\T1/ptm/m/
n/10 . This is over-ridden if
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[]\T1/ptm/m/n/10 the cut-off / tun-ing con-stant used for $\OML/cmm/m/it/10 ^^_
\OT1/cmr/m/n/10 ()$ \T1/ptm/m/n/10 and $\OML/cmm/m/it/10 \OT1/cmr/m/n/10 ()$ \
T1/ptm/m/n/10 func-tions when
[2113]
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[]\T1/ptm/m/n/10 the value of the cri-te-rion for the best so-lu-tion found, in
the case of
[2114] [2115] [2116] [2117] [2118] [2119] [2120] [2121]
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[]\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP
ACK = FALSE)
[2122]
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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")
[2123] [2124]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.npk}) has been already used, duplicate ignored
<to be read again>
\relax
l.6111 ...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.6111 ...sical N, P, K Factorial Experiment}{npk}
[2125]
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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
[2126] [2127] [2128] [2129]
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Overfull \hbox (9.78043pt too wide) in paragraph at lines 6527--6527
[] \T1/pcr/m/n/9 start = list(fixed=c(L75=c(48.7, -0.03), lsc=0.24)), verb
ose = TRUE)))[]
[2131]
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[] \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr
ellis"))[]
[2132] [2133] [2134] [2135] [2136] [2137]
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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"))[]
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[2138]
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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 ) =
[2139]
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[]\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da
ta = housing)[]
[2140] [2141]
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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
[2142] [2143]
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[]\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam
p = "exact")[]
[2144]
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[] \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC
V"), ...)[]
[2145] [2146] [2147] [2148] [2149] [2150]
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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
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[]\T1/ptm/m/n/10 where \T1/pcr/m/n/10 p1\T1/ptm/m/n/10 , \T1/pcr/m/n/10 p2\T1/p
tm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/pcr/m/n
/10 cycles \T1/ptm/m/n/10 terms or when a
[2151] [2152]
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[] \T1/pcr/m/n/10 maxit = 20, acc = 1e-4, test.vec = "resid", lqs.control =
NULL)[]
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[]\T1/ptm/m/n/10 A func-tion to spec-ify the ac-tion to be taken if \T1/pcr/m/n
/10 NA\T1/ptm/m/n/10 s are found. The
[2153] [2154] [2155] [2156] [2157] [2158] [2159] [2160] [2161] [2162] [2163]
[2164] [2165] [2166] [2167] [2168] [2169] [2170] [2171] [2172]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 9483--9483
[]\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS
E, ...)[]
[2173]
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[]\T1/ptm/m/n/10 how much the stu-dent smokes. (Fac-tor, lev-els \T1/pcr/m/n/10
"Heavy"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Regul" \T1/ptm/m/n/10 (reg-u-larly),
[2174]
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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)[]
[2175] [2176] [2177] [2178] [2179] [2180] [2181] [2182] [2183] [2184] [2185]
[2186] [2187]) (./Matrix-pkg.tex [2188]
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
[2189]
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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
[2190]
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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
[2191]
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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
[2192] [2193]
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[]\T1/pcr/m/n/10 bandSparse(n, m = n, k, diagonals, symmetric = FALSE, giveCsp
arse = TRUE)
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[]\T1/ptm/m/n/10 integer vec-tor of ``di-ag-o-nal num-bers'', with iden-ti-cal
mean-ing as in
[2194]
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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)],[]
[2195] [2196]
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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)[]
[2197]
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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 .
[2198] [2199] [2200]
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[]\T1/pcr/m/n/10 ## solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D
","P","Pt"), ...)[]
[2201]
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[]\T1/pcr/m/n/10 signature(from = "CHMfactor", to = "sparseMatrix") \T1/ptm/m/n
/10 (or equiv-a-
Underfull \hbox (badness 10000) in paragraph at lines 1045--1050
[]\T1/pcr/m/n/10 signature(x = "CHMfactor"): \T1/ptm/m/n/10 Plot the im-age of
the lower tri-
Underfull \hbox (badness 10000) in paragraph at lines 1045--1050
\T1/ptm/m/n/10 an-gu-lar fac-tor, $\OML/cmm/m/it/10 L$\T1/ptm/m/n/10 , from the
de-com-po-si-tion. This method is equiv-a-lent to
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\T1/pcr/m/n/10 image(as(x, "sparseMatrix")) \T1/ptm/m/n/10 so the com-ments in
the above de-scrip-tion of
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[]\T1/pcr/m/n/10 signature(x = "CHMfactor", logarithm = "logical")
[2202]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cho
l}) has been already used, duplicate ignored
<to be read again>
\relax
l.1134 ...- 'Matrix' S4 Generic and Methods}{chol}
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ation with the same identifier (name{Rfn.chol.1}) has been already used, duplic
ate ignored
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\relax
l.1134 ...- 'Matrix' S4 Generic and Methods}{chol}
[2203pdfTeX 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'
] [2204]
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[]\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur
e & factorization[]
[2205]
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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 1388--1391
[]\T1/ptm/m/n/10 This is a generic func-tion with spe-cial meth-ods for dif-fer
-ent types of ma-tri-ces. Use
[2206]
Underfull \hbox (badness 1609) in paragraph at lines 1435--1439
[]\T1/ptm/m/n/10 Class def-i-ni-tions [][]\T1/pcr/m/n/10 CHMfactor[][][] \T1/pt
m/m/n/10 and [][]\T1/pcr/m/n/10 dsCMatrix[][][] \T1/ptm/m/n/10 and func-tion []
[]\T1/pcr/m/n/10 expand[][][]\T1/ptm/m/n/10 . Note the ex-tra
[2207]
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[]\T1/pcr/m/n/9 ## hence, the identical() check *should* work, but fails on so
me GOTOblas:[]
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[]\T1/pcr/m/n/9 dq <- function(ch) paste(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/p
cr/m/n/9 '\T1/pcr/m/n/9 ,ch,\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/pcr/m/n/9 '\T1/
pcr/m/n/9 , sep="") ## dQuote(<UTF-8>) gives bad plots[]
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[]\T1/pcr/m/n/9 (opts <- expand.grid(perm = c(TRUE,FALSE), LDL = c(TRUE,FALSE)
, super = c(FALSE,TRUE)))[]
[2208]
Underfull \hbox (badness 6445) in paragraph at lines 1531--1538
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("Cholesky", ...) \T1/ptm/m/n/10 or
Underfull \hbox (badness 3861) in paragraph at lines 1531--1538
\T1/pcr/m/n/10 new("BunchKaufman", ...)\T1/ptm/m/n/10 , etc, or rather by calls
of the form [][]\T1/pcr/m/n/10 chol[][][](pm) \T1/ptm/m/n/10 or
Underfull \hbox (badness 1783) in paragraph at lines 1566--1570
[]\T1/ptm/m/n/10 Both these fac-tor-iza-tions can \T1/ptm/m/it/10 di-rectly \T1
/ptm/m/n/10 be treated as (tri-an-gu-lar) ma-tri-ces, as they ex-tend
Underfull \hbox (badness 1221) in paragraph at lines 1582--1588
\T1/ptm/m/n/10 ply an $\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10
n$ \T1/ptm/m/n/10 nu-meric [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 . Hen
ce, for com-pat-i-bil-ity, the \T1/pcr/m/n/10 "Cholesky" \T1/ptm/m/n/10 and
[2209]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col
Sums}) has been already used, duplicate ignored
<to be read again>
\relax
l.1623 ... Row and Column Sums and Means}{colSums}
pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.colSums.1}) has been already used, dup
licate ignored
<to be read again>
\relax
l.1623 ... Row and Column Sums and Means}{colSums}
pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.colMeans}) has been already used, dupl
icate ignored
<to be read again>
\relax
l.1624 \aliasA{colMeans}{colSums}{colMeans}
pdfTeX warning (ext4): destination w
ith the same identifier (name{Rfn.rowMeans}) has been already used, duplicate i
gnored
<to be read again>
\relax
l.1645 \aliasA{rowMeans}{colSums}{rowMeans}
pdfTeX warning (ext4): destination w
ith the same identifier (name{Rfn.rowSums}) has been already used, duplicate ig
nored
<to be read again>
\relax
l.1656 \aliasA{rowSums}{colSums}{rowSums}
[2210]
Underfull \hbox (badness 2922) in paragraph at lines 1710--1714
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sparse, i.e., i
n-her-it-ing from
Underfull \hbox (badness 1728) in paragraph at lines 1710--1714
\T1/ptm/m/n/10 class [][]\T1/pcr/m/n/10 sparseVector[][][]\T1/ptm/m/n/10 . Only
ap-pli-ca-ble when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is in-her-it-ing from a
Underfull \hbox (badness 1237) in paragraph at lines 1721--1724
[][][]\T1/pcr/m/n/10 dimnames[][][](x) \T1/ptm/m/n/10 are only kept (as [][]\T1
/pcr/m/n/10 names[][][](v)\T1/ptm/m/n/10 ) when the re-sult-ing \T1/pcr/m/n/10
v \T1/ptm/m/n/10 is [][]\T1/pcr/m/n/10 numeric[][][]\T1/ptm/m/n/10 , since
[2211]
Underfull \hbox (badness 10000) in paragraph at lines 1801--1805
[]\T1/pcr/m/n/10 signature(x = "compMatrix", value = "list")\T1/ptm/m/n/10 : se
t the
[2212]
Underfull \hbox (badness 3547) in paragraph at lines 1875--1878
[]\T1/ptm/m/n/10 a num-ber $\OML/cmm/m/it/10 > \OT1/cmr/m/n/10 0$\T1/ptm/m/n/10
, the es-ti-mated (1-norm) con-di-tion num-ber $[]$; when
[2213] [2214] [2215]
Underfull \hbox (badness 10000) in paragraph at lines 2112--2114
[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "ddenseMatrix
", where =
[2216] [2217]
Underfull \hbox (badness 10000) in paragraph at lines 2234--2236
[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "denseMatrix"
, where =
Underfull \hbox (badness 3068) in paragraph at lines 2295--2299
\T1/ptm/m/n/10 i-cally via \T1/pcr/m/n/10 as(*, "CsparseMatrix") \T1/ptm/m/n/10
or sim-i-lar. Of-ten how-ever, more eas-ily via
[2218]
Underfull \hbox (badness 4713) in paragraph at lines 2330--2332
[]\T1/pcr/m/n/10 signature(x = "dgCMatrix")\T1/ptm/m/n/10 : com-putes the LU de
-com-po-si-tion of a square
[2219]
Underfull \hbox (badness 10000) in paragraph at lines 2447--2450
[]\T1/pcr/m/n/10 signature(x = "dgeMatrix", norm = "character") \T1/ptm/m/n/10
or
[2220]
Underfull \hbox (badness 10000) in paragraph at lines 2549--2553
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("dgTMatrix", ...)\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 2549--2553
\T1/ptm/m/n/10 but more typ-i-cally via \T1/pcr/m/n/10 as(*, "dgTMatrix")\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 spMatrix[][][]()\T1/ptm/m/n/10 , or
[2221]
Underfull \hbox (badness 2707) in paragraph at lines 2605--2609
[]\T1/ptm/m/n/10 Note that both \T1/pcr/m/n/10 new(.) \T1/ptm/m/n/10 and [][]\T
1/pcr/m/n/10 spMatrix[][][] \T1/ptm/m/n/10 con-struc-tors for \T1/pcr/m/n/10 "d
gTMatrix" \T1/ptm/m/n/10 (and other
Underfull \hbox (badness 2368) in paragraph at lines 2610--2614
[]\T1/ptm/m/n/10 However this means that a ma-trix typ-i-cally can tbe stored i
n more than one pos-si-ble
Underfull \hbox (badness 10000) in paragraph at lines 2617--2620
[]\T1/ptm/m/n/10 Class [][]\T1/pcr/m/n/10 dgCMatrix[][][] \T1/ptm/m/n/10 or the
su-per-classes [][]\T1/pcr/m/n/10 dsparseMatrix[][][] \T1/ptm/m/n/10 and [][]\
T1/pcr/m/n/10 TsparseMatrix[][][]\T1/ptm/m/n/10 ;
[2222]
Underfull \hbox (badness 2689) in paragraph at lines 2673--2675
[]\T1/ptm/m/n/10 integer spec-i-fy-ing the di-men-sion of the (square) ma-trix.
If miss-ing,
Underfull \hbox (badness 10000) in paragraph at lines 2677--2682
[]\T1/ptm/m/n/10 for \T1/pcr/m/n/10 .symDiagonal \T1/ptm/m/n/10 (\T1/pcr/m/n/10
.trDiagonal\T1/ptm/m/n/10 ), the re-sult-ing sparse
Underfull \hbox (badness 3482) in paragraph at lines 2677--2682
[][]\T1/pcr/m/n/10 symmetricMatrix[][][] \T1/ptm/m/n/10 (or [][]\T1/pcr/m/n/10
triangularMatrix[][][]\T1/ptm/m/n/10 ) will have slot \T1/pcr/m/n/10 uplo
[2223]
Underfull \hbox (badness 1097) in paragraph at lines 2700--2703
[]\T1/pcr/m/n/10 Diagonal() \T1/ptm/m/n/10 re-turns an ob-ject of class [][]\T1
/pcr/m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 ldiMatrix[][][
] \T1/ptm/m/n/10 (with ``su-per-class''
Underfull \hbox (badness 1142) in paragraph at lines 2713--2718
[][]\T1/pcr/m/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 (the re-sult-ing class de
-pend-ing on \T1/pcr/m/n/10 shape \T1/ptm/m/n/10 and \T1/pcr/m/n/10 kind\T1/ptm
/m/n/10 ) rep-re-sen-ta-tion of
[2224]
Underfull \hbox (badness 3646) in paragraph at lines 2951--2954
[]\T1/ptm/m/n/10 the [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , a [][]\T
1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 , see the [][]\T1/pcr/m/n/10 Matrix[][][]
\T1/ptm/m/n/10 class de-scrip-tion. Typ-i-cally
Underfull \hbox (badness 10000) in paragraph at lines 2973--2974
[]\T1/pcr/m/n/10 signature(from = "diagonalMatrix", to = "triangularMatrix")\T1
/ptm/m/n/10 :
Underfull \hbox (badness 1810) in paragraph at lines 2980--2982
[]\T1/pcr/m/n/10 signature(a = "diagonalMatrix", b, ...)\T1/ptm/m/n/10 : is tri
v-ially im-ple-mented, of
Underfull \hbox (badness 10000) in paragraph at lines 2983--2985
[]\T1/pcr/m/n/10 signature(x = "nMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv
-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
Underfull \hbox (badness 3803) in paragraph at lines 2986--2990
[]\T1/pcr/m/n/10 signature(x = "diagonalMatrix")\T1/ptm/m/n/10 : all these grou
p meth-ods re-turn a
[2225]
Underfull \hbox (badness 1371) in paragraph at lines 2995--3001
[]\T1/pcr/m/n/10 signature(e1 = "ddiMatrix", e2="denseMatrix")\T1/ptm/m/n/10 :
the re-sult is from class
Underfull \hbox (badness 10000) in paragraph at lines 3002--3006
[]\T1/pcr/m/n/10 (object = "diagonalMatrix")\T1/ptm/m/n/10 : Re-turns an ob-jec
t of S3 class
Underfull \hbox (badness 2318) in paragraph at lines 3012--3016
[][][]\T1/pcr/m/n/10 Diagonal[][][]() \T1/ptm/m/n/10 as con-struc-tor of these
ma-tri-ces, and [][]\T1/pcr/m/n/10 isDiagonal[][][]\T1/ptm/m/n/10 . [][]\T1/pcr
/m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 and
[2226] [2227]
Underfull \hbox (badness 1859) in paragraph at lines 3196--3198
[]\T1/pcr/m/n/10 signature(x = "dMatrix", digits = "numeric")\T1/ptm/m/n/10 : t
his group con-tains
Underfull \hbox (badness 10000) in paragraph at lines 3243--3245
[][][]\T1/pcr/m/n/10 drop0[][][](x, tol=1e-10) \T1/ptm/m/n/10 is some-times pre
fer-able to (and more ef-fi-cient than)
[2228]
Underfull \hbox (badness 1168) in paragraph at lines 3363--3366
[]\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
[2229] [2230]
Underfull \hbox (badness 4967) in paragraph at lines 3528--3532
[]\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
[2231]
Overfull \hbox (2.39853pt too wide) in paragraph at lines 3533--3535
[]\T1/ptm/m/n/10 Creation ``from scratch'' most ef-fi-ciently hap-pens via [][]
\T1/pcr/m/n/10 sparseMatrix[][][](*, symmetric=TRUE)\T1/ptm/m/n/10 .
Underfull \hbox (badness 6364) in paragraph at lines 3575--3578
[]\T1/pcr/m/n/10 signature(a = "dsCMatrix", b = "....")\T1/ptm/m/n/10 : \T1/pcr
/m/n/10 x <- solve(a,b) \T1/ptm/m/n/10 solves
[2232] [2233]
Underfull \hbox (badness 10000) in paragraph at lines 3725--3730
[]\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 3725--3730
\T1/ptm/m/n/10 class \T1/pcr/m/n/10 "dsparseMatrix" \T1/ptm/m/n/10 or \T1/pcr/m
/n/10 "RsparseMatrix"\T1/ptm/m/n/10 ; class \T1/pcr/m/n/10 "compMatrix" \T1/ptm
/m/n/10 by class
Underfull \hbox (badness 10000) in paragraph at lines 3735--3737
[]\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "missing")\T1/ptm/m/n/10 : a
triv-ial
Underfull \hbox (badness 10000) in paragraph at lines 3737--3740
[]\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "character")\T1/ptm/m/n/10 :
if
[2234]
Underfull \hbox (badness 4967) in paragraph at lines 3813--3815
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 3852--3855
[]\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")\T1/ptm/m/n/10 ,
or
Underfull \hbox (badness 1735) in paragraph at lines 3852--3855
\T1/pcr/m/n/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 type = "missing
"\T1/ptm/m/n/10 : Com-putes the ma-trix norm of the
[2235]
Underfull \hbox (badness 10000) in paragraph at lines 3855--3858
[]\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")\T1/ptm/m/n/10 ,
or
Underfull \hbox (badness 2318) in paragraph at lines 3855--3858
\T1/pcr/m/n/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 type = "missing
"\T1/ptm/m/n/10 : Com-putes the re-cip-ro-cal con-di-tion
Underfull \hbox (badness 6364) in paragraph at lines 3859--3862
[]\T1/pcr/m/n/10 signature(a = "dsyMatrix", b = "....")\T1/ptm/m/n/10 : \T1/pcr
/m/n/10 x <- solve(a,b) \T1/ptm/m/n/10 solves
[2236]
Underfull \hbox (badness 4060) in paragraph at lines 3983--3986
[]\T1/pcr/m/n/10 signature(a = "dtCMatrix", b = "....")\T1/ptm/m/n/10 : sparse
tri-an-gu-lar solve (aka
[2237]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4023--4023
[]\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 4091--4095
[]\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
[2238]
Underfull \hbox (badness 10000) in paragraph at lines 4100--4103
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix", y = "dgeMatrix")\T1/ptm/m/n/10 : Ma
-
Underfull \hbox (badness 10000) in paragraph at lines 4100--4103
\T1/ptm/m/n/10 trix mul-ti-pli-ca-tion; ditto for sev-eral other sig-na-ture co
m-bi-na-tions, see
Underfull \hbox (badness 10000) in paragraph at lines 4105--4109
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix", logarithm = "logical")\T1/ptm/m/n/1
0 : the
[2239] [2240] [2241] [2242]
Underfull \hbox (badness 10000) in paragraph at lines 4393--4398
[]\T1/ptm/m/n/10 The ex-po-nen-tial of a ma-trix is de-fined as the in-fi-nite
Tay-lor se-ries
[2243] [2244]
Overfull \hbox (85.38034pt too wide) in paragraph at lines 4527--4527
[] \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 4530--4530
[] \T1/pcr/m/n/9 readMM(gzcon(url("ftp://math.nist.gov/pub/MatrixMarket2/Harwe
ll-Boeing/counterx/jgl009.mtx.gz"))))[]
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[]\T1/pcr/m/n/9 ## Store as MatrixMarket (".mtx") file, here inside temporary
dir./folder:[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4537--4537
[]\T1/pcr/m/n/9 file.info(MMfile)[,c("size", "ctime")] # (some confirmation of
the file\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s)[]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 4547--4547
[]\T1/pcr/m/n/9 ## has columns (i, j, x) -> we can use via do.call() as argume
nts to sparseMatrix():[]
[2245] [2246]
Underfull \hbox (badness 10000) in paragraph at lines 4702--4704
[][][]\T1/pcr/m/n/10 symmpart[][][] \T1/ptm/m/n/10 for the sym-met-ric part of
a ma-trix, or the co-er-cions
[2247] [2248]
Underfull \hbox (badness 10000) in paragraph at lines 4849--4854
[]\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 ,
[2249]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4930--4930
[]\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 4932--4932
[] \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 4936--4936
[] \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE,
dimnames=dns))[]
[2250]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4943--4943
[] \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 '[]
[2251]
Underfull \hbox (badness 10000) in paragraph at lines 5068--5073
[]\T1/ptm/m/n/10 color for the bor-der of each rect-an-gle. \T1/pcr/m/n/10 NA \
T1/ptm/m/n/10 means
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\T1/ptm/m/n/10 no bor-der is drawn. When \T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 as
by de-fault,
Underfull \hbox (badness 2644) in paragraph at lines 5068--5073
\T1/pcr/m/n/10 border.col <- if(lwd < .01) NA else NULL \T1/ptm/m/n/10 is used.
Con-
Underfull \hbox (badness 4108) in paragraph at lines 5068--5073
\T1/ptm/m/n/10 sider us-ing an opaque color in-stead of \T1/pcr/m/n/10 NULL \T1
/ptm/m/n/10 which cor-re-sponds to
[2252]
Underfull \hbox (badness 4120) in paragraph at lines 5087--5090
[]\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 5124--5124
[]\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 5130--5130
[] \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 5131--5131
[] \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 5134--5134
[]\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 5136--5136
[]\T1/pcr/m/n/9 if(doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CH
ECK_EXTRA")) ||[]
[2253]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5143--5143
[]\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[]
[2254]
Underfull \hbox (badness 1817) in paragraph at lines 5235--5244
[]\T1/ptm/m/n/10 While ``row-indexing'' (of more than one row \T1/ptm/m/it/10 o
r \T1/ptm/m/n/10 us-ing \T1/pcr/m/n/10 drop=FALSE\T1/ptm/m/n/10 ) stays within
the
Underfull \hbox (badness 5637) in paragraph at lines 5277--5279
[]\T1/pcr/m/n/10 signature(x = "matrix", y = "indMatrix") \T1/ptm/m/n/10 and ot
her sig-na-tures (use
[2255]
Underfull \hbox (badness 3138) in paragraph at lines 5303--5305
[]\T1/pcr/m/n/10 signature(x = "indMatrix")\T1/ptm/m/n/10 : re-turn the
[2256]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 5370--5370
[] \T1/pcr/m/n/9 if(getRversion() >= "3.2.0") identical(I12, rbind(I1
, I2)) else TRUE,[]
Underfull \hbox (badness 1603) in paragraph at lines 5391--5393
[]\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 p \T1/ptm/m/n/10 con-t
ains val-ues \T1/pcr/m/n/10 0:(n-1) \T1/ptm/m/n/10 or rather (by de-fault,
Underfull \hbox (badness 10000) in paragraph at lines 5399--5404
[]\T1/ptm/m/n/10 an in-te-ger vec-tor of the same length (\T1/pcr/m/n/10 n\T1/p
tm/m/n/10 ) as \T1/pcr/m/n/10 p\T1/ptm/m/n/10 . By de-fault,
Underfull \hbox (badness 10000) in paragraph at lines 5399--5404
\T1/ptm/m/n/10 (\T1/pcr/m/n/10 zero.p = FALSE, zero.res = FALSE\T1/ptm/m/n/10 )
, \T1/pcr/m/n/10 invPerm(p) \T1/ptm/m/n/10 is the same as
Underfull \hbox (badness 10000) in paragraph at lines 5399--5404
[][]\T1/pcr/m/n/10 order[][][](p) \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 sort.lis
t[][][](p) \T1/ptm/m/n/10 and for that case, the func-tion is equiv-a-lent to
[2257] [2258] [2259]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5628--5628
[]\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[]
[2260]
Underfull \hbox (badness 10000) in paragraph at lines 5709--5712
[][][]\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 5720--5720
[]\T1/pcr/m/n/9 isTriangular(as(M, "dgeMatrix")) # still triangular, even if n
ot "formally"[]
[2261]
Underfull \hbox (badness 1622) in paragraph at lines 5757--5762
[]\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 5757--5762
\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
[2262]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5818--5818
[]\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 5819--5819
[] \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 5826--5826
[] \T1/pcr/m/n/9 identical(dimnames(KhatriRao(m, d0, make.dimnames=TRUE)), di
mnames(Kmd)))[]
[2263]
Underfull \hbox (badness 1062) in paragraph at lines 5955--5958
[]\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
[2264]
Underfull \hbox (badness 2809) in paragraph at lines 5984--5987
[]\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
[2265]
Underfull \hbox (badness 2635) in paragraph at lines 6096--6101
[]\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 6096--6101
\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 6104--6107
[]\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.,
[2266]
Underfull \hbox (badness 10000) in paragraph at lines 6214--6224
\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 6214--6224
[][]\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
[2267]
Underfull \hbox (badness 1184) in paragraph at lines 6296--6299
[]\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
[2268]
Underfull \hbox (badness 10000) in paragraph at lines 6394--6397
[]\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.,
[2269]
Underfull \hbox (badness 10000) in paragraph at lines 6469--6472
[]\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 6485--6485
[]\T1/pcr/m/n/9 str(lutp <- as(lutr, "ltpMatrix"))# packed matrix: only 10 = (
4+1)*4/2 entries[]
[2270]
Underfull \hbox (badness 2443) in paragraph at lines 6524--6530
[]\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 6524--6530
[][]\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 6545--6548
[]\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
[2271]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6615--6615
[] \T1/pcr/m/n/9 # q is a 0-based permutation o
f the columns[]
[2272] [2273]
Underfull \hbox (badness 6268) in paragraph at lines 6751--6754
[]\T1/ptm/m/n/10 Note that when the re-sult-ing ma-trix is di-ag-o-nal (``math-
e-mat-i-cally''),
[2274]
Underfull \hbox (badness 5036) in paragraph at lines 6775--6779
[]\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 6775--6779
\T1/pcr/m/n/10 Matrix(0, nrow,ncol) \T1/ptm/m/n/10 di-rectly con-structs an ``e
mpty'' [][]sparse-Ma-trix[][][], as does
[2275]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det
}) has been already used, duplicate ignored
<to be read again>
\relax
l.6868 \aliasA{det}{Matrix-class}{det}
Underfull \hbox (badness 1348) in paragraph at lines 6948--6951
[]\T1/pcr/m/n/10 signature(x = "Matrix")\T1/ptm/m/n/10 : As [][]\T1/pcr/m/n/10
diff[][][]() \T1/ptm/m/n/10 for tra-di-tional ma-tri-ces, i.e., ap-ply-ing
Underfull \hbox (badness 10000) in paragraph at lines 6953--6956
[]\T1/pcr/m/n/10 signature(x = "Matrix", value = "ANY")\T1/ptm/m/n/10 : where \
T1/pcr/m/n/10 value \T1/ptm/m/n/10 is
Underfull \hbox (badness 10000) in paragraph at lines 6953--6956
\T1/ptm/m/n/10 in-te-ger of length 2. Al-lows to \T1/ptm/m/it/10 re-shape \T1/p
tm/m/n/10 Ma-trix ob-jects, but only when
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Underfull \hbox (badness 7326) in paragraph at lines 6981--6983
[]\T1/pcr/m/n/10 signature(from = "ANY", to = "Matrix")\T1/ptm/m/n/10 : This re
-lies on a cor-rect
[2276]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.7044 ...*\%}{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.7152 ...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.7252 ...tcrossprod}{matrix-products}{tcrossprod}
[2277]
Underfull \hbox (badness 1881) in paragraph at lines 7350--7356
\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
[2278pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cros
sprod.Rdash.methods}) has been already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox
\fi \fi
l.7412 \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.7412 \end{Details}
]
Underfull \hbox (badness 10000) in paragraph at lines 7423--7426
[]\T1/pcr/m/n/10 signature(x = "dgeMatrix", y = "dgeMatrix")\T1/ptm/m/n/10 : Ma
-
Underfull \hbox (badness 10000) in paragraph at lines 7423--7426
\T1/ptm/m/n/10 trix mul-ti-pli-ca-tion; ditto for sev-eral other sig-na-ture co
m-bi-na-tions, see
Underfull \hbox (badness 5637) in paragraph at lines 7426--7431
[]\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") \T1/ptm/m/n/10 and ot
her sig-na-tures (use
Underfull \hbox (badness 10000) in paragraph at lines 7435--7437
[]\T1/pcr/m/n/10 signature(x = "CsparseMatrix", y = "missing") \T1/ptm/m/n/10 r
e-turns
Underfull \hbox (badness 10000) in paragraph at lines 7437--7439
[]\T1/pcr/m/n/10 signature(x = "TsparseMatrix", y = "missing") \T1/ptm/m/n/10 r
e-turns
Underfull \hbox (badness 10000) in paragraph at lines 7441--7442
[]\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") \T1/ptm/m/n/10
and
[2279] [2280]
Underfull \hbox (badness 1062) in paragraph at lines 7622--7625
[]\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
[2281]
Underfull \hbox (badness 2809) in paragraph at lines 7656--7659
[]\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
[2282]
Underfull \hbox (badness 10000) in paragraph at lines 7708--7710
[]\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 X <- (X + t(X))/2 \T1/
ptm/m/n/10 should be done, af-ter
[2283]
Underfull \hbox (badness 1406) in paragraph at lines 7748--7752
[]\T1/ptm/m/n/10 Higham (2002) uses Dyk-stra's cor-rec-tion, but the ver-sion b
y Jens Oehlschlaegel did not
Underfull \hbox (badness 1019) in paragraph at lines 7748--7752
\T1/ptm/m/n/10 use it (ac-ci-den-tally), and has still lead to good re-sults; t
his sim-pli-fi-ca-tion, now only via
[2284]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 7846--7846
[]\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 [2285]
Underfull \hbox (badness 2635) in paragraph at lines 7911--7916
[]\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 7911--7916
\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 7919--7922
[]\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.,
[2286] [2287]
Underfull \hbox (badness 10000) in paragraph at lines 8113--8115
[]\T1/ptm/m/n/10 fast
[2288]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.nor
m}) has been already used, duplicate ignored
<to be read again>
\relax
l.8153 \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.8153 \HeaderA{norm}{Matrix Norms}{norm}
[2289]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8240--8240
[]\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 8241--8241
[]\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 8242--8242
[]\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 8355--8365
[]\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 ,
[2290]
Underfull \hbox (badness 1184) in paragraph at lines 8426--8429
[]\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
[2291]
Underfull \hbox (badness 10000) in paragraph at lines 8516--8519
[]\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.,
[2292]
Underfull \hbox (badness 10000) in paragraph at lines 8592--8595
[]\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.,
[2293]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 8608--8608
[]\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
[2294]
Underfull \hbox (badness 10000) in paragraph at lines 8718--8720
[]\T1/pcr/m/n/10 signature(x = "matrix", y = "pMatrix") \T1/ptm/m/n/10 and othe
r sig-na-tures (use
Underfull \hbox (badness 1596) in paragraph at lines 8734--8736
[]\T1/pcr/m/n/10 signature(from = "pMatrix", to = "ngTMatrix")\T1/ptm/m/n/10 :
co-er-cion to sparse
Underfull \hbox (badness 1721) in paragraph at lines 8740--8744
\T1/ptm/m/n/10 ma-trix; note that \T1/pcr/m/n/10 solve(P) \T1/ptm/m/n/10 is ide
n-ti-cal to \T1/pcr/m/n/10 t(P) \T1/ptm/m/n/10 for per-mu-ta-tion ma-tri-ces. S
ee
[2295] [2296]
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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 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[]
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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 8852--8862
\T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro
m
[2297] [2298]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.qr}) has been already used, duplicate ignored
<to be read again>
\relax
l.8953 \aliasA{qr}{qr-methods}{qr}
Underfull \hbox (badness 5119) in paragraph at lines 8999--9002
[]\T1/ptm/m/n/10 QR de-com-po-si-tion of a gen-eral sparse double-precision ma-
trix with
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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![]
[2299]
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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[]
[2300]
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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 9136--9139
[]\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
[2301]
Overfull \hbox (85.38034pt too wide) in paragraph at lines 9208--9208
[]\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"[]
[2302]
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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.9249 ... the Reciprocal Condition Number}{rcond}
[2303]
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[]\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not
have full rank[]
[2304] [2305] [2306]
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[]\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 gets \T1/pcr/m/n/10 x <- rand.x(nnz) \T1/ptm/m/n/10 and calls []
[]\T1/pcr/m/n/10 sparseMatrix[][][](i=i, j=j, x=x, ..)\T1/ptm/m/n/10 . When
[2307] [2308]
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[]\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
[2309]
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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:[]
[2310]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sol
ve}) has been already used, duplicate ignored
<to be read again>
\relax
l.9826 \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[]
[2311]
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 solve \T1/ptm/m/n/10 meth-ods
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[]\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 basically com-putes uses tri-an-gu-lar
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[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list
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\T1/pcr/m/n/10 ( sparse = FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : U
ses the sparse
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[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list
Underfull \hbox (badness 2165) in paragraph at lines 10002--10012
\T1/pcr/m/n/10 ( sparse=FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : Che
cks if \T1/pcr/m/n/10 a \T1/ptm/m/n/10 is sym-
[2312]
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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 , and sim-i-lar \T1/pcr/m/n/10 b\T1/ptm/m/n/10 , in-clud-ing
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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
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10095--10095
[]\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[]
[2313]
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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,
Underfull \hbox (badness 10000) in paragraph at lines 10156--10159
[]\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
[2314]
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[]\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for
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\T1/pcr/m/n/10 sparse.model.matrix \T1/ptm/m/n/10 has been changed to \T1/pcr/m
/n/10 FALSE\T1/ptm/m/n/10 , 2010-07, for
Underfull \hbox (badness 6592) in paragraph at lines 10178--10180
[]\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
[2315]
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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),[]
[2316] [2317]
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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)[]
[2318]
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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
[2319]
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[]\T1/ptm/m/n/10 The stan-dard \T1/phv/m/n/10 R [][]\T1/pcr/m/n/10 xtabs[][][](
*, sparse=TRUE)\T1/ptm/m/n/10 , for sparse ta-bles and
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[]\T1/pcr/m/n/9 (A <- sparseMatrix(i, j, x = x)) ## 8 x 10
"dgCMatrix"[]
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[]\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10
"dsCMatrix"[]
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[]\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10
"dtCMatrix"[]
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[]\T1/pcr/m/n/9 (AA <- sparseMatrix(c(1,3:8), c(2,9,6:10), x = 7 * (1:7), dims
= c(10,20)))[]
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[]\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar
e consistent[]
[2320]
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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)[]
[2321]
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[]\T1/pcr/m/n/10 (object = "sparseMatrix")\T1/ptm/m/n/10 : Re-turns an ob-ject
of S3 class
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[]\T1/pcr/m/n/10 signature(x = "sparseMatrix", value = "ANY")\T1/ptm/m/n/10 : a
l-lows to \T1/ptm/m/it/10 re-shape \T1/ptm/m/n/10 a
[2322]
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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.10821 \aliasA{qr.Q}{sparseQR-class}{qr.Q}
[2323] [2324]
Underfull \hbox (badness 1430) in paragraph at lines 10951--10953
[]\T1/pcr/m/n/10 signature(a = "sparseQR", b = "ANY")\T1/ptm/m/n/10 : For \T1/p
cr/m/n/10 solve(a,b)\T1/ptm/m/n/10 , sim-ply uses
Overfull \hbox (58.38037pt too wide) in paragraph at lines 10979--10979
[] \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
[2325]
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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 11140--11146
\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 ,
[2326]
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[]\T1/pcr/m/n/10 signature(x = "sparseVector", mode = "character") \T1/ptm/m/n/
10 co-erces
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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
[2327]
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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
Underfull \hbox (badness 10000) in paragraph at lines 11246--11248
[][][]\T1/pcr/m/n/10 sparseVector[][][]() \T1/ptm/m/n/10 for friendly con-struc
-tion of sparse vec-tors (apart from
[2328] [2329]
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[]\T1/ptm/m/n/10 The ma-trix $\OML/cmm/m/it/10 M$ \T1/ptm/m/n/10 will have \T1/
pcr/m/n/10 M[i[k], j[k]] == x[k]\T1/ptm/m/n/10 , for $\OML/cmm/m/it/10 k \OT1/c
mr/m/n/10 = 1\OML/cmm/m/it/10 ; \OT1/cmr/m/n/10 2\OML/cmm/m/it/10 ; [] ; n$\T1/
ptm/m/n/10 , where
Underfull \hbox (badness 1831) in paragraph at lines 11371--11377
[][][]\T1/pcr/m/n/10 Matrix[][][](*, sparse=TRUE) \T1/ptm/m/n/10 for the more u
sual con-struc-tor of such ma-tri-ces. Then,
[2330]
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[]\T1/pcr/m/n/10 signature(object = "symmetricMatrix")\T1/ptm/m/n/10 : re-turns
\T1/ptm/m/it/10 sym-met-ric
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[][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , even when the \T1/pcr/m/n/10
Dimnames \T1/ptm/m/n/10 slot only has row or col-umn names. This
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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 1259) in paragraph at lines 11482--11487
\T1/pcr/m/n/10 list(NULL, <character>)\T1/ptm/m/n/10 , e.g., for ef-fi-ciency.
How-ever, [][]\T1/pcr/m/n/10 dimnames[][][]() \T1/ptm/m/n/10 and other
Underfull \hbox (badness 2591) in paragraph at lines 11490--11495
\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
[2331]
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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.,
[2332] [2333]
Underfull \hbox (badness 6641) in paragraph at lines 11648--11651
[]\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
[2334]
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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
[2335] [2336] [2337]
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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
[2338]
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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)[]
[2339] [2340]
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[]\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back
[2341] [2342] [2343]) (./boot-pkg.tex [2344]
Chapter 18.
[2345] [2346] [2347] [2348] [2349] [2350] [2351]
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[]\T1/pcr/m/n/10 boot(data, statistic, R, sim = "ordinary", stype = c("i", "f"
, "w"),
[2352]
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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-
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\T1/ptm/m/n/10 lems. This may be spec-i-fied for any sim-u-la-tion, but is ig-n
ored when
[2353]
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[]\T1/ptm/m/n/10 logical, only al-lowed to be \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/1
0 for \T1/pcr/m/n/10 sim = "ordinary", stype = "i", n = 0
[2354]
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\T1/ptm/m/n/10 or \T1/pcr/m/n/10 parallel = "snow" \T1/ptm/m/n/10 us-ing the de
-fault clus-ter, a sec-ond ap-proach is used if
[2355]
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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 6493) in paragraph at lines 851--855
[][][]\T1/pcr/m/n/10 boot.array[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.c
i[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 censboot[][][]\T1/ptm/m/n/10 , [][]\
T1/pcr/m/n/10 empinf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 tilt.boot[][][]\T1/ptm/m/n/10 ,
[2356]
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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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[2358]
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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
[2359]
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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
[2360] [2361] [2362] [2363]
Underfull \hbox (badness 1571) in paragraph at lines 1443--1445
[]\T1/ptm/m/n/10 Rawlings, J.O. (1988) \T1/ptm/m/it/10 Ap-plied Re-gres-sion An
al-y-sis\T1/ptm/m/n/10 . Wadsworth and Brooks/Cole Statis-
[2364] [2365] [2366] [2367] [2368]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1735--1735
[]\T1/pcr/m/n/10 censboot(data, statistic, R, F.surv, G.surv, strata = matrix(
1,n,2),
[2369] [2370] [2371]
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[]\T1/pcr/m/n/9 mel.cox <- coxph(Surv(time, status == 1) ~ ns(thickness, df=4)
+ strata(ulcer),[]
[2373]
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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.
[2374] [2375] [2376]
Underfull \hbox (badness 1565) in paragraph at lines 2335--2340
[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est on the ori
g-i-nal data set
[2377]
Underfull \hbox (badness 4595) in paragraph at lines 2360--2365
\T1/ptm/m/n/10 are passed un-changed ev-ery time \T1/pcr/m/n/10 boot.out$statis
tic \T1/ptm/m/n/10 is called.
Underfull \hbox (badness 1881) in paragraph at lines 2429--2431
[]\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi
-cient boot-strap sim-u-la-tion.
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[][][]\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 ,
[2378] [2379]
Underfull \hbox (badness 1077) in paragraph at lines 2533--2537
[]\T1/ptm/m/n/10 The un-bi-ased es-ti-ma-tor uses a mul-ti-plier of \T1/pcr/m/n
/10 n/((n-1)*(n-2)) \T1/ptm/m/n/10 where \T1/pcr/m/n/10 n \T1/ptm/m/n/10 is the
sam-ple
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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
[2380] [2381] [2382] [2383] [2384]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2892--2892
[]\T1/pcr/m/n/10 EEF.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t
= 25,
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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,[]
[2385] [2386] [2387]
Underfull \hbox (badness 3861) in paragraph at lines 3102--3105
[][][]\T1/pcr/m/n/10 boot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.array[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.ci[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 control[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[][][
]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 linear.approx[][][]\T1/ptm/m/n/10 ,
[2388]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 3155--3155
[]\T1/pcr/m/n/10 envelope(boot.out = NULL, mat = NULL, level = 0.95, index = 1
:ncol(mat))
[2389] [2390] [2391]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3375--3375
[]\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t
he resampling
[2392] [2393] [2394] [2395] [2396] [2397] [2398]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3835--3835
[] \T1/pcr/m/n/10 t = boot.out$t[, index], w = NULL, def = TRUE, q
= NULL)[]
[2399] [2400]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3974--3974
[]\T1/pcr/m/n/9 grav.p <- imp.prob(grav.tilt.boot, w = grav.w, index = 3, t0 =
grav.z0[3])[]
[2401] [2402] [2403]
Underfull \hbox (badness 10000) in paragraph at lines 4187--4189
[]\T1/ptm/m/n/10 The quan-tiles at which the plots are re-quired. The de-fault
is
[2404]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4256--4256
[]\T1/pcr/m/n/9 # To draw the jackknife-after-bootstrap plot for the head siz
e data as in
[2405] [2406]
Underfull \hbox (badness 10000) in paragraph at lines 4359--4361
[]\T1/ptm/m/n/10 The in-dex of the vari-able of in-ter-est within the out-put o
f
Underfull \hbox (badness 1430) in paragraph at lines 4368--4372
\T1/ptm/m/n/10 If \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is sup-plied but nei-ther \T
1/pcr/m/n/10 t \T1/ptm/m/n/10 nor \T1/pcr/m/n/10 L \T1/ptm/m/n/10 are sup-plied
then \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is set to
Underfull \hbox (badness 2269) in paragraph at lines 4386--4389
[]\T1/ptm/m/n/10 The lin-ear ap-prox-i-ma-tion to a boot-strap repli-cate with
fre-quency vec-tor \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is given by
[2407] [2408] [2409] [2410] [2411] [2412] [2413] [2414] [2415]
Underfull \hbox (badness 3000) in paragraph at lines 4956--4959
[]\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put
of a call to
[2416] [2417] [2418] [2419]
Underfull \hbox (badness 2293) in paragraph at lines 5235--5238
[]\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the
boot-strap
Underfull \hbox (badness 1668) in paragraph at lines 5235--5238
\T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl
os-est to
[2420]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5314--5314
[]\T1/pcr/m/n/9 grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w", strat
a = grav1[, 2])[]
[2421] [2422] [2423] [2424] [2425] [2426] [2427] [2428]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5863--5863
[]\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c
ity.sp1$spa[1][]
[2429]
Underfull \hbox (badness 1127) in paragraph at lines 5985--6003
\T1/ptm/m/n/10 etc. un-til a point is found with a cdf ap-prox-i-ma-tion less t
han \T1/pcr/m/n/10 min(alpha)/10\T1/ptm/m/n/10 , then
[2430]
Underfull \hbox (badness 2837) in paragraph at lines 6018--6021
[]\T1/ptm/m/n/10 The re-turned value is an ob-ject of class \T1/pcr/m/n/10 "sad
dle.distn"\T1/ptm/m/n/10 . See the help file for
[2431] [2432] [2433] [2434]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6303--6303
[]\T1/pcr/m/n/9 # This example is taken from Exercise 7.5 of Gill, Murray and
Wright (1991).
[2435] [2436]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6492--6492
[]\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t
he resampling
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6494--6494
[]\T1/pcr/m/n/9 # value of the test statistic 1.84. In the book exponential t
ilting was used[]
[2437] [2438] [2439]
Underfull \hbox (badness 1596) in paragraph at lines 6739--6743
[]\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sec-ond ar-gu-m
ent ex-pected by
[2440] [2441]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6899--6899
[] \T1/pcr/m/n/9 stype = "i", sim = "balanced", alpha =
c(0.05, 0.95),[]
[2442] [2443] [2444] [2445] [2446] [2447] [2448] [2449]) (./class-pkg.tex
[2450]
Chapter 19.
[2451] [2452] [2453] [2454] [2455] [2456] [2457] [2458]
Underfull \hbox (badness 10000) in paragraph at lines 608--610
[]\T1/ptm/m/n/10 the size of the code-book. De-faults to
[2459] [2460] [2461] [2462] [2463] [2464] [2465] [2466]) (./cluster-pkg.tex
Chapter 20.
[2467]
Underfull \hbox (badness 3098) in paragraph at lines 133--142
[]\T1/ptm/b/n/10 Care \T1/ptm/m/n/10 and ex-per-tise is prob-a-bly needed when
us-ing \T1/pcr/m/n/10 method = "flexible" \T1/ptm/m/n/10 par-tic-u-
Underfull \hbox (badness 2253) in paragraph at lines 133--142
\T1/ptm/m/n/10 larly for the case when \T1/pcr/m/n/10 par.method \T1/ptm/m/n/10
is spec-i-fied of longer length than one. Since
Underfull \hbox (badness 3323) in paragraph at lines 133--142
\T1/ptm/b/n/10 clus-ter \T1/ptm/m/n/10 ver-sion 2.0, choices lead-ing to in-val
id \T1/pcr/m/n/10 merge \T1/ptm/m/n/10 struc-tures now sig-nal an er-ror
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\T1/ptm/m/n/10 as \T1/pcr/m/n/10 method="flexible", par.method = 0.5\T1/ptm/m/n
/10 . Fur-ther, \T1/pcr/m/n/10 method= "single"
Underfull \hbox (badness 10000) in paragraph at lines 133--142
\T1/ptm/m/n/10 is equiv-a-lent to \T1/pcr/m/n/10 method="flexible", par.method
= c(.5,.5,0,-.5)\T1/ptm/m/n/10 , and
Overfull \hbox (48.49016pt too wide) in paragraph at lines 133--142
\T1/pcr/m/n/10 method="complete" \T1/ptm/m/n/10 is equiv-a-lent to \T1/pcr/m/n/
10 method="flexible", par.method = c(.5,.5,0,+.5)\T1/ptm/m/n/10 .
[2468]
Underfull \hbox (badness 10000) in paragraph at lines 167--169
[]\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 method = "gaverage", par.method = 0 \
T1/ptm/m/n/10 (or \T1/pcr/m/n/10 par.method =
[2469]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 252--252
[] \T1/pcr/m/n/9 all.equal(a.wgt [iC], agnes(d.vr, method="flexible", par.met
hod = 0.5)[iC]) ,[]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 253--253
[] \T1/pcr/m/n/9 all.equal(a.sing[iC], agnes(d.vr, method="flex", par.method=
c(.5,.5,0, -.5))[iC]),[]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 254--254
[] \T1/pcr/m/n/9 all.equal(a.comp[iC], agnes(d.vr, method="flex", par.method=
c(.5,.5,0, +.5))[iC]))[]
[2470] [2471]
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[2473]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 518--518
[] \T1/pcr/m/n/10 col = c(2, 0), border = 0, axes = TRUE, frame.plot
= axes,[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 522--522
[] \T1/pcr/m/n/10 yaxRight = fromLeft, y.mar = 2.4 + max.strlen/2.5,
...)[]
[2474]
Underfull \hbox (badness 5374) in paragraph at lines 539--541
[]\T1/ptm/m/n/10 logical in-di-cat-ing the ban-ner should be framed; mainly use
d when
[2475]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 637--637
[] \T1/pcr/m/n/10 keep.data = medoids.x, rngR = FALSE, pamLike = FALSE, c
orrect.d = TRUE)[]
[2476]
Underfull \hbox (badness 3078) in paragraph at lines 688--691
[]\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
[2477] [2478]
Underfull \hbox (badness 2941) in paragraph at lines 778--781
[][][]\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 816--816
[]\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo
r this seed):[]
[2479]
Underfull \hbox (badness 10000) in paragraph at lines 863--865
[]\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p
le, see
[2480]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 928--928
[] \T1/pcr/m/n/10 arrowArgs = list(col="red3", length=1/16, angle=90, code
=3), ...)[]
[2481]
Underfull \hbox (badness 4872) in paragraph at lines 974--976
[]\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 988--992
[]\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in
2012,
[2482]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1095--1095
[] \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE.
factor = SEf)))[]
[2483]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 1112--1112
[]\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 1150--1150
[]\T1/pcr/m/n/9 plot(gsP.Z, main = "clusGap(<iid_rnorm_p=3>) ==> k = 1 clust
er is optimal")[]
[2484]
Underfull \hbox (badness 4144) in paragraph at lines 1182--1186
[]\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
[2485]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 1258--1258
[] \T1/pcr/m/n/10 col.clus = if(color) c(2, 4, 6, 3) else 5, cex = 1,
cex.txt = cex,[]
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[] \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin
t variability."),[]
[2486] [2487]
Underfull \hbox (badness 10000) in paragraph at lines 1403--1408
[]\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 1451--1454
[2488]
Underfull \hbox (badness 10000) in paragraph at lines 1468--1472
[][][]\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 1492--1492
[]\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 1502--1502
[] \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i
dent. only points[]
[2489]
Underfull \hbox (badness 5741) in paragraph at lines 1542--1545
[]\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
[2490]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1608--1608
[] \T1/pcr/m/n/10 warnBin = warnType, warnAsym = warnType, warnConst = wa
rnType,[]
[2491]
Underfull \hbox (badness 5008) in paragraph at lines 1725--1733
\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
[2492] [2493]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1816--1816
[]\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 1835--1835
[]\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st
and = FALSE,
[2494] [2495] [2496] [2497]
Underfull \hbox (badness 10000) in paragraph at lines 2143--2145
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the con-verged. This is de-fined as
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Underfull \hbox (badness 3179) in paragraph at lines 2168--2174
[][][]\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.
[2498] [2499] [2500]
Underfull \hbox (badness 10000) in paragraph at lines 2326--2329
[][][]\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 ,
[2501]
Underfull \hbox (badness 1292) in paragraph at lines 2394--2397
[]\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 2403--2405
[]\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 2426--2429
[][][]\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 ,
[2502] [2503] [2504] [2505]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2642--2642
[]\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 ):[]
[2506] [2507]
Underfull \hbox (badness 1067) in paragraph at lines 2829--2834
[]\T1/ptm/m/n/10 The de-fault \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 (or in-te-ger
\T1/pcr/m/n/10 0\T1/ptm/m/n/10 ) cor-re-sponds to the orig-i-nal ``swap'' al-g
o-rithm, whereas
[2508]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2888--2888
[]\T1/pcr/m/n/9 ## no _build_ *and* no _swap_ phase: just cluster all obs. aro
und (1, 16):[]
[2509] [2510]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 2991--2991
[]\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co
l.axis = "red")[]
[2511] [2512] [2513]
Overfull \hbox (78.78088pt too wide) in paragraph at lines 3187--3187
[] \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x
$ac, digits = 2)),[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3188--3188
[] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
= TRUE, ...)[]
[2514]
Underfull \hbox (badness 10000) in paragraph at lines 3255--3258
[]\T1/ptm/m/n/10 For the den-dro-gram, more flex-i-bil-ity than via \T1/pcr/m/n
/10 pltree() \T1/ptm/m/n/10 is pro-vided by
[2515]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3305--3305
[] \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc,
digits = 2)),[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3306--3306
[] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
= TRUE, ...)[]
[2516] [2517] [2518]
Underfull \hbox (badness 10000) in paragraph at lines 3491--3494
[]\T1/ptm/m/n/10 when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 does not have a \T1/pcr/m
/n/10 diss \T1/ptm/m/n/10 com-po-nent as for
Underfull \hbox (badness 3471) in paragraph at lines 3491--3494
[][]\T1/pcr/m/n/10 pam[][][](*, keep.diss=FALSE)\T1/ptm/m/n/10 , \T1/pcr/m/n/10
dist \T1/ptm/m/n/10 must be the dis-sim-i-lar-ity if a
[2519]
Underfull \hbox (badness 10000) in paragraph at lines 3554--3559
[][][]\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 ,
[2520]
Underfull \hbox (badness 4621) in paragraph at lines 3616--3621
[]\T1/ptm/m/n/10 Note that cur-rently the method func-tion sim-ply calls \T1/pc
r/m/n/10 plot([][]as.hclust[][][](x), ...)\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1990) in paragraph at lines 3616--3621
\T1/ptm/m/n/10 which dis-patches to [][]\T1/pcr/m/n/10 plot.hclust[][][](..)\T1
/ptm/m/n/10 . If more flex-i-ble plots are needed, con-sider
Underfull \hbox (badness 6268) in paragraph at lines 3628--3631
[][][]\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 ,
[2521] [2522] [2523]
Underfull \hbox (badness 10000) in paragraph at lines 3813--3816
[][][]\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 3844--3847
[][][]\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 ,
[2524]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 3897--3897
[] \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right =
TRUE, ...)[]
Underfull \hbox (badness 2035) in paragraph at lines 3908--3910
[]\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
[2525] [2526] [2527] [2528]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 4101--4101
[] \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 4103--4103
[] \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat
= TRUE, ...)[]
Underfull \hbox (badness 1946) in paragraph at lines 4132--4137
[]\T1/ptm/m/n/10 arguments passed [][]\T1/pcr/m/n/10 barplot[][][]()\T1/ptm/m/n
/10 ; note that the de-fault used to be \T1/pcr/m/n/10 col
[2529]
Underfull \hbox (badness 10000) in paragraph at lines 4199--4207
\T1/pcr/m/n/10 attr(sil, "Ordered") \T1/ptm/m/n/10 is a log-i-cal in-di-cat-ing
if \T1/pcr/m/n/10 sil \T1/ptm/m/it/10 is \T1/ptm/m/n/10 or-dered as by
[2530]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4241--4241
[]\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 4250--4250
[] \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 4252--4252
[] \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 4255--4255
[]\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 4257--4257
[] \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 4264--4264
[]\T1/pcr/m/n/9 str(xc1k <- xclara[ sample(nrow(xclara), size = 1000) ,]) # ro
wnames == indices[]
[2531] [2532] [2533] [2534] [2535] [2536]
Underfull \hbox (badness 10000) in paragraph at lines 4622--4628
[]\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 4638--4640
[]\T1/ptm/m/n/10 Sample data set ac-com-pa-ny-ing the ref-er-ence be-low (file
`\T1/pcr/m/n/10 xclara.dat\T1/ptm/m/n/10 ' in side
Overfull \hbox (52.98038pt too wide) in paragraph at lines 4651--4651
[]\T1/pcr/m/n/9 ## Visualization: Assuming groups are defined as {1:1000}, {10
01:2000}, {2001:3000}
Overfull \hbox (9.78043pt too wide) in paragraph at lines 4653--4653
[]\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)$id.med[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4663--4663
[] \T1/pcr/m/n/9 ## We see 3 + 2 + 2 = 7 clear "outlier"s or "wrong group" o
bservations:[]
[2537]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4667--4667
[] \T1/pcr/m/n/9 ## Apart from these, what are the robust ranges of indices? -
- Robust range:[]
[2538]) (./codetools-pkg.tex
Chapter 21.
Overfull \hbox (24.78088pt too wide) in paragraph at lines 16--16
[] \T1/pcr/m/n/10 suppressParamUnused = !all, suppressFundefMismatch
= FALSE,[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 17--17
[] \T1/pcr/m/n/10 suppressLocalUnused = FALSE, suppressNoLocalFun =
!all,[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 18--18
[] \T1/pcr/m/n/10 skipWith = FALSE, suppressUndefined = dfltSuppress
Undefined,[]
[2539]
Underfull \hbox (badness 10000) in paragraph at lines 65--70
[]\T1/pcr/m/n/10 checkUsageEnv \T1/ptm/m/n/10 and \T1/pcr/m/n/10 checkUsagePack
age \T1/ptm/m/n/10 are con-ve-nience func-tions that ap-ply
[2540]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 119--119
[]\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e
nterInternal,[]
[2541] [2542] [2543]) (./foreign-pkg.tex [2544]
Chapter 22.
[2545]
Underfull \hbox (badness 1231) in paragraph at lines 67--70
[]\T1/ptm/m/n/10 a char-ac-ter string with the name of the ARFF file to read fr
om, or a
Underfull \hbox (badness 6708) in paragraph at lines 78--81
[]\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / /
www . cs . waikato . ac . nz / ~ml / weka / arff .
[2546] [2547]
Underfull \hbox (badness 3601) in paragraph at lines 235--243
[]\T1/ptm/m/n/10 A data frame with at-tributes. These will in-clude \T1/pcr/m/n
/10 "datalabel"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "time.stamp"\T1/ptm/m/n/10 ,
[2548]
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[]\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates =
FALSE,
[2549] [2550] [2551]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 462--462
[] \T1/pcr/m/n/10 trim_values = TRUE, reencode = NA, use.missings = t
o.data.frame,[]
[2552]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 463--463
[] \T1/pcr/m/n/10 sub = ".", add.undeclared.levels = c("sort", "appen
d", "no"),[]
Underfull \hbox (badness 10000) in paragraph at lines 506--515
[]\T1/ptm/m/n/10 character: what to do with du-pli-cated value la-bels for dif-
fer-
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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
Underfull \hbox (badness 10000) in paragraph at lines 506--515
\T1/ptm/m/n/10 la-bel is kept while fur-ther du-pli-cated la-bels are re-named
to
Underfull \hbox (badness 10000) in paragraph at lines 506--515
\T1/pcr/m/n/10 paste0(label, duplicated.value.labels.infix, level)\T1/ptm/m/n/1
0 ,
Underfull \hbox (badness 10000) in paragraph at lines 516--519
[]\T1/ptm/m/n/10 character: the in-fix used for la-bels of fac-tor lev-els with
du-
Underfull \hbox (badness 10000) in paragraph at lines 516--519
\T1/ptm/m/n/10 pli-cated value la-bels in SPSS (de-fault \T1/pcr/m/n/10 "_dupli
cated_"\T1/ptm/m/n/10 ) if
[2553]
Underfull \hbox (badness 10000) in paragraph at lines 551--559
[]\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 http : / / msdn . microsoft . com / en
-[]us / library / ms776446(VS . 85 ) .aspx$[][]
Underfull \hbox (badness 7613) in paragraph at lines 569--575
[]\T1/ptm/m/n/10 There may be at-tributes \T1/pcr/m/n/10 "label.table" \T1/ptm/
m/n/10 and \T1/pcr/m/n/10 "variable.labels"\T1/ptm/m/n/10 . At-tribute
[2554]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 624--624
[]\T1/pcr/m/n/9 ### hence may need some special treatment with appropriate arg
ument settings.[]
Overfull \hbox (112.38031pt too wide) in paragraph at lines 625--625
[]\T1/pcr/m/n/9 ### Expect lots of warnings as value labels (corresponding to
R factor labels) are uncomplete,[]
[2555]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 658--658
[]\T1/pcr/m/n/9 ## Long Strings (>255 chars) are imported in consecutive separ
ate variables[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 662--662
[]\T1/pcr/m/n/9 cat.long.string <- function(x, w=70) cat(paste(strwrap(x, widt
h=w), "\n"))[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 669--669
[]\T1/pcr/m/n/9 long.string <- apply(x[,c("string_500", "STRIN0")], 1, paste,
collapse="")[]
[2556] [2557]
Underfull \hbox (badness 10000) in paragraph at lines 813--814
Overfull \hbox (4.38043pt too wide) in paragraph at lines 823--823
[]\T1/pcr/m/n/9 iris.s <- read.systat(system.file("files/Iris.syd", package="f
oreign")[1])[]
[2558] [2559]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 899--899
[] \T1/pcr/m/n/10 data.restore(file, print = FALSE, verbose = FALSE, env = .G
lobalEnv)
[2560]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 963--963
[]\T1/pcr/m/n/10 write.arff(x, file, eol = "\n", relation = deparse(substitute
(x)))
Underfull \hbox (badness 6708) in paragraph at lines 989--992
[]\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / /
www . cs . waikato . ac . nz / ~ml / weka / arff .
[2561] [2562]
Underfull \hbox (badness 10000) in paragraph at lines 1073--1074
[][][]$\T1/pcr/m/n/10 http : / / www . clicketyclick . dk / databases / xbase /
format / data _ types .
Overfull \hbox (24.78088pt too wide) in paragraph at lines 1109--1109
[] \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric",
"codes"))[]
[2563]
Underfull \hbox (badness 1286) in paragraph at lines 1194--1198
[]\T1/ptm/m/n/10 Unless dis-abled by ar-gu-ment \T1/pcr/m/n/10 convert.dates =
FALSE\T1/ptm/m/n/10 , \T1/phv/m/n/10 R \T1/ptm/m/n/10 date and date-time ob-jec
ts
[2564]
Underfull \hbox (badness 10000) in paragraph at lines 1267--1273
[]\T1/ptm/m/n/10 The work for this func-tion is done by \T1/pcr/m/n/10 foreign:
::writeForeignStata\T1/ptm/m/n/10 ,
[2565]
Underfull \hbox (badness 6725) in paragraph at lines 1293--1296
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 package="SPSS"\T1/ptm/m/n/10 , as a side ef
-fect, the dec-i-mal in-di-ca-tor is al-ways set by
[2566]) (./lattice-pkg.tex
Chapter 23.
[2567] [2568] [2569]
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"),[]
[2570]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 298--298
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defaul
t.dotplot"),[]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 305--305
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.barchart"),[]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 313--313
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.stripplot"),[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 334--334
[] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 338--338
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.bwplot"),[]
[2571]
Underfull \hbox (badness 4060) in paragraph at lines 357--369
[]\T1/ptm/m/n/10 For the func-tions doc-u-mented here, the for-mula is gen-er-a
lly of the
Underfull \hbox (badness 10000) in paragraph at lines 357--369
\T1/ptm/m/n/10 form \T1/pcr/m/n/10 y ~ x | g1 * g2 * ... \T1/ptm/m/n/10 (or equ
iv-a-lently, \T1/pcr/m/n/10 y ~ x |
Underfull \hbox (badness 1028) in paragraph at lines 397--412
\T1/ptm/m/n/10 This for-mula would be taken to mean that the user wants to plot
both
Underfull \hbox (badness 10000) in paragraph at lines 413--415
[]\T1/ptm/m/n/10 To in-ter-pret \T1/pcr/m/n/10 y1 + y2 \T1/ptm/m/n/10 as a sum,
one can ei-ther set
[2572]
Underfull \hbox (badness 7631) in paragraph at lines 479--484
[]\T1/ptm/m/n/10 A po-ten-tially use-ful com-po-nent of \T1/pcr/m/n/10 scales \
T1/ptm/m/n/10 in this case may be
[2573] [2574]
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
[2575] [2576] [2577] [2578]
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.
[2579]
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
[2580] [2581]
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
[2582] [2583] [2584]
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 ,
[2585]
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 ,
[2586]
Underfull \vbox (badness 10000) has occurred while \output is active [2587]
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
[2588]
Underfull \hbox (badness 6808) in paragraph at lines 1755--1759
[]\T1/ptm/m/n/10 graphical ar-gu-ments, which are pro-cessed and even-tu-ally p
assed to
Underfull \hbox (badness 10000) in paragraph at lines 1772--1775
[]\T1/ptm/m/n/10 style set-tings be-yond the stan-dard \T1/pcr/m/n/10 col\T1/pt
m/m/n/10 , \T1/pcr/m/n/10 lty\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lwd\T1/ptm/m/n/10
, etc; see
[2589]
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
[2590] [2591] [2592]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2071--2071
[] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl
ot"),[]
Underfull \hbox (badness 10000) in paragraph at lines 2086--2093
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 formula \T1/ptm/m/n/10 method, \T1/pcr/
m/n/10 x \T1/ptm/m/n/10 can be a for-mula of the form
Underfull \hbox (badness 1997) in paragraph at lines 2086--2093
\T1/pcr/m/n/10 ~ x | g1 * g2 * ...\T1/ptm/m/n/10 , in-di-cat-ing that his-togra
ms or ker-nel den-sity
[2593]
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
[2594] [2595] [2596]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 2345--2345
[] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 2349--2349
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.qqmath"),[]
Underfull \hbox (badness 4441) in paragraph at lines 2362--2366
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 method, \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 should be a for-mula of the form
[2597] [2598] [2599]
Underfull \hbox (badness 4441) in paragraph at lines 2547--2554
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 method, \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 should be a for-mula of the form
[2600] [2601]
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"),[]
[2602]
Underfull \hbox (badness 10000) in paragraph at lines 2761--2766
[]\T1/ptm/m/n/10 for the \T1/pcr/m/n/10 formula \T1/ptm/m/n/10 method, a for-mu
la of the form \T1/pcr/m/n/10 z ~ x * y
[2603]
Underfull \hbox (badness 2913) in paragraph at lines 2791--2796
[]\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix.
Underfull \hbox (badness 3058) in paragraph at lines 2791--2796
\T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p
tm/m/n/10 must have the same lengths as
Underfull \hbox (badness 6758) in paragraph at lines 2877--2881
[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the col-orkey should be
Underfull \hbox (badness 7576) in paragraph at lines 2877--2881
\T1/ptm/m/n/10 ren-dered as a raster im-age us-ing [][]\T1/pcr/m/n/10 grid.rast
er[][][]\T1/ptm/m/n/10 . See also
Underfull \hbox (badness 10000) in paragraph at lines 2883--2885
[]\T1/ptm/m/n/10 Logical flag, passed to [][]\T1/pcr/m/n/10 rasterGrob[][][] \T
1/ptm/m/n/10 when
[2604]
Underfull \hbox (badness 1609) in paragraph at lines 2935--2941
[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether raster rep-re-sen-ta-ti
ons should be used,
Underfull \hbox (badness 2772) in paragraph at lines 2935--2941
\T1/ptm/m/n/10 both for the false color im-age and the color key (if present).
Ef-
Underfull \hbox (badness 1400) in paragraph at lines 2935--2941
\T1/ptm/m/n/10 fec-tively, set-ting this to \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10
changes the de-fault panel func-tion from
Underfull \hbox (badness 2486) in paragraph at lines 2959--2963
[]\T1/ptm/m/n/10 Other use-ful ar-gu-ments are men-tioned in the help page for
the de-fault panel func-tion
[2605] [2606]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3060--3060
[] \T1/pcr/m/n/10 xlim = if (is.factor(x)) levels(x) else range(x, finite
= TRUE),[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3061--3061
[] \T1/pcr/m/n/10 ylim = if (is.factor(y)) levels(y) else range(y, finite
= TRUE),[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3062--3062
[] \T1/pcr/m/n/10 zlim = if (is.factor(z)) levels(z) else range(z, finite
= TRUE),[]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3073--3073
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
cloud"),[]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 3085--3085
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.wireframe"),[]
[2607]
Underfull \hbox (badness 10000) in paragraph at lines 3110--3118
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 meth-ods, a fo
r-mula of the form \T1/pcr/m/n/10 z ~ x
Underfull \hbox (badness 2913) in paragraph at lines 3143--3150
[]\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix.
Underfull \hbox (badness 3058) in paragraph at lines 3143--3150
\T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p
tm/m/n/10 must have the same lengths as
[2608] [2609] [2610] [2611]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.parallel}) has been already used, duplicate ignored
<to be read again>
\relax
l.3431 \aliasA{parallel}{B\_08\_splom}{parallel}
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3473--3473
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
splom"),[]
[2612]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3496--3496
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.parallel"),[]
[2613] [2614] [2615] [2616] [2617]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3832--3832
[]\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt(
var(x)))
[2618]
Underfull \hbox (badness 10000) in paragraph at lines 3922--3926
\T1/ptm/m/n/10 fy-ing \T1/pcr/m/n/10 lattice.options(default.theme = "col.white
bg")\T1/ptm/m/n/10 .
Underfull \hbox (badness 2435) in paragraph at lines 3922--3926
\T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa
ded) set to
[2619] [2620]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4052--4052
[]\T1/pcr/m/n/10 trellis.par.set(name, value, ..., theme, warn = TRUE, strict
= FALSE)
Underfull \hbox (badness 1173) in paragraph at lines 4061--4065
[]\T1/ptm/m/n/10 A char-ac-ter string giv-ing the name of a com-po-nent. If un-
spec-i-fied in
Underfull \hbox (badness 3219) in paragraph at lines 4088--4090
[]\T1/ptm/m/n/10 A log-i-cal flag, in-di-cat-ing whether a warn-ing should be i
s-sued when
Underfull \hbox (badness 1728) in paragraph at lines 4105--4109
\T1/pcr/m/n/10 theme\T1/ptm/m/n/10 ). These are used to mod-ify the cur-rent se
t-tings (ob-tained by
[2621]
Underfull \hbox (badness 5161) in paragraph at lines 4170--4174
[]\T1/ptm/m/n/10 The ac-tual list of the com-po-nents in \T1/pcr/m/n/10 trellis
.settings \T1/ptm/m/n/10 has not been fi-nal-ized,
Underfull \hbox (badness 4913) in paragraph at lines 4170--4174
\T1/ptm/m/n/10 so I'm not at-tempt-ing to list them here. The cur-rent value ca
n be ob-tained by
[2622] [2623]
Underfull \hbox (badness 1067) in paragraph at lines 4284--4294
[]\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. \T1/pcr/m/n/10 col \T1/ptm/m/n/10 i
s used for com-po-nents \T1/pcr/m/n/10 "plot.symbol"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 4284--4294
\T1/pcr/m/n/10 "plot.line"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "plot.polygon"\T1/ptm
/m/n/10 , \T1/pcr/m/n/10 "superpose.symbol"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1735) in paragraph at lines 4284--4294
\T1/pcr/m/n/10 "superpose.line"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "superpose.p
olygon"\T1/ptm/m/n/10 . \T1/pcr/m/n/10 col.points
Underfull \hbox (badness 10000) in paragraph at lines 4284--4294
\T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col\T1/ptm/m/n/10 , but is used only f
or \T1/pcr/m/n/10 "plot.symbol" \T1/ptm/m/n/10 and
Underfull \hbox (badness 5231) in paragraph at lines 4284--4294
\T1/pcr/m/n/10 "superpose.symbol"\T1/ptm/m/n/10 . Sim-i-larly, \T1/pcr/m/n/10 c
ol.line \T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col \T1/ptm/m/n/10 for
Underfull \hbox (badness 1701) in paragraph at lines 4309--4312
[]\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 plot
.symbol\T1/ptm/m/n/10 , \T1/pcr/m/n/10 plot.polygon\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 4312--4314
[]\T1/ptm/m/n/10 border color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 pl
ot.polygon \T1/ptm/m/n/10 and
[2624] [2625] [2626] [2627] [2628] [2629]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4716--4716
[]\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab
= "Height")[]
[2630] [2631]
Underfull \hbox (badness 10000) in paragraph at lines 4903--4906
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 trellis\T1/ptm/m/n/10 , by
de-fault plot-ted by \T1/pcr/m/n/10 print.trellis\T1/ptm/m/n/10 .
[2632] [2633]
Underfull \hbox (badness 1442) in paragraph at lines 5035--5038
[]\T1/pcr/m/n/10 plot.shingle \T1/ptm/m/n/10 dis-plays the ranges of shin-gles
via rect-an-gles. \T1/pcr/m/n/10 print.shingle \T1/ptm/m/n/10 and
[2634] [2635] [2636] [2637] [2638] [2639]
Underfull \hbox (badness 3646) in paragraph at lines 5367--5370
[][][]\T1/pcr/m/n/10 Lattice[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 draw.key[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 trellis.par.get[][][]\T1/ptm/m/n/10 ,
and [][]\T1/pcr/m/n/10 xyplot[][][]\T1/ptm/m/n/10 , specif-i-cally the en-try f
or
Overfull \hbox (36.78088pt too wide) in paragraph at lines 5397--5397
[] \T1/pcr/m/n/10 bg = trellis.par.get("strip.background")$col[wh
ich.given],[]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 5398--5398
[] \T1/pcr/m/n/10 fg = trellis.par.get("strip.shingle")$col[which
.given],[]
[2640]
Underfull \hbox (badness 10000) in paragraph at lines 5486--5489
[]\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i
-zon-tal.
Underfull \hbox (badness 2103) in paragraph at lines 5486--5489
\T1/pcr/m/n/10 horizontal=FALSE \T1/ptm/m/n/10 is use-ful for strips on the lef
t of pan-els us-ing
Underfull \hbox (badness 6412) in paragraph at lines 5503--5509
[]\T1/ptm/m/n/10 default strip func-tion for trel-lis func-tions. Use-ful mostl
y be-cause of the \T1/pcr/m/n/10 style
Underfull \hbox (badness 10000) in paragraph at lines 5503--5509
\T1/ptm/m/n/10 ar-gu-ment --- non-default styles are of-ten more in-for-ma-tive
, es-pe-cially when
Underfull \hbox (badness 10000) in paragraph at lines 5503--5509
\T1/ptm/m/n/10 the names of the lev-els of the fac-tor \T1/pcr/m/n/10 x \T1/ptm
/m/n/10 are small. Tra-di-tional use is as
Underfull \hbox (badness 10000) in paragraph at lines 5503--5509
\T1/pcr/m/n/10 strip = function(...) strip.default(style=2,...)\T1/ptm/m/n/10 ,
though this can be
[2641]
Underfull \hbox (badness 1635) in paragraph at lines 5512--5517
[]\T1/pcr/m/n/10 strip.default \T1/ptm/m/n/10 is called for its side-effect, wh
ich is to draw a strip ap-pro-pri-ate for
[2642]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5661--5661
[]\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la
bels,[]
[2643]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 5675--5675
[]\T1/pcr/m/n/10 panel.link.splom(threshold = 18, verbose = getOption("verbose
"), ...)[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 5676--5676
[]\T1/pcr/m/n/10 panel.brush.splom(threshold = 18, verbose = getOption("verbos
e"), ...)[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5679--5679
[]\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location"
, "toplevel",[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5682--5682
[] \T1/pcr/m/n/10 "xlab", "ylab", "xlab.top", "ylab.rig
ht", "page"),[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 5684--5684
[] \T1/pcr/m/n/10 side = c("left", "top", "right", "bottom", "in
side"),[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 5690--5690
[] \T1/pcr/m/n/10 which.given = lattice.getStatus("current.whi
ch.given",[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5691--5691
[] \T1/pcr/m/n/10 prefix = pre
fix),[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 5692--5692
[] \T1/pcr/m/n/10 which.panel = lattice.getStatus("current.whi
ch.panel",[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5693--5693
[] \T1/pcr/m/n/10 prefix = pre
fix),[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5694--5694
[] \T1/pcr/m/n/10 column = lattice.getStatus("current.focus.co
lumn",[]
Underfull \hbox (badness 10000) in paragraph at lines 5710--5712
[]\T1/ptm/m/n/10 variables defin-ing the con-tents of the panel. In the case of
[2644]
Underfull \hbox (badness 2376) in paragraph at lines 5721--5723
[]\T1/ptm/m/n/10 an op-tional vec-tor of la-bels as-so-ci-ated with each point.
De-faults to
[2645]
Underfull \hbox (badness 2538) in paragraph at lines 5846--5850
\T1/ptm/m/n/10 For \T1/pcr/m/n/10 trellis.focus\T1/ptm/m/n/10 , the de-fault is
\T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 in in-ter-ac-tive mode, and
Underfull \hbox (badness 4205) in paragraph at lines 5857--5864
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 panel.identify.qqmath\T1/ptm/m/n/10 , ex-tr
a pa-ram-e-ters are passed on to
Underfull \hbox (badness 4792) in paragraph at lines 5857--5864
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 trellis.switchFocus\T1/ptm/m/n/10 , these are
used (in com-bi-na-tion with
[2646] [2647]
Underfull \hbox (badness 10000) in paragraph at lines 6010--6014
[][][]\T1/pcr/m/n/10 identify[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Lattice[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.trellis[][][]\T1/ptm/m/n/10 , []
[]\T1/pcr/m/n/10 trellis.currentLayout[][][]\T1/ptm/m/n/10 ,
[2648] [2649]
Underfull \hbox (badness 4242) in paragraph at lines 6157--6162
[]\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li
s pa-ram-e-
[2650] [2651]
Underfull \hbox (badness 3601) in paragraph at lines 6273--6278
[]\T1/ptm/m/n/10 Creates Box and Whisker plot of \T1/pcr/m/n/10 x \T1/ptm/m/n/1
0 for ev-ery level of \T1/pcr/m/n/10 y \T1/ptm/m/n/10 (or the other way round
Underfull \hbox (badness 2486) in paragraph at lines 6273--6278
\T1/ptm/m/n/10 if \T1/pcr/m/n/10 horizontal=FALSE\T1/ptm/m/n/10 ). By de-fault,
the ac-tual box-plot statis-tics are cal-cu-lated us-ing
[2652] [2653]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 6360--6360
[] \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co
lors")$palette,[]
[2654]
Underfull \hbox (badness 1888) in paragraph at lines 6492--6499
\T1/pcr/m/n/10 at \T1/ptm/m/n/10 can be a nu-meric vec-tor, \T1/pcr/m/n/10 col.
regions \T1/ptm/m/n/10 a vec-tor of col-ors, and
[2655]
Underfull \hbox (badness 10000) in paragraph at lines 6549--6552
[]\T1/ptm/m/n/10 All three num-bers should be be-tween 0 and 1. The
Underfull \hbox (badness 1558) in paragraph at lines 6549--6552
\T1/pcr/m/n/10 shade.colors.palette \T1/ptm/m/n/10 func-tion should re-turn a v
alid color. The
[2656]
Underfull \hbox (badness 1005) in paragraph at lines 6599--6607
\T1/ptm/m/n/10 fer-ent pur-poses. For cloud, the data is un-struc-tured, and \T
1/pcr/m/n/10 x\T1/ptm/m/n/10 , \T1/pcr/m/n/10 y \T1/ptm/m/n/10 and \T1/pcr/m/n/
10 z \T1/ptm/m/n/10 are all passed to
Underfull \hbox (badness 1571) in paragraph at lines 6599--6607
\T1/ptm/m/n/10 the \T1/pcr/m/n/10 panel.3d.cloud \T1/ptm/m/n/10 func-tion. For
wire-frame, on the other hand, \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/
10 y \T1/ptm/m/n/10 are in-
[2657] [2658] [2659] [2660] [2661]
Underfull \hbox (badness 1320) in paragraph at lines 6955--6962
[]\T1/pcr/m/n/10 panel.levelplot.raster \T1/ptm/m/n/10 is an al-ter-na-tive pan
el func-tion that uses the raster draw-
Underfull \hbox (badness 1715) in paragraph at lines 6955--6962
\T1/ptm/m/n/10 can only ren-der data on an eq-ui-s-paced grid), but can be more
ef-fi-cient. When us-ing
[2662]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 7025--7025
[] \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels =
NULL,[]
[2663]
Underfull \hbox (badness 10000) in paragraph at lines 7055--7059
[]\T1/ptm/m/n/10 The panel func-tion used for the di-ag-o-nals. See ar-gu-ments
to
Underfull \hbox (badness 1584) in paragraph at lines 7055--7059
\T1/pcr/m/n/10 diag.panel.splom \T1/ptm/m/n/10 to know what ar-gu-ments this fu
nc-tion is passed
[2664]
Underfull \hbox (badness 10000) in paragraph at lines 7160--7163
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 diag.panel \T1/ptm/m/n/10 from \T1/pcr/m/n/10
panel.pairs\T1/ptm/m/n/10 . Cur-rently ig-nored by
[2665] [2666]
Underfull \hbox (badness 2012) in paragraph at lines 7326--7329
[]\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu
-ally passed on to
[2667]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7372--7372
[] \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta
ils.n = 50))[]
[2668] [2669]
Underfull \hbox (badness 2644) in paragraph at lines 7513--7517
\T1/ptm/m/n/10 ig-nores these. For types "r" and "smooth", these are passed on
to
Underfull \hbox (badness 2772) in paragraph at lines 7526--7529
[]\T1/ptm/m/n/10 Most gen-er-ally, \T1/pcr/m/n/10 grid \T1/ptm/m/n/10 can be a
list of ar-gu-ments to be sup-plied to
Underfull \hbox (badness 4242) in paragraph at lines 7540--7548
\T1/ptm/m/n/10 which is called with those ar-gu-ments. If spec-i-fied as a (pos
-si-bly
Underfull \hbox (badness 1147) in paragraph at lines 7540--7548
\T1/ptm/m/n/10 named) nu-meric vec-tor, \T1/pcr/m/n/10 abline \T1/ptm/m/n/10 is
co-erced to a list. This al-lows ar-
Underfull \hbox (badness 2351) in paragraph at lines 7540--7548
\T1/ptm/m/n/10 gu-ments of the form \T1/pcr/m/n/10 abline = c(0, 1)\T1/ptm/
m/n/10 , which adds the di-
Underfull \hbox (badness 1675) in paragraph at lines 7540--7548
\T1/ptm/m/n/10 ag-o-nal line, or \T1/pcr/m/n/10 abline = c(h = 0, v = 0)\T1
/ptm/m/n/10 , which adds the
Underfull \hbox (badness 1769) in paragraph at lines 7540--7548
\T1/ptm/m/n/10 x- and y-axes to the plot. Use the list form for finer con-trol;
e.g.,
[2670]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 7596--7596
[] \T1/pcr/m/n/9 ylab = list(c("horizontal=TRUE", "horizontal=FALSE"), y
= c(1/6, 4/6)),[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7606--7606
[] \T1/pcr/m/n/9 scales = list(alternating = c(0, 2), tck = c(0, 0.7), d
raw = FALSE),[]
[2671]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 7667--7667
[] \T1/pcr/m/n/10 font, fontfamily, fontface, cex, ..., identifier, nam
e.type)[]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 7672--7672
[] \T1/pcr/m/n/10 adj = c(0.5, 0.5), pos = NULL, offset = 0.5, ..., ident
ifier, name.type)[]
[2672] [2673] [2674]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 7857--7857
[]\T1/pcr/m/n/10 panel.grid(h=3, v=3, col, col.line, lty, lwd, x, y, ..., iden
tifier = "grid")[]
[2675]
Underfull \hbox (badness 1436) in paragraph at lines 7912--7918
[]\T1/ptm/m/n/10 A log-i-cal flag de-ter-min-ing whether the de-fault graph-i-c
al pa-ram-e-ters for
Underfull \hbox (badness 1231) in paragraph at lines 7912--7918
\T1/ptm/m/n/10 tings. The de-fault is to take them from the ``add.line'' set-ti
ngs. The
[2676] [2677] [2678] [2679] [2680] [2681] [2682] [2683]
Underfull \hbox (badness 10000) in paragraph at lines 8470--8473
[]\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to \T1/pcr/m/n/10 panel.superpo
se
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\T1/ptm/m/n/10 from \T1/pcr/m/n/10 panel.superpose.2\T1/ptm/m/n/10 , and to \T1
/pcr/m/n/10 panel.groups \T1/ptm/m/n/10 from
[2684] [2685]
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[]\T1/pcr/m/n/10 prepanel.default.bwplot(x, y, horizontal, nlevels, origin, st
ack, ...)[]
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[]\T1/pcr/m/n/10 prepanel.default.histogram(x, breaks, equal.widths, type, nin
t, ...)[]
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[]\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr
ipts, ...)[]
[2686]
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[]\T1/ptm/m/n/10 details of his-togram cal-cu-la-tions. \T1/pcr/m/n/10 type \T1
/ptm/m/n/10 has a dif-fer-ent mean-ing in
[2687]
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[]\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti
es. If used with
[2688]
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[]\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr
ibed in
[2689] [2690]
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[] \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b
ottom$labels$labels)[]
[2691] [2692]
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[]\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su
nspot.year)),[]
[2693]
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[]\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
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\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
[2694] [2695] [2696] [2697] [2698] [2699] [2700]
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[]\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 ,
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\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 ,
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[]\T1/ptm/m/n/10 Factor with 6 lev-els: \T1/pcr/m/n/10 "Grand Rapids"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "Duluth"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "University Farm"
\T1/ptm/m/n/10 ,
[2701] [2702] [2703]pdfTeX warning (ext4): destination with the same identifier
(name{Rfn.melanoma}) has been already used, duplicate ignored
<to be read again>
\relax
l.9853 \aliasA{melanoma}{H\_melanoma}{melanoma}
[2704] [2705] [2706]
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[]\T1/ptm/m/n/10 Cause of death. A fac-tor with lev-els \T1/pcr/m/n/10 Alzheime
rs\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Cancer\T1/ptm/m/n/10 ,
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\T1/pcr/m/n/10 Cerebrovascular diseases\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Diabetes
\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Flu and pneumonia\T1/ptm/m/n/10 ,
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\T1/pcr/m/n/10 Heart disease\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Lower respiratory\T
1/ptm/m/n/10 , \T1/pcr/m/n/10 Nephritis\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Suicide\
T1/ptm/m/n/10 , and
[2707]
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[] \T1/pcr/m/n/9 par.settings = simpleTheme(pch = 16), auto.key = list(
columns = 2),[]
[2708]) (./mgcv-pkg.tex
Chapter 24.
[2709] [2710]
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[]\T1/pcr/m/n/10 bam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL,
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[] \T1/pcr/m/n/10 paraPen=NULL,chunk.size=10000,rho=0,AR.start=NULL,discret
e=FALSE,[]
[2711]
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[] \T1/pcr/m/n/10 coef=NULL,drop.unused.levels=TRUE,G=NULL,fit=TRUE,drop.in
tercept=NULL,...)[]
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
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\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known
scale.
[2712] [2713] [2714] [2715]
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[][][]\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 ,
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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 ,
[2716]
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[]\T1/pcr/m/n/9 system.time(b2 <- bam(y ~ s(x0,bs=bs,k=k)+s(x1,bs=bs,k=k)+s(x2
,bs=bs,k=k)+[]
[2717] [2718] [2719]
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[]\T1/ptm/m/n/10 The link func-tion: one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/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
[2720] [2721]
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[]\T1/ptm/m/n/10 First con-sider \T1/pcr/m/n/10 choldrop\T1/ptm/m/n/10 . If \T1
/pcr/m/n/10 R \T1/ptm/m/n/10 is up-per tri-an-gu-lar then
[2722]
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[]\T1/ptm/m/n/10 Choosing the ba-sis di-men-sion, and check-ing the choice, whe
n us-ing pe-nal-ized re-gres-sion
[2723]
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[]\T1/ptm/m/n/10 Wood, S.N. (2017) Gen-er-al-ized Ad-di-tive Mod-els: An In-tro
-duc-tion with R (2nd edi-tion).
[2724]
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[2726] [2727] [2728] [2729]
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[]\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h + 2*b$family$data$
q^.5),col=2)[]
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[]\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$
q^.5),col=2)[]
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[]\T1/pcr/m/n/9 bs <- gam(cbind(time,strata)~s(age,by=sex)+sex+s(nodes)+perfor
+rx+obstruct+adhere,[]
[2730]
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[]\T1/pcr/m/n/9 ## create index picking out elements of stored hazard info for
this stratum...[]
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[]\T1/pcr/m/n/9 if (i==1) plot(bs$family$data$tr[ind],exp(-bs$family$data$h[in
d]),type="l",ylim=c(0,1),[]
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[] \T1/pcr/m/n/9 lines(bs$family$data$tr[ind],exp(-bs$family$data$h[ind])
,lwd=2,col=i)[]
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[]\T1/pcr/m/n/9 b <- gam(t~s(x0)+s(x1)+s(x2,k=15)+s(x3),family=cox.ph,weights=
d,data=surv)[]
[2731]
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[] \T1/pcr/m/n/9 if (inter) prg <- txtProgressBar(min = 0, max = length(sid),
initial = 0,[]
[2732]
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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$day,to=te)) ## inter
polate to te[]
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[2734] [2735] [2736] [2737] [2738] [2739] [2740] [2741]
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[]\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str
ict=FALSE)
[2742] [2743] [2744] [2745] [2746] [2747]
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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,[]
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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
[2748]
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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.
[2749] [2750]
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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
[2751] [2752]
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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 ,
[2753]
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[2757] [2758] [2759] [2760] [2761] [2762] [2763]
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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)),[]
[2764] [2765] [2766] [2767] [2768] [2769]
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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
[2770] [2771]
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[]\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat
,method="ML")[]
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[]\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix
ed penalty, if
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[] \T1/pcr/m/n/9 mod <- gam(y~s(a,bs="re")+s(b,bs="re")+s(a,b,bs="re")+s(x0,i
d=1)+s(x1,id=1)+[]
[2782] [2783] [2784]
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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,
[2785]
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[]\T1/pcr/m/n/10 niterPQL=20,verbosePQL=TRUE,method="ML",drop.unused.levels=TR
UE,...)[]
[2786]
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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
[2787]
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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
[2788] [2789]
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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 ( []
[]$\T1/pcr/m/n/10 https : / / cran . r-[]project .
[2790]
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[]\T1/ptm/m/n/10 If `outer' it-er-a-tion has been used to fit the model (see []
[]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 ar-gu-ment
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[]\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic-
tion, used by
[2794] [2795] [2796] [2797] [2798] [2799] [2800]
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[]\T1/ptm/m/n/10 A pre-fit gam ob-ject, as pro-duced by \T1/pcr/m/n/10 gam(...,
fit=FALSE) \T1/ptm/m/n/10 or
[2801]
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[] \T1/pcr/m/n/9 ## example using a scale location model for the motorcycle d
ata. A simple plotting[]
[2802]
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[] \T1/pcr/m/n/9 } else lines(xg,predict(din,xg)$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[]
[2804] [2805] [2806] [2807] [2808] [2809]
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[]\T1/pcr/m/n/10 jagam(formula,family=gaussian,data=list(),file,weights=NULL,n
a.action,
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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
[2810] [2811] [2812] [2813] [2814] [2815]
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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)
[2816] [2817] [2818] [2819]
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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)[]
[2824] [2825] [2826] [2827] [2828] [2829] [2830] [2831] [2832]
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[]\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra
nts EP/K005251/1 and
[2833] [2834]
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[]\T1/pcr/m/n/9 ## Alternative, better scaling example, using the discrete opt
ion with bam...[]
[2835] [2836]
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[]\T1/pcr/m/n/9 for (sim in c(1,7)) { ## cycle over uncorrelated and correlate
d covariates[]
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[] \T1/pcr/m/n/9 dat1[[dname[i]]][dat1[[by.name]]] <- mean(dat1[[dname[i]]]
,na.rm=TRUE)[]
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[2849] [2850] [2851] [2852] [2853] [2854]
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[2856]
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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 8655--8658
\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 8655--8658
\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 .
[2857]
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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 8711--8714
\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
[2858] [2859] [2860]
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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,[]
[2861] [2862] [2863]
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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
[2864] [2865] [2866] [2867]
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[] \T1/pcr/m/n/10 na.action=na.pass,cluster=NULL,discrete=TRUE,n.thread
s=1,...)[]
[2868] [2869]
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[] \T1/pcr/m/n/10 na.action=na.pass,unconditional=FALSE,iterms.type=NUL
L,...)[]
[2870] [2871] [2872] [2873]
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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[]
[2875]
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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
[2876]
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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
[2877]
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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,
[2878] [2879]
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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,
[2880] [2881] [2882] [2883]
Underfull \hbox (badness 1946) in paragraph at lines 10241--10248
[]\T1/ptm/m/n/10 The sec-ond method rep-re-sents the con-ven-tional ran-dom ef-
fects in a GAM in the same
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\T1/ptm/m/n/10 way that the smooths are rep-re-sented --- as pe-nal-ized re-gre
s-sion terms. This method
Underfull \hbox (badness 2042) in paragraph at lines 10241--10248
\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.
[2884]
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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")[]
Underfull \hbox (badness 10000) in paragraph at lines 10344--10347
[]\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 ,
[2885] [2886] [2887] [2888] [2889]
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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)
[2890] [2891] [2892] [2893] [2894] [2895]
Underfull \hbox (badness 3861) in paragraph at lines 10972--10975
[]\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-
[2896]
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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-
[2897] [2898] [2899]
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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
[2900]
Underfull \hbox (badness 1803) in paragraph at lines 11261--11265
\T1/ptm/m/n/10 The last en-try will be the \T1/pcr/m/n/10 by \T1/ptm/m/n/10 var
i-able, if \T1/pcr/m/n/10 object$by \T1/ptm/m/n/10 is not \T1/pcr/m/n/10 "NA"\T
1/ptm/m/n/10 .
Underfull \hbox (badness 1502) in paragraph at lines 11273--11285
\T1/pcr/m/n/10 cs.smooth.spec \T1/ptm/m/n/10 (cu-bic re-gres-sion splines with
shrinkage-to-zero); \T1/pcr/m/n/10 cc.smooth.spec
Underfull \hbox (badness 2401) in paragraph at lines 11290--11294
\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 11290--11294
\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 ,
[2901] [2902] [2903]
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Underfull \hbox (badness 6876) in paragraph at lines 11485--11491
[][][]\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
Underfull \hbox (badness 10000) in paragraph at lines 11526--11527
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[2905] [2906]
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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
[2907] [2908]
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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 (25.98041pt too wide) in paragraph at lines 11720--11720
[] \T1/pcr/m/n/9 "1st order penalties: red tps; blue bs over (0,1); black bs
over (-.5,1.5)")[]
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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[]
[2909]
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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:[]
[2910]
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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
Underfull \hbox (badness 10000) in paragraph at lines 11802--11804
\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
[2911] [2912]
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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
[2913]
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[]\T1/pcr/m/n/9 b <- gam(y~s(x,z,bs="ds",m=c(1,.5),k=50),data=data) ## first
deriv penalty[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 12012--12012
[]\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[]
[2914] [2915] [2916]
Underfull \hbox (badness 10000) in paragraph at lines 12162--12163
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[2917] [2918] [2919] [2920]
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[]\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m
ethod="REML")[]
[2921]
Underfull \hbox (badness 10000) in paragraph at lines 12462--12464
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[2922] [2923]
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Underfull \hbox (badness 10000) in paragraph at lines 12621--12624
[]\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 12621--12624
\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 12621--12624
\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"
[2925] [2926]
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[]\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with
2 variances[]
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[]\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a
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\T1/pcr/m/n/10 s(...,bs="so",xt=list(bnd=bnd,...)) \T1/ptm/m/n/10 term in a \T1
/pcr/m/n/10 gam \T1/ptm/m/n/10 for-
[2927] [2928] [2929]
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[]\T1/pcr/m/n/9 ## notice NULL element in \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 xt\TS1
/pcr/m/n/9 ' \T1/pcr/m/n/9 list - to indicate no xt object for "cr" basis...[]
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[2932]
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[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths on the
sphere, via terms like
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[2933] [2934] [2935] [2936]
Underfull \hbox (badness 3396) in paragraph at lines 13352--13355
[][][]\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
[2937]
Underfull \hbox (badness 10000) in paragraph at lines 13397--13399
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[2938] [2939] [2940] [2941]
Underfull \hbox (badness 10000) in paragraph at lines 13621--13624
[]\T1/pcr/m/n/10 bs="fs" \T1/ptm/m/n/10 Smooth fac-tor in-ter-ac-tions are of-t
en pro-
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\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
[2942]
Underfull \hbox (badness 10000) in paragraph at lines 13654--13658
[][][]\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 13654--13658
[][]\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 13654--13658
[][]\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 ,
[2943] [2944] [2945] [2946] [2947]
Underfull \hbox (badness 2158) in paragraph at lines 13944--13944
[]\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma-
trix from
[2948]
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[]\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0,
centre=FALSE)[]
[2949] [2950]
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[] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars
"),...)[]
[2951] [2952] [2953]
Underfull \hbox (badness 4846) in paragraph at lines 14288--14291
[]\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
[2954] [2955] [2956] [2957] [2958]
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[2960] [2961] [2962] [2963] [2964] [2965] [2966]
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[]\T1/ptm/m/n/10 Suppose that \T1/pcr/m/n/10 m=1 \T1/ptm/m/n/10 and you fill an
ar-ray us-ing code like
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\T1/pcr/m/n/10 for(i in 1:K) for(j in i:K) for(k in j:K) for(l in k:K)
[2967] [2968] [2969] [2970] [2971] [2972]
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[]\T1/pcr/m/n/10 vcov(object, freq = FALSE, dispersion = NULL,unconditional=FA
LSE, ...)[]
[2973] [2974] [2975] [2976] [2977]
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[]\T1/pcr/m/n/9 ## 1. If the zero inflation rate becomes decoupled from the li
near predictor,[]
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[]\T1/pcr/m/n/9 ## it is possible for the linear predictor to be almost unboun
ded in regions[]
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[]\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val
ues, to check we[]
[2978] [2979] [2980]) (./nlme-pkg.tex
Chapter 25.
[2981]
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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
[2982]
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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
[2983] [2984] [2985] [2986] [2987]
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[] \T1/pcr/m/n/9 lme(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[]
[2988] [2989]
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[]\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 251-254 ---------------------------
---------------[]
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[]\T1/pcr/m/n/9 # Compare an "lme" object with a "gls" object (test would be n
on-sensical!)[]
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[]\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 ---------------------------
---------------[]
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[] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxil
lary fissure"),[]
[2998]
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
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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 ,
[3006]
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
[3007] [3008] [3009] [3010] [3011]
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 ,
[3012]
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")[]
[3013]
Underfull \hbox (badness 1132) in paragraph at lines 2144--2146
[]\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac
ted us-ing the
[3014] [3015]
Underfull \hbox (badness 4168) in paragraph at lines 2255--2261
[][][]\T1/pcr/m/n/10 ACF.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corARMA[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T
1/pcr/m/n/10 Dim.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize
.corStruct[][][]\T1/ptm/m/n/10 ,
[3016]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2280--2280
[] \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[]
[3017] [3018] [3019] [3020] [3021] [3022] [3023] [3024]
Underfull \hbox (badness 10000) in paragraph at lines 2843--2847
[][][]\T1/pcr/m/n/10 corFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corMatr
ix.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 recalc.corStruct[][][]\T1
/ptm/m/n/10 ,
[3025] [3026] [3027] [3028] [3029] [3030] [3031] [3032] [3033] [3034] [3035]
[3036]
Underfull \hbox (badness 6493) in paragraph at lines 3579--3587
[][][]\T1/pcr/m/n/10 corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corGaus[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corSpher[][][]\T1/ptm
/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 ,
[3037] [3038] [3039] [3040] [3041] [3042] [3043] [3044] [3045] [3046] [3047]
[3048] [3049] [3050] [3051] [3052] [3053] [3054] [3055] [3056] [3057] [3058]
[3059] [3060]
Underfull \hbox (badness 10000) in paragraph at lines 5159--5163
[][][]\T1/pcr/m/n/10 getCovariate.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m
/n/10 getCovariate.data.frame[][][]\T1/ptm/m/n/10 ,
[3061] [3062] [3063] [3064] [3065]
Underfull \hbox (badness 10000) in paragraph at lines 5476--5480
[]\T1/ptm/m/n/10 Note that as from ver-sion 3.1-102, this only omits rows omit-
ted in the fit if
Underfull \hbox (badness 2671) in paragraph at lines 5476--5480
\T1/pcr/m/n/10 na.action = na.omit\T1/ptm/m/n/10 , and does not omit at all if
\T1/pcr/m/n/10 na.action = na.exclude\T1/ptm/m/n/10 .
[3066] [3067]
Underfull \hbox (badness 10000) in paragraph at lines 5591--5594
[][][]\T1/pcr/m/n/10 getGroupsFormula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10
getGroups.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getGroups.gls[][]
[]\T1/ptm/m/n/10 ,
[3068] [3069] [3070] [3071] [3072] [3073] [3074] [3075] [3076]
Underfull \hbox (badness 2799) in paragraph at lines 6097--6103
\T1/ptm/m/n/10 covariance ma-trix, ei-ther \T1/pcr/m/n/10 "random.effects" \T1/
ptm/m/n/10 for the random-effects
[3077]
Underfull \hbox (badness 7133) in paragraph at lines 6158--6162
[]\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in \
T1/pcr/m/n/10 model\T1/ptm/m/n/10 ,
[3078]
Underfull \hbox (badness 2057) in paragraph at lines 6242--6253
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsCon
trol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsObject[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gls[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gls[][][]\T1/ptm/m/n/10 ,
[3079]
Underfull \hbox (badness 10000) in paragraph at lines 6306--6308
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6338--6338
[]\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[]
[3080] [3081] [3082] [3083]
Underfull \hbox (badness 7133) in paragraph at lines 6556--6560
[]\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in \
T1/pcr/m/n/10 model\T1/ptm/m/n/10 ,
[3084]
Underfull \hbox (badness 10000) in paragraph at lines 6655--6661
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsCo
ntrol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsObject[][][]\T1/ptm/m/n/10 ,
[][]\T1/pcr/m/n/10 gnlsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict
.gnls[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (54.78088pt too wide) in paragraph at lines 6682--6682
[]\T1/pcr/m/n/10 gnlsControl(maxIter = 50, nlsMaxIter = 7, msMaxIter = 50, min
Scale = 0.001,
[3085]
Underfull \hbox (badness 10000) in paragraph at lines 6720--6722
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3086]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6750--6750
[]\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[]
[3087] [3088] [3089]
Underfull \hbox (badness 10000) in paragraph at lines 6993--7000
[][][]\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 ,
[3090]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7010--7010
[] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla
ry fissure" ),[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7018--7018
[]\T1/pcr/m/n/9 fm1 <- lme( Orth.new ) # fixed and groups formulae extracted
from object[]
Underfull \hbox (badness 2875) in paragraph at lines 7040--7042
[]\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
[3091] [3092] [3093]
Underfull \hbox (badness 10000) in paragraph at lines 7255--7260
[][][]\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 ,
[3094] [3095] [3096]
Underfull \hbox (badness 10000) in paragraph at lines 7407--7415
[]\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 7407--7415
\T1/ptm/m/n/10 tion and op-ti-miza-tion al-go-rithms used in \T1/pcr/m/n/10 lme
\T1/ptm/m/n/10 . De-faults to
Underfull \hbox (badness 1817) in paragraph at lines 7407--7415
\T1/pcr/m/n/10 list(niterEM=20, gradHess=TRUE)\T1/ptm/m/n/10 , im-ply-ing that
20 EM it-er-a-
Underfull \hbox (badness 3118) in paragraph at lines 7430--7433
[][][]\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 ,
[3097] [3098] [3099]
Underfull \hbox (badness 3354) in paragraph at lines 7645--7647
[]\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
[3100] [3101] [3102] [3103] [3104] [3105]
Underfull \hbox (badness 1642) in paragraph at lines 8037--8059
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o
f the form
[3106] [3107]
Underfull \hbox (badness 10000) in paragraph at lines 8157--8174
[][][]\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 8157--8174
[][]\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 8200--8200
[] \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data
= TRUE)[]
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[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o
f the form
[3108] [3109] [3110] [3111] [3112]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 8474--8474
[]\T1/pcr/m/n/10 lmeControl(maxIter = 50, msMaxIter = 50, tolerance = 1e-6, ni
terEM = 25,
Underfull \hbox (badness 10000) in paragraph at lines 8520--8522
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3113]
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[]\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.8565 \aliasA{sigma}{lmeObject}{sigma}
[3114] [3115] [3116]
Underfull \hbox (badness 10000) in paragraph at lines 8726--8738
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 lmList\T1/ptm/m/n/10 , ei-ther a lin-ear fo
r-mula ob-ject of the form
[3117] [3118] [3119] [3120] [3121] [3122] [3123] [3124] [3125]
Underfull \hbox (badness 10000) in paragraph at lines 9317--9324
[][][]\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 9328--9328
[]\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me
thod = "ML")
[3126]
Underfull \hbox (badness 6300) in paragraph at lines 9410--9413
[]\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
[3127] [3128] [3129] [3130]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.Matrix}) has been already used, duplicate ignored
<to be read again>
\relax
l.9679 ...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.9679 ...rA{Matrix}{Assign Matrix Values}{Matrix}
[3131]
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[]\T1/ptm/m/n/10 a ma-trix, or list of ma-tri-ces, with the same di-men-sions a
s
Underfull \hbox (badness 3108) in paragraph at lines 9743--9746
[]\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 9743--9746
\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
[3132] [3133] [3134]
Underfull \hbox (badness 2435) in paragraph at lines 9917--9922
[]\T1/ptm/m/n/10 The model ma-tri-ces for each el-e-ment of \T1/pcr/m/n/10 form
ula(object)\T1/ptm/m/n/10 , cal-cu-lated us-ing \T1/pcr/m/n/10 data\T1/ptm/m/n/
10 ,
[3135] [3136] [3137] [3138] [3139]
Underfull \hbox (badness 7291) in paragraph at lines 10207--10209
[]\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
[3140] [3141] [3142]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10423--10423
[]\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation,
weights,
[3143]
Underfull \hbox (badness 1596) in paragraph at lines 10452--10478
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o
f the form
[3144] [3145] [3146]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10628--10628
[]\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation,
weights,[]
[3147] [3148]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 10779--10779
[] \T1/pcr/m/n/10 opt = c("nlminb", "nlm"), natural = TRUE, sigma =
NULL, ...)[]
Underfull \hbox (badness 2213) in paragraph at lines 10790--10795
[]\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[][][]
[3149]
Underfull \hbox (badness 10000) in paragraph at lines 10812--10816
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 10831--10833
[]\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 10867--10867
[]\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[]
[3150] [3151] [3152] [3153]
Overfull \hbox (96.18033pt too wide) in paragraph at lines 11123--11123
[]\T1/pcr/m/n/9 cfm1 <- confint(fm1) # via profiling each % FIXME: only *one*
message instead of one *each*[]
[3154] [3155] [3156] [3157] [3158] [3159] [3160] [3161] [3162] [3163] [3164]
[3165]
Underfull \hbox (badness 6268) in paragraph at lines 11902--11912
[][][]\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 ,
[3166] [3167] [3168] [3169]
Underfull \hbox (badness 10000) in paragraph at lines 12163--12169
[][][]\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 ,
[3170] [3171] [3172] [3173] [3174]
Underfull \hbox (badness 6876) in paragraph at lines 12485--12487
[]\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
[3175] [3176]
Underfull \hbox (badness 2452) in paragraph at lines 12641--12648
[][][]\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 ,
[3177]
Underfull \hbox (badness 10000) in paragraph at lines 12706--12712
[][][]\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 ,
[3178] [3179] [3180] [3181] [3182] [3183] [3184] [3185] [3186] [3187] [3188]
[3189] [3190] [3191]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13658--13658
[]\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline =
0, id = 0.05)[]
[3192]
Underfull \hbox (badness 10000) in paragraph at lines 13685--13688
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nffGroupedD
ata\T1/ptm/m/n/10 , rep-re-sent-ing a
Underfull \hbox (badness 6016) in paragraph at lines 13713--13716
[]\T1/ptm/m/n/10 an op-tional char-ac-ter string with the la-bel for the hor-i-
zon-tal axis.
Underfull \hbox (badness 2653) in paragraph at lines 13713--13716
\T1/ptm/m/n/10 De-fault is the \T1/pcr/m/n/10 y \T1/ptm/m/n/10 el-e-ments of \T
1/pcr/m/n/10 attr(object, "labels") \T1/ptm/m/n/10 and
Underfull \hbox (badness 1975) in paragraph at lines 13720--13723
[]\T1/ptm/m/n/10 an op-tional func-tion passed as the \T1/pcr/m/n/10 strip \T1/
ptm/m/n/10 ar-gu-ment to the \T1/pcr/m/n/10 dotplot
Underfull \hbox (badness 1838) in paragraph at lines 13728--13735
[]\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 13728--13735
\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
[3193]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 13785--13785
[]\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect,
panel,[]
Underfull \hbox (badness 10000) in paragraph at lines 13792--13795
[]\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 13792--13795
\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
[3194]
Underfull \hbox (badness 4582) in paragraph at lines 13820--13823
[]\T1/ptm/m/n/10 optional char-ac-ter strings with the la-bels for the plot. De
-fault is
Underfull \hbox (badness 2418) in paragraph at lines 13820--13823
\T1/ptm/m/n/10 the cor-re-spond-ing el-e-ments of \T1/pcr/m/n/10 attr(object,
"labels") \T1/ptm/m/n/10 and
Underfull \hbox (badness 2990) in paragraph at lines 13824--13827
[]\T1/ptm/m/n/10 an op-tional func-tion passed as the \T1/pcr/m/n/10 strip \T1/
ptm/m/n/10 ar-gu-ment to the \T1/pcr/m/n/10 xyplot
[3195]
Underfull \hbox (badness 10000) in paragraph at lines 13900--13903
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nmGroupedDa
ta\T1/ptm/m/n/10 , rep-re-sent-ing a
Underfull \hbox (badness 1472) in paragraph at lines 13925--13932
\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 ,
[3196]
Underfull \hbox (badness 10000) in paragraph at lines 13994--13996
[][][]\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 ,
[3197] [3198] [3199] [3200]
Underfull \hbox (badness 1540) in paragraph at lines 14209--14214
\T1/ptm/m/n/10 a \T1/pcr/m/n/10 loess \T1/ptm/m/n/10 smoother is added to the p
lot. If \T1/pcr/m/n/10 showModel = TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n/10 x \T1
/ptm/m/n/10 in-cludes an
Underfull \hbox (badness 1215) in paragraph at lines 14256--14258
[]\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis.
De-faults to
[3201] [3202] [3203] [3204] [3205]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 14500--14500
[]\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female",
"Male","Male"),[]
[3206] [3207] [3208] [3209] [3210] [3211] [3212] [3213] [3214]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.15153 ...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.15153 ...Extract Random Effects}{random.effects}
[3215] [3216] [3217]
[3218] [3219] [3220] [3221] [3222] [3223] [3224]
Underfull \hbox (badness 1009) in paragraph at lines 15810--15819
\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
[3225] [3226] [3227]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 15957--15957
[] \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi
st = FALSE, ...)[]
[3228] [3229] [3230] [3231]
Underfull \hbox (badness 10000) in paragraph at lines 16235--16253
[]\T1/ptm/m/n/10 any of the fol-low-ing: (i) a one-sided for-mula of the form
Underfull \hbox (badness 1708) in paragraph at lines 16235--16253
\T1/pcr/m/n/10 ~x1+...+xn | g1/.../gm\T1/ptm/m/n/10 , with \T1/pcr/m/n/10 x1+..
.+xn \T1/ptm/m/n/10 spec-i-fy-ing the model
[3232]
Underfull \hbox (badness 10000) in paragraph at lines 16292--16298
[][][]\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 ,
[3233]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 16323--16323
[] \T1/pcr/m/n/10 method = c("REML", "ML"), niterEM = c(40, 200), useG
en, ...)[]
[3234] [3235] [3236] [3237] [3238] [3239] [3240]
Underfull \hbox (badness 1728) in paragraph at lines 16812--16815
[]\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou
t-put in the
[3241] [3242] [3243] [3244] [3245]
Underfull \hbox (badness 1867) in paragraph at lines 17147--17156
\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 17147--17156
\T1/pcr/m/n/10 "Compound Symmetry" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdCompSymm
\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Diagonal"
Underfull \hbox (badness 10000) in paragraph at lines 17147--17156
\T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdDiag\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Multip
le of an Identity" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdIdent\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17147--17156
\T1/pcr/m/n/10 "General Positive-Definite, Natural Parametrization"
[3246]
Underfull \hbox (badness 10000) in paragraph at lines 17211--17219
[]\T1/ptm/m/n/10 an op-tional char-ac-ter string with a de-scrip-tion of the
Underfull \hbox (badness 10000) in paragraph at lines 17211--17219
\T1/pcr/m/n/10 varFunc \T1/ptm/m/n/10 class. De-fault de-pends on the method fu
nc-tion:
Underfull \hbox (badness 10000) in paragraph at lines 17211--17219
\T1/pcr/m/n/10 "Combination of variance functions" \T1/ptm/m/n/10 for \T1/pcr/m
/n/10 varComb\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17211--17219
\T1/pcr/m/n/10 "Constant plus power of covariate" \T1/ptm/m/n/10 for \T1/pcr/m/
n/10 varConstPower\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17211--17219
\T1/pcr/m/n/10 "Exponential of variance covariate" \T1/ptm/m/n/10 for \T1/pcr/m
/n/10 varExp\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17211--17219
\T1/pcr/m/n/10 "Different standard deviations per stratum" \T1/ptm/m/n/10 for
Underfull \hbox (badness 10000) in paragraph at lines 17211--17219
\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 ,
[3247] [3248] [3249] [3250]
Underfull \hbox (badness 10000) in paragraph at lines 17458--17465
[][][]\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 ,
[3251] [3252] [3253] [3254] [3255] [3256] [3257] [3258]
Underfull \hbox (badness 10000) in paragraph at lines 17993--18003
[][][]\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 17993--18003
[][]\T1/pcr/m/n/10 Variogram.corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10
Variogram.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corSphe
r[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 3579) in paragraph at lines 18031--18036
\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
[3259]
Underfull \hbox (badness 3579) in paragraph at lines 18095--18100
\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
[3260]
Underfull \hbox (badness 3579) in paragraph at lines 18158--18163
\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
[3261]
Underfull \hbox (badness 1577) in paragraph at lines 18219--18221
[]\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 18221--18226
\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
[3262]
Underfull \hbox (badness 3579) in paragraph at lines 18284--18289
\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
[3263]
Underfull \hbox (badness 10000) in paragraph at lines 18317--18326
[][][]\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 18317--18326
[][]\T1/pcr/m/n/10 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 V
ariogram.corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corRatio[][]
[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 3579) in paragraph at lines 18356--18361
\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
[3264] [3265] [3266]
Underfull \hbox (badness 1009) in paragraph at lines 18505--18514
\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
[3267] [3268]
Underfull \hbox (badness 1009) in paragraph at lines 18639--18648
\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
[3269] [3270] [3271] [3272] [3273] [3274] [3275] [3276]) (./nnet-pkg.tex
Chapter 26.
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.multinom}
) has been already used, duplicate ignored
<to be read again>
\relax
l.47 ...t Multinomial Log-linear Models}{multinom}
pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.multinom.1}) has been already used, du
plicate ignored
<to be read again>
\relax
l.47 ...t Multinomial Log-linear Models}{multinom}
[3277]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 70--70
[] \T1/pcr/m/n/10 contrasts = NULL, Hess = FALSE, summ = 0, censored =
FALSE,[]
Underfull \hbox (badness 10000) in paragraph at lines 78--87
[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[3278] [3279] [3280]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 369--369
[]\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size =
2, rang = 0.1,[]
[3281]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 426--426
[]\T1/pcr/m/n/9 targets <- matrix(c(rep(c(1,0,0),50), rep(c(0,1,0),50), rep(c(
0,0,1),50)),[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 429--429
[]\T1/pcr/m/n/9 ir1 <- nnet(ir[samp,], targets[samp,], size=2, rang=0.1, decay
=5e-4, maxit=200)[]
[3282]
Underfull \hbox (badness 4013) in paragraph at lines 474--477
\T1/ptm/m/n/10 the cor-re-spond-ing class (which is prob-a-bly only use-ful if
the net was gen-er-ated by
[3283]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 509--509
[]\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size =
2, rang = 0.1,[]
[3284]) (./rpart-pkg.tex
Chapter 27.
[3285] [3286] [3287] [3288]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 324--324
[]\T1/pcr/m/n/10 labels(object, digits = 4, minlength = 1L, pretty, collapse =
TRUE, ...)[]
[3289]
Underfull \hbox (badness 10000) in paragraph at lines 373--377
[]\T1/ptm/m/n/10 Vector of split la-bels (\T1/pcr/m/n/10 collapse = TRUE\T1/ptm
/m/n/10 ) or ma-trix of left and right splits
[3290] [3291] [3292]
Underfull \hbox (badness 1442) in paragraph at lines 591--597
[]\T1/ptm/m/n/10 if \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 , the leaf nodes will be
at the hor-i-zon-tal plot co-or-di-nates of
[3293] [3294]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 728--728
[] \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep =
""),[]
[3295]
Underfull \hbox (badness 2941) in paragraph at lines 785--787
[]\T1/ptm/m/n/10 a plot of \T1/pcr/m/n/10 rpart \T1/ptm/m/n/10 is cre-ated us-i
ng the \T1/pcr/m/n/10 postscript \T1/ptm/m/n/10 driver, or the cur-rent de-vice
if
[3296]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 902--902
[]\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie
s, probabilities[]
[3297]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 921--921
[]\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d
igits"), ...)[]
[3298] [3299] [3300]
Underfull \hbox (badness 2310) in paragraph at lines 1113--1116
[]\T1/ptm/m/n/10 For re-gres-sion or \T1/pcr/m/n/10 anova \T1/ptm/m/n/10 trees
all three resid-ual def-i-ni-tions re-duce to
Overfull \hbox (6.78088pt too wide) in paragraph at lines 1163--1163
[]\T1/pcr/m/n/10 rpart(formula, data, weights, subset, na.action = na.rpart, m
ethod,
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1164--1164
[] \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos
t, ...)[]
Underfull \hbox (badness 2837) in paragraph at lines 1187--1196
[]\T1/ptm/m/n/10 one of \T1/pcr/m/n/10 "anova"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "
poisson"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "class" \T1/ptm/m/n/10 or \T1/pcr/m/n/1
0 "exp"\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 method
Underfull \hbox (badness 2088) in paragraph at lines 1187--1196
\T1/ptm/m/n/10 is miss-ing then the rou-tine tries to make an in-tel-li-gent gu
ess. If \T1/pcr/m/n/10 y
Underfull \hbox (badness 1817) in paragraph at lines 1187--1196
\T1/ptm/m/n/10 is a sur-vival ob-ject, then \T1/pcr/m/n/10 method = "exp" \T1/p
tm/m/n/10 is as-sumed, if \T1/pcr/m/n/10 y \T1/ptm/m/n/10 has 2
[3301]
Underfull \hbox (badness 2846) in paragraph at lines 1226--1228
[]\T1/ptm/m/n/10 a list of op-tions that con-trol de-tails of the \T1/pcr/m/n/1
0 rpart \T1/ptm/m/n/10 al-go-rithm. See
[3302]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1270--1270
[]\T1/pcr/m/n/9 par(mfrow = c(1,2), xpd = NA) # otherwise on some devices the
text is clipped[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 1286--1286
[]\T1/pcr/m/n/10 rpart.control(minsplit = 20, minbucket = round(minsplit/3), c
p = 0.01,
Overfull \hbox (60.78088pt too wide) in paragraph at lines 1287--1287
[] \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate
= 2, xval = 10,[]
[3303] [3304] [3305] [3306] [3307] [3308]
Underfull \hbox (badness 1565) in paragraph at lines 1739--1742
[]\T1/ptm/m/n/10 the ploidy sta-tus of the tu-mor, from flow cy-tom-e-try. Val-
ues are `\T1/pcr/m/n/10 diploid\T1/ptm/m/n/10 ',
[3309] [3310]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1833--1833
[] \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n =
FALSE,[]
[3311] [3312] [3313]) (./spatial-pkg.tex [3314]
Chapter 28.
[3315] [3316] [3317] [3318] [3319] [3320]
Underfull \hbox (badness 10000) in paragraph at lines 423--427
[3321] [3322] [3323] [3324] [3325] [3326] [3327] [3328] [3329] [3330] [3331]
[3332] [3333]) (./survival-pkg.tex [3334]
Chapter 29.
[3335] [3336]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 171--171
[]\T1/pcr/m/n/9 aareg(formula = Surv(time, status) ~ age + sex + ph.ecog, data
= lung, nmin = 1[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 190--190
[]\T1/pcr/m/n/9 ## Not run: lines(lfit2[4], col=2) # Nearly the same, until t
he last point[]
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[]\T1/pcr/m/n/9 # Chronic Granuomatous Disease. See section 8.5 of Therneau a
nd Grambsch.[]
[3337] [3338]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}
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\relax
l.326 ... Myelogenous Leukemia survival data}{aml}
[3339] [3340]
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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)[]
[3341]
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[] \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog),
lung)[]
[3342] [3343]
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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"),[]
[3345] [3346]
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[] \T1/pcr/m/n/9 subcoh = ~subcohort, id=~seqno, stratum=~instit, cohort.siz
e=stratsizes,[]
[3347] [3348] [3349]
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[]\T1/ptm/m/n/10 F.J. Anscombe (1949). Trans-for-ma-tions of Pois-son, bi-no-mi
al and negative-binomial data.
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[]\T1/pcr/m/n/9 ppois(4, 10.24153) #chance of seeing 4 or fewer events wit
h large rate[]
[3350] [3351]
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[]\T1/pcr/m/n/9 ## Not run: clogit(case ~ spontaneous + induced + strata(strat
um), data=infert)
[3352]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col
on}) has been already used, duplicate ignored
<to be read again>
\relax
l.1178 ...erapy for Stage B/C colon cancer}{colon}
[3353]
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[] \T1/pcr/m/n/10 cluster, ymin, ymax, timewt= c("n", "S", "S/G", "n/G", "n/G
2", "I"),[]
[3354] [3355] [3356] [3357] [3358] [3359]
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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 ,
[3360]
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[]\T1/pcr/m/n/10 iter.max = 20, toler.inf = sqrt(eps), outer.max = 10, timefix
=TRUE)[]
[3361] [3362] [3363] [3364] [3365] [3366]
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[] \T1/pcr/m/n/9 [1] "extreme" "logistic" "gaussian" "weibull" "
exponential"[]
[3367] [3368] [3369] [3370]
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[]\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t
df = 5,[]
[3371] [3372] [3373] [3374] [3375]
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[]\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt
y(id), kidney)
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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
[3377]
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[]\T1/ptm/m/n/10 this pa-ram-e-ter is no longer nec-es-sary and is ig-nored. Se
e the note in
[3378]
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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 )))[]
[3379] [3380] [3381] [3382] [3383]
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[]\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential
ly the same.[]
[3384] [3385] [3386] [3387]
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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 )))[]
[3388]
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[3390] [3391] [3392] [3393] [3394]
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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,[]
[3395] [3396]
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[]\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign),
collapse,[]
[3397]
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[]\T1/pcr/m/n/9 mresid <- (lung$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[]
[3398]
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[] \T1/pcr/m/n/9 predict(fit, reference="sample") + sum(coef(fit) * fit$means
, na.rm=TRUE)[]
[3399]
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[]\T1/pcr/m/n/9 pct <- 1:98/100 # The 100th percentile of predicted survival
is at +infinity[]
[3400] [3401]
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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
[3402] [3403]
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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, ...)[]
[3404] [3405] [3406]
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[] \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year=
entry.dt),[]
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[]\T1/ptm/m/n/10 an ar-ray con-tain-ing the ex-pected num-ber of events (or per
-son years if
[3407]
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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)) +[]
[3408] [3409] [3410] [3411] [3412]
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[3414]
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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
[3415] [3416] [3417] [3418] [3419]
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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)[]
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has been already used, duplicate ignored
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\relax
l.5705 ...ata from a soldering experiment}{solder}
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ation with the same identifier (name{Rfn.solder.1}) has been already used, dupl
icate ignored
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l.5705 ...ata from a soldering experiment}{solder}
[3420]
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[]\T1/pcr/m/n/10 statefig(layout, connect, margin = 0.03, box = TRUE, cex = 1,
col = 1,
[3421] [3422] [3423] [3424] [3425] [3426]
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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,[]
[3427] [3428] [3429] [3430]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 6459--6459
[] \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 ),[]
[3431] [3432]
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 length \T1/ptm/m/n/10 of a \T1/pcr/m/n/10 S
urv \T1/ptm/m/n/10 ob-ject is the num-ber of sur-vival times
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\T1/ptm/m/n/10 it con-tains, not the num-ber of items re-quired to en-code it,
e.g.,
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\T1/pcr/m/n/10 x <- Surv(1:4, 5:9, c(1,0,1,0)); length(x) \T1/ptm/m/n/10 has a
value of 4. Like-
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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
[3434] [3435]
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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
[3436]
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[] \T1/pcr/m/n/9 rmap= list(age=(accept.dt - birth.dt), sex=1
, year=accept.dt),[]
[3437]
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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
[3438]
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[]\T1/ptm/m/n/10 numeric value to scale the re-sults. If \T1/pcr/m/n/10 ratetab
le \T1/ptm/m/n/10 is in units/day,
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[] \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d
t-entry.dt)),[]
[3439]
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[]\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival
by 1/2 years[]
[3440] [3441] [3442]
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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 ,
[3443]
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[] \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit",
"arcsin"),[]
[3444] [3445]
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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/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the er-ror. Pos-si-ble val-
ues are
[3448] [3449]
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[]\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored
(status=3),[]
[3450] [3451] [3452] [3453]
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[]\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit,
survtype,
[3454]
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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
[3455] [3456]
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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 ,
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\T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 ,\T1/pcr/m/n/10 "lognormal" \T1/ptm/m/n
/10 and \T1/pcr/m/n/10 "loglogistic"\T1/ptm/m/n/10 . Oth-er-wise, it is
[3457]
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[]\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi
on. The survreg[]
[3458]
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[3459] [3460]
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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 )[]
[3461]
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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 )[]
[3462] [3463] [3464] [3465] [3466]
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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)[]
[3467] [3468] [3469] [3470] [3471] [3472]pdfTeX warning (ext4): destination wit
h the same identifier (name{Rfn.xtfrm.Surv}) has been already used, duplicate i
gnored
<to be read again>
\relax
l.9488 ...ting order for Surv objects}{xtfrm.Surv}
[3473]
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[]\T1/pcr/m/n/10 levels, test = c("global", "trend", "pairwise"), predict = "l
inear",[]
[3474] [3475] [3476]) (./fullrefman.ind [3477] [3478] [3479] [3480] [3481]
[3482] [3483] [3484] [3485] [3486] [3487] [3488] [3489] [3490] [3491] [3492]
[3493] [3494] [3495] [3496] [3497]
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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 ,
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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 Logic,CsparseMatrix,CsparseMatrix-method
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[]\T1/pcr/m/n/10 Logic,triangularMatrix,diagonalMatrix-method
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[]\T1/pcr/m/n/10 Ops,atomicVector,sparseVector-method
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[]\T1/pcr/m/n/10 qr.resid,sparseQR,numeric-method
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[]\T1/pcr/m/n/10 rcond,ddenseMatrix,character-method
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[]\T1/pcr/m/n/10 Schur,diagonalMatrix,logical-method
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(/usr/share/texmf-dist/tex/latex/psnfss/t1pcr.fd) [1] [2] [3] [4] [5] [6]
[7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21]
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Chapter 1.
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[]\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h
igh-est, for
[3]
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[]\T1/pcr/m/n/10 .Devices \T1/ptm/m/n/10 is a [][]pairlist[][][] of length-one
char-ac-ter vec-tors. The first en-try is al-ways
[4]
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[]\T1/ptm/m/n/10 the small-est pos-i-tive floating-point num-ber \T1/pcr/m/n/10
x \T1/ptm/m/n/10 such that
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\T1/pcr/m/n/10 1 + x != 1\T1/ptm/m/n/10 . It equals \T1/pcr/m/n/10 double.base
^ ulp.digits \T1/ptm/m/n/10 if ei-
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\T1/ptm/m/n/10 ther \T1/pcr/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/pcr/m
/n/10 double.rounding \T1/ptm/m/n/10 is 0; oth-er-wise,
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\T1/ptm/m/n/10 it is \T1/pcr/m/n/10 (double.base ^ double.ulp.digits) / 2\T1/pt
m/m/n/10 . Nor-mally
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[]\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/pcr/m/n/10 x \T1
/ptm/m/n/10 such that \T1/pcr/m/n/10 1 - x != 1\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 It equals \T1/pcr/m/n/10 double.base ^ double.neg.ulp.digits \T1
/ptm/m/n/10 if
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\T1/pcr/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/pcr/m/n/10 double.roundin
g \T1/ptm/m/n/10 is 0; oth-er-wise, it is
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\T1/pcr/m/n/10 (double.base ^ double.neg.ulp.digits) / 2\T1/ptm/m/n/10 . Nor-ma
lly
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[]\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-
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\T1/ptm/m/n/10 i-cally, it is equal to \T1/pcr/m/n/10 (1 - double.neg.eps) *
[5] [6] [7]
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[][][]\T1/pcr/m/n/10 R.version[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 Sys.
info[][][] \T1/ptm/m/n/10 give more de-tails about the OS. In par-tic-u-lar,
[8]
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[]\T1/ptm/m/n/10 logical: should \T1/pcr/m/n/10 minlength \T1/ptm/m/n/10 be ob-
served strictly? Note that set-ting
[9] [10]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T
1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ',
[11] [12] (/usr/share/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [13] [14] [15]
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[]\T1/pcr/m/n/10 all.names(expr, functions = TRUE, max.names = -1L, unique = F
ALSE)
[16] [17] [18] [19]
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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
[20] [21] [22] [23]
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[]\T1/pcr/m/n/10 %% \T1/ptm/m/n/10 in-di-cates \T1/pcr/m/n/10 x mod y \T1/ptm/m
/n/10 and \T1/pcr/m/n/10 %/% \T1/ptm/m/n/10 in-di-cates in-te-ger di-vi-sion. I
t is guar-an-teed that
[24] [25] [26]
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[] \T1/pcr/m/n/10 cut.names = FALSE, col.names = names(x), fix.em
pty.names = TRUE,[]
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[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , set-ting row n
ames and con-vert-ing col-umn names
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\T1/ptm/m/n/10 (to syn-tac-tic names: see [][]\T1/pcr/m/n/10 make.names[][][]\T
1/ptm/m/n/10 ) is op-tional. Note that all
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\T1/ptm/m/n/10 of \T1/phv/m/n/10 R\T1/ptm/m/n/10 's \T1/ptm/b/n/10 base \T1/ptm
/m/n/10 pack-age \T1/pcr/m/n/10 as.data.frame() \T1/ptm/m/n/10 meth-ods use \T1
/pcr/m/n/10 optional
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\T1/ptm/m/n/10 only for col-umn names treat-ment, ba-si-cally with the mean-ing
of
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[][]\T1/pcr/m/n/10 data.frame[][][](*, check.names = !optional)\T1/ptm/m/n/10 .
See also the
[27]
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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
[28]
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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
[29] [30]
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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)[]
[31]
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[]\T1/ptm/m/n/10 If it is a list, the equiv-a-lent of [][]\T1/pcr/m/n/10 list2e
nv[][][](x, parent = emptyenv())
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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]
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[]\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by
[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]
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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
[38] [39]
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[]\T1/pcr/m/n/10 attach(what, pos = 2L, name = deparse(substitute(what), backt
ick=FALSE),
[40] [41] [42]
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[]\T1/ptm/m/n/10 The ex-trac-tion func-tion first looks for an ex-act match to
\T1/pcr/m/n/10 which \T1/ptm/m/n/10 amongst the at-
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\T1/ptm/m/n/10 tributes of \T1/pcr/m/n/10 x\T1/ptm/m/n/10 , then (un-less \T1/p
cr/m/n/10 exact = TRUE\T1/ptm/m/n/10 ) a unique par-tial match. (Set-ting
[43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56]
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[]\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim
-ited by set-ting
[57] [58] [59]
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[] \T1/pcr/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...)
, recursive=recursive)
[60] [61] [62] [63]
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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
[64] [65]
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[]\T1/ptm/m/n/10 is ICU avail-able for col-la-tion? See the help on [][]Com-par
-i-son[][][] and
[66] [67]
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[]\T1/pcr/m/n/9 cat(paste(letters, 100* 1:26), fill = TRUE, labels = paste0("{
", 1:10, "}:"))[]
[68]
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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
[69]
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 cbind \T1/ptm/m/n/10 data frame method is j
ust a wrap-per for
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[][]\T1/pcr/m/n/10 data.frame[][][](..., check.names = FALSE)\T1/ptm/m/n/10 . T
his means that it will split ma-
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\T1/ptm/m/n/10 trix columns in data frame ar-gu-ments, and con-vert char-ac-ter
columns to fac-tors un-less
[70]
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[]\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna
mes (default)[]
[71] [72] [73] [74]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c
har-ac-ter by
[75] [76] [77] [78] [79] [80]
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[]\T1/ptm/m/n/10 When a generic func-tion \T1/pcr/m/n/10 fun \T1/ptm/m/n/10 is
ap-plied to an ob-ject with class at-tribute
[81] [82] [83] [84] [85] [86] [87] [88]
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[]\T1/ptm/m/n/10 Collation of char-ac-ter strings is a com-plex topic. For an i
n-tro-duc-tion see [][]$\T1/pcr/m/n/10 https : / /
[89] [90]
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[]\T1/pcr/m/n/9 ## The exact result of this *depends* on the platform, compile
r, math-library:[]
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[]\T1/pcr/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex
_)), is.na(Im(NA_complex_)))[]
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[]\T1/pcr/m/n/9 showC(NpNA)# but not always is {shows \TS1/pcr/m/n/9 '\T1/pcr
/m/n/9 (R = NaN, I = NA)\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 on some platforms}[]
[91] [92] [93]
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[]\T1/ptm/m/n/10 User in-ter-rupts sig-nal a con-di-tion of class \T1/pcr/m/n/1
0 interrupt \T1/ptm/m/n/10 that in-her-its di-rectly from class
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[]\T1/ptm/m/n/10 Restarts are used for es-tab-lish-ing re-cov-ery pro-to-cols.
They can be es-tab-lished us-ing
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[]\T1/ptm/m/n/10 New restarts for \T1/pcr/m/n/10 withRestarts \T1/ptm/m/n/10 ca
n be spec-i-fied in sev-eral ways. The sim-plest is in
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[]\T1/ptm/m/n/10 One ad-di-tional field that can be spec-i-fied for a restart i
s \T1/pcr/m/n/10 interactive\T1/ptm/m/n/10 . This should
[94] [95]
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[]\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e
ncoding"))[]
[96]
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[]\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 :
[97] [98]
Underfull \hbox (badness 10000) in paragraph at lines 6580--6583
[]\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 6580--6583
\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
[99] [100]
Underfull \hbox (badness 1248) in paragraph at lines 6762--6768
\T1/ptm/m/n/10 Byte Or-der Mark if present (which it of-ten is for files and we
b-pages gen-er-ated by Mi-
Underfull \hbox (badness 2080) in paragraph at lines 6762--6768
\T1/ptm/m/n/10 crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not rec-o
m-mended) when writ-ing it
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[]\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in
g from
[101]
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\T1/ptm/m/n/10 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http : / / standar
ds . freedesktop . org / clipboards-[]spec /
[102] [103]
Underfull \vbox (badness 10000) has occurred while \output is active [104]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7016--7016
[]\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE"))
; close(con)[]
[105]
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\T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the
first el-e-
[106] [107] [108] [109]
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[]\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th
e call to
[110] [111]
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[]\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org") ## this redirect
s to https://[]
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[]\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h
igh-est, for
[112] [113] [114]
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[]\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng
th.out = 24)[]
[115] [116]
Underfull \hbox (badness 8132) in paragraph at lines 7836--7840
[]\T1/ptm/m/n/10 logical: should char-ac-ter vec-tors be con-verted to fac-tors
? The
Underfull \hbox (badness 4543) in paragraph at lines 7836--7840
\T1/ptm/m/n/10 `factory-fresh' de-fault is \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ,
but this can be changed by set-ting
Underfull \hbox (badness 10000) in paragraph at lines 7855--7865
[]\T1/pcr/m/n/10 data.frame \T1/ptm/m/n/10 con-verts each of its ar-gu-ments to
a data frame by call-ing
Underfull \hbox (badness 1062) in paragraph at lines 7855--7865
[][]\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
[117]
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[]\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")
Underfull \hbox (badness 7451) in paragraph at lines 7926--7936
[][][]\T1/pcr/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.data.frame
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10
, [][]\T1/pcr/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 names[]
[][] \T1/ptm/m/n/10 (for the col-
Underfull \hbox (badness 3449) in paragraph at lines 7926--7936
\T1/ptm/m/n/10 umn names), [][]\T1/pcr/m/n/10 [.data.frame[][][] \T1/ptm/m/n/10
for sub-set-ting meth-ods and \T1/pcr/m/n/10 I(matrix(..)) \T1/ptm/m/n/10 ex-a
m-
[118] [119] [120] [121] [122] [123]
Underfull \hbox (badness 10000) in paragraph at lines 8358--8370
\T1/pcr/m/n/10 23:59:59", format = "%Y-%m-%d %H:%M:%S", tz = "UTC") \T1/ptm/m/n
/10 may give \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 8358--8370
\T1/ptm/m/n/10 and hence \T1/pcr/m/n/10 as.POSIXct("1969-12-31 23:59:59", tz =
"UTC") \T1/ptm/m/n/10 will give
[124] [125] [126]
Underfull \hbox (badness 5802) in paragraph at lines 8585--8589
[]\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 read.dcf(all = FALSE) \T1/ptm/m/n/10
reads the file byte-by-byte. This al-lows a
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[][][]$\T1/pcr/m/n/10 https : / / www . debian . org / doc / debian-[]policy /
index . html #
[127] [128] [129]
Underfull \hbox (badness 10000) in paragraph at lines 8805--8809
[]\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
[130]
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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})[]
[131]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 8920--8920
[] \T1/pcr/m/n/10 backtick = mode(expr) %in% c("call", "expression", "(
", "function"),[]
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[] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "sh
owAttributes"),[]
[132] [133]
Underfull \hbox (badness 5403) in paragraph at lines 9039--9041
[]\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 9058--9060
[]\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
[134]
Underfull \hbox (badness 1132) in paragraph at lines 9130--9137
\T1/ptm/m/n/10 at-tributes as well, but not to use any of the other op-tions to
make the re-sult parseable.
[135]
Underfull \hbox (badness 1603) in paragraph at lines 9266--9269
[]\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
[136] [137] [138] [139] [140] [141] [142] [143] [144]
Underfull \hbox (badness 1917) in paragraph at lines 9872--9877
[]\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
[145]
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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 9928--9928
[]\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling
on both levels[]
[146] [147]
Underfull \hbox (badness 1168) in paragraph at lines 10030--10035
\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 10069--10075
[]\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 10076--10079
[]\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
[148] [149]
Underfull \hbox (badness 2828) in paragraph at lines 10235--10239
[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / IEEE _ 754-[]19
85$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / en . wikipedia .
Underfull \hbox (badness 10000) in paragraph at lines 10235--10239
\T1/pcr/m/n/10 org / wiki / IEEE _ 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr
/m/n/10 https : / / en . wikipedia . org / wiki / Double _
[150]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 10268--10268
[] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "showA
ttributes"))[]
[151] [152] [153]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10483--10483
[]\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon
th.abb[5:9]))
[154]
Underfull \hbox (badness 1629) in paragraph at lines 10557--10561
[]\T1/ptm/m/n/10 Promises will nor-mally only be en-coun-tered by users as a re
-sult of lazy-loading (when
[155] [156]
Underfull \hbox (badness 2150) in paragraph at lines 10658--10661
[]\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered
from the re-verse
Underfull \hbox (badness 3690) in paragraph at lines 10672--10680
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 anyDuplicated\T1/ptm/m/n/10 , \T1/pcr/m/n/10
anyDuplicated(x, ...) \T1/ptm/m/n/10 is a ``gen-er-al-ized'' short-cut for
Underfull \hbox (badness 10000) in paragraph at lines 10681--10683
[]\T1/pcr/m/n/10 duplicated(x, fromLast = TRUE) \T1/ptm/m/n/10 is equiv-a-lent
to but faster than
[157]
Underfull \hbox (badness 3735) in paragraph at lines 10701--10708
[]\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \
T1/pcr/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to
[158] [159]
Underfull \hbox (badness 10000) in paragraph at lines 10897--10900
[]\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
[160] [161] [162] [163] [164] [165] [166] [167] [168] [169]
Underfull \hbox (badness 5288) in paragraph at lines 11594--11596
[]\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val
ue of
Underfull \hbox (badness 3039) in paragraph at lines 11604--11609
[]\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
[170]
Underfull \hbox (badness 10000) in paragraph at lines 11664--11666
[]\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for
[171]
Underfull \hbox (badness 4569) in paragraph at lines 11781--11785
[]\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 11781--11785
\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
[172] [173]
Underfull \hbox (badness 10000) in paragraph at lines 11896--11898
[]\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
[174]
Underfull \hbox (badness 2790) in paragraph at lines 11939--11941
[]\T1/pcr/m/n/10 get0(): \T1/ptm/m/n/10 The object---as from [][]\T1/pcr/m/n/10
get[][][](x, *)\T1/ptm/m/n/10 --- if \T1/pcr/m/n/10 exists(x, *) \T1/ptm/m/n/1
0 is true, oth-er-wise
[175] [176]
Underfull \hbox (badness 4048) in paragraph at lines 12110--12120
[]\T1/pcr/m/n/10 as.expression \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-me
nt into an ex-pres-sion ob-ject. It is
Underfull \hbox (badness 3657) in paragraph at lines 12110--12120
\T1/ptm/m/n/10 generic, and only the de-fault method is de-scribed here. (The d
e-fault method calls
[177] [178] [179]
Underfull \hbox (badness 5460) in paragraph at lines 12358--12367
[]\T1/ptm/m/n/10 Both \T1/pcr/m/n/10 $ \T1/ptm/m/n/10 and \T1/pcr/m/n/10 [[ \T1
/ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a
l-
Underfull \hbox (badness 2221) in paragraph at lines 12358--12367
\T1/ptm/m/n/10 lowed and no par-tial match-ing is done. The se-man-tics of thes
e op-er-a-tions are those
Underfull \hbox (badness 2707) in paragraph at lines 12358--12367
\T1/ptm/m/n/10 of \T1/pcr/m/n/10 get(i, env = x, inherits = FALSE)\T1/ptm/m/
n/10 . If no match is found then \T1/pcr/m/n/10 NULL
Underfull \hbox (badness 2818) in paragraph at lines 12358--12367
\T1/ptm/m/n/10 is re-turned. The re-place-ment ver-sions, \T1/pcr/m/n/10 $<- \T
1/ptm/m/n/10 and \T1/pcr/m/n/10 [[<-\T1/ptm/m/n/10 , can also be used. Again,
Underfull \hbox (badness 6978) in paragraph at lines 12358--12367
\T1/ptm/m/n/10 only char-ac-ter ar-gu-ments are al-lowed. The se-man-tics in th
is case are those of
[180] [181] [182] [183] [184] [185]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12732--12732
[]\T1/pcr/m/n/9 ## "avector" := vector that keeps attributes. Could provide
a constructor[]
[186] [187] [188] [189]
Underfull \hbox (badness 5119) in paragraph at lines 13017--13020
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 iconv \T1/ptm/m/n/10 this will give the im-
ple-men-ta-tion as well as the ver-sion, for ex-am-ple
[190] [191]
Underfull \hbox (badness 2221) in paragraph at lines 13178--13187
\T1/ptm/m/n/10 en-tries. If ar-gu-ment \T1/pcr/m/n/10 ordered \T1/ptm/m/n/10 is
true (or \T1/pcr/m/n/10 ordered() \T1/ptm/m/n/10 is used) the re-sult has clas
s
[192] [193] [194] [195]
Underfull \hbox (badness 2253) in paragraph at lines 13439--13441
[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
done: see
[196] [197]
Underfull \hbox (badness 10000) in paragraph at lines 13554--13556
[]\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/pcr/m
/n/10 PATH \T1/ptm/m/n/10 and \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 with
[198] [199]
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[]\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See
[200]
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[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac
cess[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][][]\T1/ptm/m/n/10 ,
[201]
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[][][]$\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[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 13868--13868
[]\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode
= "0777")[]
[202]
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[][][]\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 ,
[203]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13970--13970
[]\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu
rsive = TRUE)[]
[204]
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[]\T1/pcr/m/n/9 ## will not give an error, maybe a warning about *all* locatio
ns it is found:[]
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[]\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F
ALSE,
Underfull \hbox (badness 7238) in paragraph at lines 14098--14105
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 findInterval \T1/ptm/m/n/10 finds
the in-dex of one vec-tor \T1/pcr/m/n/10 x \T1/ptm/m/n/10 in an-other, \T1/pcr
/m/n/10 vec\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 14098--14105
\T1/ptm/m/n/10 where the lat-ter must be non-decreasing. Where this is triv-ial
, equiv-a-lent to
Underfull \hbox (badness 2126) in paragraph at lines 14098--14105
\T1/pcr/m/n/10 apply( outer(x, vec, ">="), 1, sum)\T1/ptm/m/n/10 , as a mat-ter
of fact, the in-ter-nal al-go-
[205]
Underfull \hbox (badness 3965) in paragraph at lines 14106--14110
[]\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,
[206] [207]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 14269--14269
[] \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING)
Overfull \hbox (0.78088pt too wide) in paragraph at lines 14270--14270
[] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING)[]
[208] [209]
Underfull \hbox (badness 10000) in paragraph at lines 14349--14353
[]\T1/ptm/m/n/10 The C type \T1/pcr/m/n/10 Rcomplex \T1/ptm/m/n/10 is de-fined
in `\T1/pcr/m/n/10 Complex.h\T1/ptm/m/n/10 ' as a
Underfull \hbox (badness 1389) in paragraph at lines 14349--14353
\T1/pcr/m/n/10 typedef struct {double r; double i;}\T1/ptm/m/n/10 . It may or m
ay not be equiv-a-lent to
[210] [211]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 14497--14497
[]\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[]
[212]
Underfull \hbox (badness 1168) in paragraph at lines 14584--14588
[]\T1/ptm/m/n/10 Either a log-i-cal spec-i-fy-ing whether el-e-ments of a real
or com-plex vec-
Underfull \hbox (badness 2012) in paragraph at lines 14584--14588
\T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger
penalty (see
[213]
Underfull \hbox (badness 6944) in paragraph at lines 14679--14682
[][][]\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 ,
[214]
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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),[]
[215] [216]
Underfull \hbox (badness 10000) in paragraph at lines 14838--14840
[]\T1/pcr/m/n/10 prettyNum() \T1/ptm/m/n/10 is used for ``pret-ti-fy-ing'' (pos
-si-bly for-mat-ted) num-bers, also in
Overfull \hbox (48.78088pt too wide) in paragraph at lines 14857--14857
[] \T1/pcr/m/n/10 decimal.mark = getOption("OutDec"), input.d.mark =
decimal.mark,[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 14859--14859
[] \T1/pcr/m/n/10 zero.print = NULL, drop0trailing = FALSE, is.cmplx
= NA,[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 14862--14862
[]\T1/pcr/m/n/10 .format.zeros(x, zero.print, nx = suppressWarnings(as.numeric
(x)))[]
Underfull \hbox (badness 2790) in paragraph at lines 14868--14871
[]\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/ptm/m/n/10 the to-tal field width; if both \T1/pcr/m/n/10 digits \T1/ptm/
m/n/10 and \T1/pcr/m/n/10 width \T1/ptm/m/n/10 are un-spec-i-fied,
Underfull \hbox (badness 1024) in paragraph at lines 14899--14903
[]\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
[217]
Underfull \hbox (badness 10000) in paragraph at lines 14968--14970
[]\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
[218]
Underfull \hbox (badness 10000) in paragraph at lines 14974--14978
[]\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,
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\T1/ptm/m/n/10 so \T1/pcr/m/n/10 formatC(c(6.11, 13.1), digits = 2, format = "f
g") \T1/ptm/m/n/10 gives
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[]\T1/pcr/m/n/10 prettyNum \T1/ptm/m/n/10 is the util-ity func-tion for pret-ti
-fy-ing \T1/pcr/m/n/10 x\T1/ptm/m/n/10 . \T1/pcr/m/n/10 x \T1/ptm/m/n/10 can be
com-plex (or
Underfull \hbox (badness 3601) in paragraph at lines 15013--15017
[]\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 decimal.mark \T1/ptm/m/n/10 in
\T1/pcr/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt
m/m/n/10 3.2.0: for use
Underfull \hbox (badness 3302) in paragraph at lines 15013--15017
\T1/ptm/m/n/10 within [][]\T1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in
pack-ages which might be used with ear-lier ver-sions: use
[219]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 15080--15080
[]\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 [220]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 15102--15102
[]\T1/pcr/m/n/9 doLC <- FALSE # R warns, so change to TRUE manually if you wan
t see the effect[]
[221] [222] [223] [224] [225] [226] [227] [228] [229] [230] [231]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 15920--15920
[]\T1/pcr/m/n/9 utils::tail(getLoadedDLLs(), 2) # the last 2 loaded ones, stil
l a DLLInfoList[]
[232] [233]
Underfull \hbox (badness 2418) in paragraph at lines 16029--16033
\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 16036--16039
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 name \T1/ptm/m/n/10 con-tains only one sym-b
ol name and \T1/pcr/m/n/10 unlist \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\T1/ptm/
m/n/10 , then the sin-gle
Underfull \hbox (badness 2326) in paragraph at lines 16064--16071
[][][]\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 ,
[234] [235] [236] [237]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 16310--16310
[]\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F
ALSE,
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[]\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][]
[] (or char-ac-ter string for
[238] [239] [240] [241]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 16603--16603
[] \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around
"checking hack"[]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 16632--16632
[]\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 16683--16683
[] \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F
ALSE)[]
Underfull \hbox (badness 10000) in paragraph at lines 16689--16693
[]\T1/ptm/m/n/10 raw vec-tor con-tain-ing a [][]reg-u-lar ex-pres-sion[][][] (o
r fixed pat-tern for
Underfull \hbox (badness 1028) in paragraph at lines 16689--16693
\T1/pcr/m/n/10 fixed = TRUE\T1/ptm/m/n/10 ) to be matched in the given raw vec-
tor. Co-erced by
[243] [244] [245] [246] [247]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17048--17048
[]\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)))
[248] [249] [250] [251]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 17302--17302
[]\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F
ALSE)
[252] [253] [254]
Underfull \hbox (badness 2435) in paragraph at lines 17563--17565
[]\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/pcr/m/n/10 http : / / www
. unicode . org / reports / tr35 /
[255]
Underfull \hbox (badness 1867) in paragraph at lines 17605--17612
[]\T1/ptm/m/n/10 It is op-tional on Win-dows: if \T1/phv/m/n/10 R \T1/ptm/m/n/1
0 has been built against ICU, it will only be used if
Underfull \hbox (badness 1490) in paragraph at lines 17605--17612
\T1/ptm/m/n/10 en-vi-ron-ment vari-able \T1/pcr/m/n/10 R_ICU_LOCALE \T1/ptm/m/n
/10 is set or once \T1/pcr/m/n/10 icuSetCollate \T1/ptm/m/n/10 is called to se-
Underfull \hbox (badness 1490) in paragraph at lines 17605--17612
\T1/ptm/m/n/10 lect the lo-cale (as ICU and Win-dows dif-fer in their idea of l
o-cale names). Note that
Underfull \hbox (badness 2285) in paragraph at lines 17620--17622
[]\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\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.[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17638--17638
[] \T1/pcr/m/n/9 icuSetCollate(locale = "da_DK", case_first = "default"); p
rint(sort(x))[]
[256]
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[]\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se
t = TRUE,
[257] [258]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 17792--17792
[]\T1/pcr/m/n/9 ### For functions ("closure"s): ------------------------------
----------------[]
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[]\T1/pcr/m/n/9 identical(f, g) # TRUE, as bytecode is
ignored by default[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 17801--17801
[]\T1/pcr/m/n/9 ## GLM families contain several functions, some of which share
an environment:[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17807--17807
[]\T1/pcr/m/n/9 op <- options(keep.source = TRUE) # and so, these have differi
ng "srcref" :[]
[259] [260]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 17934--17934
[]\T1/pcr/m/n/9 ## This is a (not atypical) case where it is better *not* to u
se ifelse(),[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17942--17942
[]\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):[]
[261] [262] [263]
Underfull \hbox (badness 10000) in paragraph at lines 18147--18149
[]\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
[264]
Underfull \hbox (badness 4217) in paragraph at lines 18231--18240
[][][]\T1/pcr/m/n/10 length[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 length<-[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 dimnames<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dim[][][]\T1/ptm
/m/n/10 , [][]\T1/pcr/m/n/10 dim<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 nam
es[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 names<-[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 2057) in paragraph at lines 18246--18262
[][][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.c
omplex[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.double[][][]\T1/ptm/m/n/10 ,
[][]\T1/pcr/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.logi
cal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.raw[][][]\T1/ptm/m/n/10 ,
[265] [266] [267] [268] [269] [270]
Underfull \hbox (badness 4699) in paragraph at lines 18660--18663
[]\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 ,
[271] [272]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 18783--18783
[]\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = "
GMT")[]
[273] [274]
Underfull \hbox (badness 4739) in paragraph at lines 18918--18920
[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
[275] [276] [277] [278] [279] [280] [281]
Underfull \hbox (badness 1430) in paragraph at lines 19331--19336
\T1/ptm/m/n/10 if \T1/pcr/m/n/10 simplify = "array"\T1/ptm/m/n/10 , an ar-ray i
f ap-pro-pri-ate, by ap-ply-ing \T1/pcr/m/n/10 simplify2array()\T1/ptm/m/n/10 .
Underfull \hbox (badness 10000) in paragraph at lines 19331--19336
\T1/pcr/m/n/10 sapply(x, f, simplify = FALSE, USE.NAMES = FALSE) \T1/ptm/m/n/10
is the same as
[282]
Underfull \hbox (badness 10000) in paragraph at lines 19392--19397
[]\T1/ptm/m/n/10 logical; if true, \T1/pcr/m/n/10 simplify2array() \T1/ptm/m/n/
10 will pro-duce a (``higher
Underfull \hbox (badness 10000) in paragraph at lines 19392--19397
\T1/ptm/m/n/10 rank'') ar-ray when ap-pro-pri-ate, whereas \T1/pcr/m/n/10 highe
r = FALSE \T1/ptm/m/n/10 would
Underfull \hbox (badness 5008) in paragraph at lines 19392--19397
\T1/ptm/m/n/10 re-turn a ma-trix (or vec-tor) only. These two cases cor-re-spon
d to
Underfull \hbox (badness 10000) in paragraph at lines 19392--19397
\T1/pcr/m/n/10 sapply(*, simplify = "array") \T1/ptm/m/n/10 or \T1/pcr/m/n/10 s
implify = TRUE\T1/ptm/m/n/10 , re-
[283]
Underfull \hbox (badness 10000) in paragraph at lines 19452--19459
[]\T1/pcr/m/n/10 vapply \T1/ptm/m/n/10 re-turns a vec-tor or ar-ray of type mat
ch-ing the \T1/pcr/m/n/10 FUN.VALUE\T1/ptm/m/n/10 . If
Underfull \hbox (badness 6364) in paragraph at lines 19452--19459
\T1/pcr/m/n/10 length(FUN.VALUE) == 1 \T1/ptm/m/n/10 a vec-tor of the same leng
th as \T1/pcr/m/n/10 X \T1/ptm/m/n/10 is re-turned, oth-
Underfull \hbox (badness 5064) in paragraph at lines 19452--19459
\T1/ptm/m/n/10 er-wise an ar-ray. If \T1/pcr/m/n/10 FUN.VALUE \T1/ptm/m/n/10 is
not an [][]\T1/pcr/m/n/10 array[][][]\T1/ptm/m/n/10 , the re-sult is a ma-trix
with
Underfull \hbox (badness 5908) in paragraph at lines 19452--19459
\T1/pcr/m/n/10 length(FUN.VALUE) \T1/ptm/m/n/10 rows and \T1/pcr/m/n/10 length(
X) \T1/ptm/m/n/10 columns, oth-er-wise an ar-ray \T1/pcr/m/n/10 a \T1/ptm/m/n/1
0 with
Underfull \hbox (badness 10000) in paragraph at lines 19468--19470
[]\T1/pcr/m/n/10 sapply(*, simplify = FALSE, USE.NAMES = FALSE) \T1/ptm/m/n/10
is equiv-a-lent to
[284]
Underfull \hbox (badness 1975) in paragraph at lines 19540--19543
[]\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
[285] [286] [287] [288] [289] [290]
Underfull \hbox (badness 1077) in paragraph at lines 19935--19940
[]\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
[291]
Underfull \hbox (badness 10000) in paragraph at lines 19949--19956
[][][]$\T1/pcr/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][]
\T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 http : / / curl . haxx . se /
[292]
Underfull \hbox (badness 10000) in paragraph at lines 20023--20027
[]\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
[293]
Underfull \hbox (badness 10000) in paragraph at lines 20153--20157
[]\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 20153--20157
[][]\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
[294] [295]
Underfull \hbox (badness 10000) in paragraph at lines 20251--20258
[][][]\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 ,
[296] [297]
Underfull \hbox (badness 10000) in paragraph at lines 20372--20376
[]\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
[298]
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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 20442--20447
\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 20442--20447
\T1/ptm/m/n/10 this li-cense is in file `\T1/pcr/m/n/10 $R_SHARE_DIR/licenses/L
GPL-2.1\T1/ptm/m/n/10 ' and can be viewed
Underfull \hbox (badness 10000) in paragraph at lines 20442--20447
\T1/ptm/m/n/10 by \T1/pcr/m/n/10 RShowDoc("LGPL-2.1")\T1/ptm/m/n/10 . Ver-sion
3 of the li-cense can be dis-played by
[299] [300]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 20609--20609
[] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. =
FALSE)[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 20613--20613
[] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. =
FALSE)[]
[301]
Underfull \hbox (badness 3343) in paragraph at lines 20669--20673
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac
cess[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 files[][][] \T1/ptm/m/n/10 for
many more file han-dling func-tions and
[302]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20755--20755
[] \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments
as for lists[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 20766--20766
[] \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1,
pr = 0.2))),[]
[303] [304]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 20877--20877
[]\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 20880--20880
[]\T1/pcr/m/n/9 attach("all.rda") # safer and will warn about masked objects w
/ same name in .GlobalEnv[]
[305]
Underfull \hbox (badness 6380) in paragraph at lines 20925--20930
[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways
be sup-
Underfull \hbox (badness 1337) in paragraph at lines 20983--20990
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 category = "LC_ALL" \T1/ptm/m/n/10 the de-t
ails of the string are system-specific: it might be
Underfull \hbox (badness 1960) in paragraph at lines 20983--20990
\T1/ptm/m/n/10 a sin-gle lo-cale name or a set of lo-cale names sep-a-rated by
\T1/pcr/m/n/10 "/" \T1/ptm/m/n/10 (So-laris, ma-cOS) or
Underfull \hbox (badness 1043) in paragraph at lines 20983--20990
\T1/ptm/m/n/10 not nec-es-sar-ily the case that the re-sult of \T1/pcr/m/n/10 f
oo <- Sys.getlocale() \T1/ptm/m/n/10 can be used in
[306]
Underfull \hbox (badness 2564) in paragraph at lines 21016--21019
[]\T1/ptm/m/n/10 Almost all the out-put rou-tines used by \T1/phv/m/n/10 R \T1/
ptm/m/n/10 it-self un-der Win-dows ig-nore the set-ting of
Overfull \hbox (4.38043pt too wide) in paragraph at lines 21046--21046
[]\T1/pcr/m/n/9 Sys.setlocale("LC_TIME", "de_DE.UTF-8") # Linux, macOS, other
Unix-alikes[]
[307]
Underfull \hbox (badness 1205) in paragraph at lines 21069--21074
\T1/ptm/m/n/10 10) log-a-rithms, and \T1/pcr/m/n/10 log2 \T1/ptm/m/n/10 com-put
es bi-nary (i.e., base 2) log-a-rithms. The gen-eral form
[308] [309]
Underfull \hbox (badness 1400) in paragraph at lines 21214--21218
[][][]\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
Overfull \hbox (36.83002pt too wide) in paragraph at lines 21234--21241
[]\T1/pcr/m/n/10 isTRUE(x) \T1/ptm/m/n/10 is the same as \T1/pcr/m/n/10 { is.lo
gical(x) && length(x) == 1 && !is.na(x) && x }\T1/ptm/m/n/10 ;
Underfull \hbox (badness 4886) in paragraph at lines 21234--21241
\T1/ptm/m/n/10 In ear-lier \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions, \T1/pcr/m
/n/10 isTRUE <- function(x) identical(x, TRUE)\T1/ptm/m/n/10 , had the
[310] [311]
Underfull \hbox (badness 2469) in paragraph at lines 21384--21390
[]\T1/pcr/m/n/10 as.logical \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-ment
to be of log-i-cal type. For [][]\T1/pcr/m/n/10 factor[][][]\T1/ptm/m/n/10 s,
Underfull \hbox (badness 1939) in paragraph at lines 21384--21390
\T1/ptm/m/n/10 this uses the [][]\T1/pcr/m/n/10 levels[][][] \T1/ptm/m/n/10 (la
-bels). Like [][]\T1/pcr/m/n/10 as.vector[][][] \T1/ptm/m/n/10 it strips at-tri
butes in-clud-ing names.
Underfull \hbox (badness 10000) in paragraph at lines 21384--21390
\T1/ptm/m/n/10 Char-ac-ter strings \T1/pcr/m/n/10 c("T", "TRUE", "True", "true"
) \T1/ptm/m/n/10 are re-garded as true,
[312] [313] [314] [315] [316]
Underfull \hbox (badness 10000) in paragraph at lines 21701--21703
[]\T1/ptm/m/n/10 The al-go-rithm used by \T1/pcr/m/n/10 make.unique \T1/ptm/m/n
/10 has the prop-erty that
[317] [318] [319] [320] [321]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 22005--22005
[]\T1/pcr/m/n/9 zN <- c(complex(real = NA , imaginary = r ), complex(real =
r , imaginary = NA ),[]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 22006--22006
[] \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 22009--22009
[]\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)[]
[322] [323]
Underfull \hbox (badness 1655) in paragraph at lines 22133--22137
[]\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion
(also known as a `clo-sure'):
[324] [325] [326]
Underfull \hbox (badness 2277) in paragraph at lines 22382--22385
[]\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.
[327] [328] [329] [330] [331] [332] [333] [334]
Underfull \hbox (badness 10000) in paragraph at lines 22867--22873
[]\T1/ptm/m/n/10 There are also lim-its on in-di-vid-ual ob-jects. The stor-age
space can-not ex-ceed
Underfull \hbox (badness 6316) in paragraph at lines 22867--22873
\T1/ptm/m/n/10 the ad-dress limit, and if you try to ex-ceed that limit, the er
-ror mes-sage be-gins
Underfull \hbox (badness 1484) in paragraph at lines 22899--22907
[]\T1/ptm/m/n/10 The address-space limit is 2Gb un-der 32-bit Win-dows un-less
the OS's de-fault has been
Underfull \hbox (badness 2951) in paragraph at lines 22899--22907
\T1/ptm/m/n/10 changed to al-low more (up to 3Gb). See [][]$\T1/pcr/m/n/10 http
s : / / www . microsoft . com / whdc /
Underfull \hbox (badness 3460) in paragraph at lines 22899--22907
\T1/pcr/m/n/10 system / platform / server / PAE / PAEmem . mspx$[][] \T1/ptm/m/
n/10 and [][]$\T1/pcr/m/n/10 https : / / msdn . microsoft .
[335]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 22976--22976
[] \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y =
all,[]
[336]
Underfull \hbox (badness 10000) in paragraph at lines 23030--23034
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 by \T1/ptm/m/n/10 or both \T1/pcr/m/n/10 by.
x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 by.y \T1/ptm/m/n/10 are of length 0 (a leng
th zero vec-
Underfull \hbox (badness 10000) in paragraph at lines 23030--23034
\T1/ptm/m/n/10 tor or \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 ), the re-sult, \T1/pcr
/m/n/10 r\T1/ptm/m/n/10 , is the \T1/ptm/m/it/10 Carte-sian prod-uct \T1/ptm/m/
n/10 of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , i.
e.,
[337] [338] [339] [340] [341] [342]
Underfull \hbox (badness 10000) in paragraph at lines 23481--23489
\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 ;
[343] [344]
Underfull \hbox (badness 3849) in paragraph at lines 23595--23600
[]\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
[345]
Underfull \hbox (badness 7308) in paragraph at lines 23672--23678
[]\T1/ptm/m/n/10 For an [][]\T1/pcr/m/n/10 environment[][][] env\T1/ptm/m/n/10
, \T1/pcr/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond-
ing
Underfull \hbox (badness 5077) in paragraph at lines 23672--23678
\T1/ptm/m/n/10 list, i.e., \T1/pcr/m/n/10 names(as.list(env, all.names = TRUE))
\T1/ptm/m/n/10 which are also given by
Underfull \hbox (badness 10000) in paragraph at lines 23682--23685
[]\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute
via the gen-eral rules:
Underfull \hbox (badness 10000) in paragraph at lines 23682--23685
\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
[346] [347]
Underfull \hbox (badness 10000) in paragraph at lines 23834--23836
[]\T1/ptm/m/n/10 character string: par-tial match-ing to one of
[348] [349] [350] [351]
Underfull \hbox (badness 6188) in paragraph at lines 24053--24056
[]\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
[352] [353] [354] [355] [356] [357] [358]
Underfull \hbox (badness 2197) in paragraph at lines 24535--24539
[]\T1/ptm/m/n/10 Loading a names-pace should where pos-si-ble be silent, with s
tartup mes-sages given by
Underfull \hbox (badness 4048) in paragraph at lines 24535--24539
\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 24549--24553
[]\T1/ptm/m/n/10 Uses of \T1/pcr/m/n/10 library \T1/ptm/m/n/10 with ar-gu-ment
\T1/pcr/m/n/10 help \T1/ptm/m/n/10 to dis-play ba-sic in-for-ma-tion about the
pack-
Underfull \hbox (badness 1990) in paragraph at lines 24549--24553
\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
[359]
Underfull \hbox (badness 10000) in paragraph at lines 24642--24648
[]\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 24642--24648
\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
[360]
Underfull \hbox (badness 10000) in paragraph at lines 24655--24657
[]\T1/pcr/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m
ore ef-fi-cient than
Overfull \hbox (4.38043pt too wide) in paragraph at lines 24706--24706
[] \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:[]
[361] [362] [363]
Underfull \hbox (badness 10000) in paragraph at lines 24899--24905
[]\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 is.numeric \T1/ptm/m/n/
10 re-turns \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of
Underfull \hbox (badness 10000) in paragraph at lines 24899--24905
[][]\T1/ptm/m/n/10 mode[][][] \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/10 ([][]type
[][][] \T1/pcr/m/n/10 "double" \T1/ptm/m/n/10 or type \T1/pcr/m/n/10 "integer"\
T1/ptm/m/n/10 ) and not a fac-tor,
Underfull \hbox (badness 10000) in paragraph at lines 24899--24905
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 oth-er-wise. That is, \T
1/pcr/m/n/10 is.integer(x) || is.double(x)\T1/ptm/m/n/10 , or
[364]
Underfull \hbox (badness 4120) in paragraph at lines 24985--24992
[]\T1/ptm/m/n/10 Hexadecimal con-stants start with \T1/pcr/m/n/10 0x \T1/ptm/m/
n/10 or \T1/pcr/m/n/10 0X \T1/ptm/m/n/10 fol-lowed by a nonempty se-quence from
[365] [366]
Underfull \hbox (badness 1694) in paragraph at lines 25121--25124
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor with suit-able nu-meric ver-sion strings
(see `De-tails');
[367] [368] [369] [370]
Underfull \hbox (badness 1603) in paragraph at lines 25368--25370
[]\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a
re con-verted by
[371]
Overfull \hbox (73.28088pt too wide) in paragraph at lines 25491--25499
\T1/pcr/m/n/10 c("datasets", "utils", "grDevices", "graphics", "stats",
"methods")\T1/ptm/m/n/10 .
[372] [373]
Underfull \hbox (badness 5475) in paragraph at lines 25628--25638
[]\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/pcr/m
/n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to
Underfull \hbox (badness 3271) in paragraph at lines 25670--25673
[]\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men
t vari-able
Underfull \hbox (badness 10000) in paragraph at lines 25685--25687
[]\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v
alue
[374] [375] [376]
Underfull \hbox (badness 3138) in paragraph at lines 25948--25954
[]\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 25948--25954
\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 25948--25954
\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
[377]
Underfull \hbox (badness 1194) in paragraph at lines 25961--25964
[]\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/pcr/m/n/10 create.post[][
][] \T1/ptm/m/n/10 (and hence[][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/n/10
and
Underfull \hbox (badness 1389) in paragraph at lines 25987--25989
[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
l HTTP server, see
Underfull \hbox (badness 10000) in paragraph at lines 25999--26003
[]\T1/ptm/m/n/10 string used as the user agent in HTTP(S) re-quests. If
Underfull \hbox (badness 6592) in paragraph at lines 25999--26003
\T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 , re-quests will be made with-out a user agen
t header. The de-fault is
Underfull \hbox (badness 10000) in paragraph at lines 26004--26010
[]\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by
Underfull \hbox (badness 3826) in paragraph at lines 26019--26024
[]\T1/ptm/m/n/10 Used by [][]\T1/pcr/m/n/10 install.packages[][][] \T1/ptm/m/n/
10 (and in-di-rectly
Overfull \hbox (49.4607pt too wide) in paragraph at lines 26025--26036
[]\T1/ptm/m/n/10 Used by [][]\T1/pcr/m/n/10 install.packages[][][](type = "both
")
Underfull \hbox (badness 1009) in paragraph at lines 26037--26040
[]\T1/ptm/m/n/10 default email-ing method used by [][]\T1/pcr/m/n/10 create.pos
t[][][] \T1/ptm/m/n/10 and hence [][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/
n/10 and
Underfull \hbox (badness 10000) in paragraph at lines 26047--26059
[]\T1/ptm/m/n/10 The de-fault type of pack-ages to be down-loaded and in-stalle
d -- see
Underfull \hbox (badness 1072) in paragraph at lines 26047--26059
[][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 . Pos-si-ble val-ues ar
e \T1/pcr/m/n/10 "source" \T1/ptm/m/n/10 (the de-fault ex-cept un-der a
[378]
Underfull \hbox (badness 10000) in paragraph at lines 26061--26068
[]\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/pcr/m/n/10 upda
te.packages[][][]\T1/ptm/m/n/10 . De-faults to
Underfull \hbox (badness 10000) in paragraph at lines 26061--26068
\T1/pcr/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i
-ties to prompt for a
Underfull \hbox (badness 6380) in paragraph at lines 26061--26068
\T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi
ng like
Overfull \hbox (34.78088pt too wide) in paragraph at lines 26061--26068
\T1/pcr/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr
an";
[379] [380] [381] [382]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26392--26392
[]\T1/pcr/m/n/9 system.time(o <- sort.list(xx, method = "radix")) # 0.007 sec,
300X faster[]
Underfull \hbox (badness 10000) in paragraph at lines 26405--26409
[]\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/pcr/m/n/10 X \T1/ptm/m/n
/10 and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/pcr/m/n/10 A \T1/ptm/
m/n/10 with di-men-sion
Underfull \hbox (badness 10000) in paragraph at lines 26405--26409
\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)]
[383] [384] [385] [386] [387]
Underfull \hbox (badness 4341) in paragraph at lines 26729--26731
[]\T1/pcr/m/n/10 paste0(..., collapse) \T1/ptm/m/n/10 is equiv-a-lent to \T1/pc
r/m/n/10 paste(..., sep = "", collapse)\T1/ptm/m/n/10 ,
Underfull \hbox (badness 4518) in paragraph at lines 26765--26771
[][][]\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
[388]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 26787--26787
[]\T1/pcr/m/n/9 ## Notice that the recycling rules make every input as long as
the longest input.[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26799--26799
[]\T1/pcr/m/n/9 paste("1st", "2nd", "3rd", collapse = ", ") # probably not wha
t you wanted[]
[389] [390] [391] [392] [393] [394] [395]
Underfull \hbox (badness 10000) in paragraph at lines 27233--27237
[]\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,
[396]
Underfull \hbox (badness 1796) in paragraph at lines 27299--27302
[]\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
[397] [398] [399]
Underfull \hbox (badness 10000) in paragraph at lines 27499--27502
[]\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
[400] [401] [402] [403] [404] [405] [406] [407] [408]
Underfull \hbox (badness 1226) in paragraph at lines 28131--28136
\T1/pcr/m/n/10 ncol(X) <= nrow(X)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 complete \T
1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 or the ar-gu-ment \T1/pcr/m/
n/10 ncol \T1/ptm/m/n/10 is greater than
[409]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 28176--28176
[] \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))[]
[410] [411] [412] [413]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 28442--28442
[]\T1/pcr/m/n/9 (nn <- "\u0126\u0119\u1114\u022d\u2001\u03e2\u0954\u0f3f\u13d3
\u147b\u203c")[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 28453--28453
[]\T1/pcr/m/n/9 n2 <- "\U0126\U0119\U1114\U022d\U2001\U03e2\U0954\U0f3f\U13d3\
U147b\U203c"[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 28459--28459
[]\T1/pcr/m/n/9 ## https://cran.r-project.org/doc/manuals/r-release/R-lang.htm
l#Literal-constants[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 28460--28460
[]\T1/pcr/m/n/9 ## and bug 16098 https://bugs.r-project.org/bugzilla3/show_bug
.cgi?id=16098[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 28463--28463
[]\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow
ed (parse errors)[]
[414]
Underfull \hbox (badness 7415) in paragraph at lines 28538--28542
[]\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
[415]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 28559--28559
[]\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu
l bottom-right note[]
[416]
Underfull \hbox (badness 2418) in paragraph at lines 28718--28729
[]\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
[417] [418]
Underfull \hbox (badness 1248) in paragraph at lines 28852--28859
\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 28852--28859
\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 /
[419] [420]
Underfull \hbox (badness 1533) in paragraph at lines 28968--28971
[]\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
[421]
Underfull \hbox (badness 1337) in paragraph at lines 29065--29068
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 finite \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE
\T1/ptm/m/n/10 , the min-i-mum and max-i-mum of all fi-nite val-ues is com-pute
d, i.e.,
[422]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 29113--29113
[] \T1/pcr/m/n/10 ties.method = c("average", "first", "last", "random", "m
ax", "min"))[]
Underfull \hbox (badness 1038) in paragraph at lines 29131--29142
[]\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/pcr/m/n/10 NA\
T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in
Underfull \hbox (badness 10000) in paragraph at lines 29143--29146
[]\T1/pcr/m/n/10 NA \T1/ptm/m/n/10 val-ues are never con-sid-ered to be equal:
for \T1/pcr/m/n/10 na.last = TRUE \T1/ptm/m/n/10 and
[423] [424]
Underfull \hbox (badness 1117) in paragraph at lines 29238--29244
\T1/ptm/m/n/10 e-ments which have a class in-cluded in \T1/pcr/m/n/10 classes \
T1/ptm/m/n/10 are re-placed by the re-sult of ap-ply-ing
[425] [426] [427] [428] [429] [430]
Underfull \hbox (badness 4048) in paragraph at lines 29616--29621
[]\T1/ptm/m/n/10 Either an ob-ject whose mode will give the mode of the vec-tor
to
Underfull \hbox (badness 4582) in paragraph at lines 29616--29621
\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 29616--29621
\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 ,
[431] [432] [433] [434] [435] [436] [437] [438]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 30162--30162
[]\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene
d as needed.[]
[439] [440] [441] [442]
Overfull \hbox (13.9408pt too wide) in paragraph at lines 30448--30450
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 ! " # $ % & \TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 ( )
* + , - . / : ; < = > ? @ [ \ ] ^ _ \TS1/pcr/m/n/10 ` \T1/pcr/m/n/10 { | } ~\T
1/ptm/m/n/10 '.
[443] [444] [445]
Underfull \hbox (badness 7558) in paragraph at lines 30664--30668
[]\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 30674--30676
[]\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 30679--30682
[][][]\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 30683--30685
[]\T1/ptm/m/n/10 The TRE doc-u-men-ta-tion at [][]$\T1/pcr/m/n/10 http : / / la
urikari . net / tre / documentation /
Underfull \hbox (badness 10000) in paragraph at lines 30686--30688
[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 http : / / p
ubs . opengroup . org / onlinepubs /
[446] [447] [448] [449] [450] [451]
Underfull \hbox (badness 10000) in paragraph at lines 31091--31095
[][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] []
[]NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple
x_[][][]
[452] [453] [454] [455] [456]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 31422--31422
[] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"))[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 31425--31425
[] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"),[]
[457] [458] [459]
Underfull \hbox (badness 3375) in paragraph at lines 31653--31660
\T1/ptm/m/n/10 pen if the spec-i-fied row names, i.e., \T1/pcr/m/n/10 value\T1/
ptm/m/n/10 , are in-valid, e.g., du-
Underfull \hbox (badness 2359) in paragraph at lines 31653--31660
\T1/ptm/m/n/10 pli-cated or \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 . The de-fault (is
back com-pat-i-ble), \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 , will sig-nal
Underfull \hbox (badness 2582) in paragraph at lines 31653--31660
\T1/ptm/m/n/10 an er-ror, where \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 will ``au-to-m
atic'' row names and \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 will call
[460] [461] [462]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 31806--31806
[] \T1/pcr/m/n/10 useHash = (!replace && is.null(prob) && size <= n/
2 && n > 1e7))[]
[463] [464]
Underfull \hbox (badness 10000) in paragraph at lines 31937--31941
[]\T1/pcr/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c
ur-rent
Underfull \hbox (badness 10000) in paragraph at lines 31937--31941
\T1/ptm/m/n/10 workspace', i.e., \T1/pcr/m/n/10 save(list = ls(all.names = TRUE
), file =
[465] [466] [467]
Underfull \hbox (badness 2302) in paragraph at lines 32188--32195
[]\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d
e-fined as $[]$,
Underfull \hbox (badness 2837) in paragraph at lines 32188--32195
\T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no
n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non
-missing
Underfull \hbox (badness 3815) in paragraph at lines 32188--32195
\T1/ptm/m/n/10 val-ues. In the case \T1/pcr/m/n/10 center = TRUE\T1/ptm/m/n/10
, this is the same as the stan-dard de-vi-a-tion,
Underfull \hbox (badness 2181) in paragraph at lines 32188--32195
\T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti
ons with-out cen-ter-ing, use
[468]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 32240--32240
[] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul =
FALSE)[]
[469]
Underfull \hbox (badness 1158) in paragraph at lines 32344--32349
[]\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
[470]
Underfull \hbox (badness 10000) in paragraph at lines 32371--32377
[]\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac-
ters
Underfull \hbox (badness 1953) in paragraph at lines 32371--32377
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 \a, \b, \f, \n, \r, \t, \v\T1/ptm/m/n/10 ' and o
c-tal and hex-adec-i-mal rep-re-
[471]
Underfull \hbox (badness 10000) in paragraph at lines 32447--32452
[]\T1/ptm/m/n/10 Note that since \T1/pcr/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r
a-tor and not a ter-mi-na-tor, read-ing a file by
Underfull \hbox (badness 6725) in paragraph at lines 32447--32452
\T1/pcr/m/n/10 scan("foo", sep = "\n", blank.lines.skip = FALSE) \T1/ptm/m/n/10
will give an empty
[472]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 32529--32529
[]\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data
", sep = "\n")
[473] [474] [475]
Underfull \hbox (badness 2809) in paragraph at lines 32793--32799
[]\T1/ptm/m/n/10 The fifth form gen-er-ates the se-quence \T1/pcr/m/n/10 1, 2,
..., length(from) \T1/ptm/m/n/10 (as if ar-gu-ment
Underfull \hbox (badness 7759) in paragraph at lines 32800--32803
[]\T1/ptm/m/n/10 The fi-nal form gen-er-ates the in-te-ger se-quence \T1/pcr/m/
n/10 1, 2, ..., length.out \T1/ptm/m/n/10 un-less
[476] [477] [478] [479] [480] [481] [482] [483] [484] [485] [486] [487]
Underfull \hbox (badness 1735) in paragraph at lines 33605--33611
\T1/ptm/m/n/10 Only prompts and (most) mes-sages con-tinue to ap-pear on the co
n-sole. Mes-sages sent
[488]
Underfull \hbox (badness 4303) in paragraph at lines 33621--33624
[]\T1/pcr/m/n/10 split = TRUE \T1/ptm/m/n/10 only splits \T1/phv/m/n/10 R \T1/p
tm/m/n/10 out-put (via \T1/pcr/m/n/10 Rvprintf\T1/ptm/m/n/10 ) and the de-fault
out-put from
[489] [490] [491] [492]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 33939--33939
[] \T1/pcr/m/n/10 method = c("auto", "shell", "quick", "radix"), index
.return = FALSE)[]
[493] [494] [495] [496]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 34191--34191
[] \T1/pcr/m/n/10 print. = TRUE, echo = TRUE, max.deparse.length
= Inf,[]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 34193--34193
[] \T1/pcr/m/n/10 deparseCtrl = c("keepInteger", "showAttributes"
, "keepNA"),[]
[497]
Underfull \hbox (badness 10000) in paragraph at lines 34236--34242
[][][]\T1/pcr/m/n/10 character[][][] \T1/ptm/m/n/10 vec-tor, passed as \T1/pcr/
m/n/10 control \T1/ptm/m/n/10 to [][]\T1/pcr/m/n/10 deparse[][][]()\T1/ptm/m/n/
10 , see
Underfull \hbox (badness 10000) in paragraph at lines 34236--34242
\T1/ptm/m/n/10 also [][]\T1/pcr/m/n/10 .deparseOpts[][][]\T1/ptm/m/n/10 . In \T
1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion <= 3.3.x, this was hard-
Underfull \hbox (badness 10000) in paragraph at lines 34236--34242
\T1/ptm/m/n/10 coded to \T1/pcr/m/n/10 "showAttributes"\T1/ptm/m/n/10 , which i
s the de-fault cur-rently;
Underfull \hbox (badness 2512) in paragraph at lines 34251--34253
[]\T1/ptm/m/n/10 integer; how many com-ment lines at the start of the file to s
kip if
[498]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 34347--34347
[]\T1/pcr/m/n/9 ## (all should look "as if on top level", e.g. non-assignments
should print:)[]
[499] [500] [501] [502] [503]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 34675--34675
[]\T1/pcr/m/n/9 ### Calculate \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 z-scores\TS1/pcr/m
/n/9 ' \T1/pcr/m/n/9 by group (standardize to mean zero, variance one)[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 34690--34690
[]\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is
being added[]
[504] [505] [506] [507] [508] [509]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 35129--35129
[]\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un
known")
Overfull \hbox (12.78088pt too wide) in paragraph at lines 35130--35130
[]\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile =
FALSE)[]
[510] [511] [512] [513]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 35394--35394
[]\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS
E, nowadays often three
[514]
Underfull \hbox (badness 10000) in paragraph at lines 35478--35488
[]\T1/ptm/m/n/10 A func-tion \T1/pcr/m/n/10 .First \T1/ptm/m/n/10 (and [][]\T1/
pcr/m/n/10 .Last[][][]\T1/ptm/m/n/10 ) can be de-fined in ap-pro-pri-ate `\T1/p
cr/m/n/10 .Rprofile\T1/ptm/m/n/10 '
Underfull \hbox (badness 10000) in paragraph at lines 35478--35488
\T1/ptm/m/n/10 or `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' files or have b
een saved in `\T1/pcr/m/n/10 .RData\T1/ptm/m/n/10 '. If you want
Underfull \hbox (badness 8113) in paragraph at lines 35478--35488
\T1/ptm/m/n/10 a dif-fer-ent set of pack-ages than the de-fault ones when you s
tart, in-sert a call
Underfull \hbox (badness 10000) in paragraph at lines 35478--35488
\T1/ptm/m/n/10 to [][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 in the `\T1/p
cr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n
/10 ' file. For ex-am-ple,
Underfull \hbox (badness 6542) in paragraph at lines 35478--35488
\T1/pcr/m/n/10 options(defaultPackages = character()) \T1/ptm/m/n/10 will at-ta
ch no ex-tra pack-ages on
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\T1/ptm/m/n/10 startup (only the \T1/ptm/b/n/10 base \T1/ptm/m/n/10 pack-age) (
or set \T1/pcr/m/n/10 R_DEFAULT_PACKAGES=NULL \T1/ptm/m/n/10 as an en-vi-
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\T1/ptm/m/n/10 ron-ment vari-able be-fore run-ning \T1/phv/m/n/10 R\T1/ptm/m/n/
10 ). Us-ing \T1/pcr/m/n/10 options(defaultPackages = "") \T1/ptm/m/n/10 or
[515]
Underfull \hbox (badness 10000) in paragraph at lines 35522--35528
[]\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 35522--35528
\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 35522--35528
\T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/i386/R
environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/pcr/m/n/10 .Renviron.i386\T1/ptm/m/
n/10 ' will be
Underfull \hbox (badness 1728) in paragraph at lines 35534--35541
[]\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 here is a
lso a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/Renviron\T1/ptm
/m/n/10 ' which is read
Underfull \hbox (badness 1038) in paragraph at lines 35534--35541
\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 35534--35541
\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
[516] [517] [518] [519] [520]
Underfull \hbox (badness 10000) in paragraph at lines 35875--35881
[]\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/pcr/m/n/10 form
at \T1/ptm/m/n/10 meth-ods is
[521] [522] [523]
Underfull \hbox (badness 1163) in paragraph at lines 36064--36071
[]\T1/ptm/m/n/10 Specific to \T1/phv/m/n/10 R \T1/ptm/m/n/10 is \T1/pcr/m/n/10
%OSn\T1/ptm/m/n/10 , which for out-put gives the sec-onds trun-cated to \T1/pcr
/m/n/10 0 <= n <= 6
Underfull \hbox (badness 8132) in paragraph at lines 36064--36071
\T1/ptm/m/n/10 dec-i-mal places (and if \T1/pcr/m/n/10 %OS \T1/ptm/m/n/10 is no
t fol-lowed by a digit, it uses the set-ting of
[524] [525] [526] [527]
Underfull \hbox (badness 1142) in paragraph at lines 36346--36352
[]\T1/ptm/m/n/10 Note that split-ting into sin-gle char-ac-ters can be done \T1
/ptm/m/it/10 via \T1/pcr/m/n/10 split = character(0) \T1/ptm/m/n/10 or
Overfull \hbox (0.78088pt too wide) in paragraph at lines 36361--36361
[] \T1/pcr/m/n/10 add the string to the left of the match to the ou
tput.[]
[528] [529] [530] [531]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 36609--36609
[] \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p
refix)[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 36653--36653
[]\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll
apse = "\n")[]
[532] [533] [534] [535] [536] [537] [538]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 37087--37087
[]\T1/pcr/m/n/9 ## In fact, you can pass vectors into several arguments, and e
verything gets added.[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 37090--37090
[]\T1/pcr/m/n/9 ## If there are missing values, the sum is unknown, i.e., also
missing, ....[]
[539]
Underfull \hbox (badness 10000) in paragraph at lines 37141--37148
[]\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 37141--37148
\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 37192--37192
[]\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau
lt precision
[540] [541] [542] [543]
Underfull \hbox (badness 2762) in paragraph at lines 37431--37440
\T1/ptm/m/n/10 of the el-e-ments in \T1/pcr/m/n/10 ...\T1/ptm/m/n/10 . If there
is a match then that el-e-ment is eval-u-ated un-less
Underfull \hbox (badness 1466) in paragraph at lines 37431--37440
\T1/ptm/m/n/10 it is miss-ing, in which case the next non-missing el-e-ment is
eval-u-ated, so for ex-am-ple
[544]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 37493--37493
[] \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw
ise: last"),"\n")[]
[545] [546]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 37658--37658
[]\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.
[547]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 37696--37696
[]\T1/pcr/m/n/9 if(.Platform$OS.type == "unix") ## on Unix-alikes such Linux,
macOS, FreeBSD:[]
[548]
Underfull \hbox (badness 3219) in paragraph at lines 37745--37750
[]\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 37745--37750
\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
[549]
Underfull \hbox (badness 2452) in paragraph at lines 37835--37838
\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 37835--37838
\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
[550] [551] [552]
Underfull \hbox (badness 10000) in paragraph at lines 38022--38026
[]\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 38037--38040
[]\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
[553] [554]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 38169--38169
[]\T1/pcr/m/n/9 is.symlink <- function(paths) isTRUE(nzchar(Sys.readlink(paths
), keepNA=TRUE))[]
[555]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 38239--38239
[]\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
[556] [557] [558]
Underfull \hbox (badness 1082) in paragraph at lines 38377--38380
[]\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
[559] [560]
Underfull \hbox (badness 1038) in paragraph at lines 38564--38567
[]\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
[561] [562] [563] [564] [565] [566]
Underfull \hbox (badness 1515) in paragraph at lines 38928--38931
[]\T1/ptm/m/n/10 Because of the way it is im-ple-mented, on a Unix-alike \T1/pc
r/m/n/10 stderr = TRUE \T1/ptm/m/n/10 im-plies
[567] [568] [569]
Underfull \hbox (badness 4096) in paragraph at lines 39169--39172
[]\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 ,
[570] [571]
Underfull \hbox (badness 10000) in paragraph at lines 39283--39287
[]\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.,
[572] [573]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 39437--39437
[] \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 39439--39439
[] \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),[]
[574]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 39441--39441
[] \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 39454--39456
[]\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
[575]
Underfull \hbox (badness 10000) in paragraph at lines 39534--39537
[][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$https : / / developer .
[576] [577]
Underfull \hbox (badness 1867) in paragraph at lines 39652--39656
[][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getTaskCallbackNames
[][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 https : / /
Underfull \hbox (badness 5475) in paragraph at lines 39714--39718
[][][]\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 \ [][]$\T1/pcr/m/n/10 https : / /
[578] [579] [580] [581] [582] [583] [584]
Underfull \hbox (badness 10000) in paragraph at lines 40132--40139
\T1/ptm/m/n/10 is also known as `\T1/pcr/m/n/10 GB\T1/ptm/m/n/10 ', `\T1/pcr/m/
n/10 GB-Eire\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 Europe/Belfast\T1/ptm/m/n/10 ', `
\T1/pcr/m/n/10 Europe/Guernsey\T1/ptm/m/n/10 ',
Underfull \hbox (badness 4467) in paragraph at lines 40188--40197
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 OlsonNames \T1/ptm/m/n/10 re-turn
s the time-zone names known to the cur-rently se-
Underfull \hbox (badness 3954) in paragraph at lines 40188--40197
\T1/ptm/m/n/10 lected Ol-son/IANA database. The system-specific lo-ca-tion in t
he file sys-tem varies,
Underfull \hbox (badness 10000) in paragraph at lines 40198--40206
[]\T1/ptm/m/n/10 Where \T1/phv/m/n/10 R \T1/ptm/m/n/10 was con-fig-ured with op
-tion `\T1/pcr/m/n/10 --with-internal-tzcode\T1/ptm/m/n/10 ' (the de-
Underfull \hbox (badness 10000) in paragraph at lines 40198--40206
\T1/ptm/m/n/10 fault on ma-cOS and Win-dows: rec-om-mended on So-laris), the da
tabase at
Underfull \hbox (badness 1303) in paragraph at lines 40198--40206
\T1/pcr/m/n/10 file.path(R.home("share"), "zoneinfo") \T1/ptm/m/n/10 is used by
de-fault: file `\T1/pcr/m/n/10 VERSION\T1/ptm/m/n/10 '
[585]
Underfull \hbox (badness 1337) in paragraph at lines 40264--40272
\T1/ptm/m/n/10 a file `\T1/pcr/m/n/10 localtime\T1/ptm/m/n/10 ', usu-ally un-de
r `\T1/pcr/m/n/10 /etc\T1/ptm/m/n/10 ' (but pos-si-bly un-der `\T1/pcr/m/n/10 /
usr/local/etc\T1/ptm/m/n/10 ' or
Underfull \hbox (badness 10000) in paragraph at lines 40273--40276
[]\T1/ptm/m/n/10 `Because the time zone iden-ti-fier is ex-tracted from the sym
-link tar-get name of
[586]
Underfull \hbox (badness 4429) in paragraph at lines 40330--40332
[][][]$\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-
Overfull \hbox (31.3804pt too wide) in paragraph at lines 40339--40339
[]\T1/pcr/m/n/9 ## typically some acronyms/aliases such as "UTC", "NZ", "MET",
"Eire", ..., but[]
[587] [588] [589]
Underfull \hbox (badness 10000) in paragraph at lines 40556--40558
[]\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
[590] [591]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 40678--40678
[]\T1/pcr/m/n/9 trace(pt, tracer = quote(cat(sprintf("tracing pt(*, ncp = %.15
g)\n", ncp))),[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 40680--40680
[]\T1/pcr/m/n/9 power.t.test(20, 1, power=0.8, sd=NULL) ##--> showing the ncp
root finding:[]
Underfull \vbox (badness 10000) has occurred while \output is active [592]
[593] [594] [595] [596]
Underfull \hbox (badness 6542) in paragraph at lines 41042--41044
[]\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
[597] [598] [599]
Underfull \hbox (badness 3460) in paragraph at lines 41208--41211
[]\T1/ptm/m/n/10 a [][]con-nec-tion[][][], or a char-ac-ter string nam-ing the
file to print to (via
Underfull \hbox (badness 1708) in paragraph at lines 41215--41223
[]\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 41215--41223
\T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][
]\T1/pcr/m/n/10 stderr[][][] \T1/ptm/m/n/10 con-nec-tion un-less
Underfull \hbox (badness 10000) in paragraph at lines 41224--41228
[]\T1/pcr/m/n/10 try \T1/ptm/m/n/10 is im-ple-mented us-ing [][]\T1/pcr/m/n/10
tryCatch[][][]\T1/ptm/m/n/10 ; for pro-gram-ming, in-
Underfull \hbox (badness 10000) in paragraph at lines 41224--41228
\T1/ptm/m/n/10 stead of \T1/pcr/m/n/10 try(expr, silent = TRUE)\T1/ptm/m/n/10 ,
some-thing like
Underfull \hbox (badness 3281) in paragraph at lines 41224--41228
\T1/pcr/m/n/10 tryCatch(expr, error = function(e) e) \T1/ptm/m/n/10 (or other s
im-ple er-ror han-dler func-
Underfull \hbox (badness 4859) in paragraph at lines 41245--41250
[][][]\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;
[600]
Underfull \hbox (badness 3895) in paragraph at lines 41307--41319
[]\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 41307--41319
\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 ,
[601] [602] [603]
Underfull \hbox (badness 10000) in paragraph at lines 41492--41495
[]\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an
d sock-ets.
[604] [605]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 41629--41629
[]\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp
ression(1+x))[]
[606] [607] [608] [609] [610] [611]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 42096--42096
[]\T1/pcr/m/n/9 (xx <- intToUtf8(x, , TRUE)) # will only display in some local
es and fonts[]
[612]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 42105--42105
[]\T1/pcr/m/n/9 system(paste("od -x", foo)) # 2-byte units, correct on little-
endian platform[]
[613]
Underfull \hbox (badness 1803) in paragraph at lines 42222--42225
[]\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 2334) in paragraph at lines 42226--42233
[]\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
[614]
Underfull \hbox (badness 4726) in paragraph at lines 42252--42256
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 is.vector\T1/ptm/m/n/10 , \T1/pcr/m/n/10 TR
UE \T1/ptm/m/n/10 or \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 . \T1/pcr/m/n/10 is.vec
tor(x, mode = "numeric") \T1/ptm/m/n/10 can be
Underfull \hbox (badness 1122) in paragraph at lines 42252--42256
\T1/ptm/m/n/10 true for vec-tors of types \T1/pcr/m/n/10 "integer" \T1/ptm/m/n/
10 or \T1/pcr/m/n/10 "double" \T1/ptm/m/n/10 whereas \T1/pcr/m/n/10 is.vector(x
, mode =
[615] [616]
Underfull \hbox (badness 3668) in paragraph at lines 42441--42443
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di-
ately, even if
[617] [618]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 42545--42545
[] \T1/pcr/m/n/10 header = ngettext(n, "Warning message:\n", "Warning mes
sages:\n"),[]
[619]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 42620--42620
[]\T1/pcr/m/n/9 ## at the end prints all three warnings, from the \TS1/pcr/m/n
/9 '\T1/pcr/m/n/9 option(warn = 0)\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 above[]
Overfull \hbox (90.78033pt too wide) in paragraph at lines 42628--42628
[]\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 ...[]
[620] [621]
Underfull \hbox (badness 6220) in paragraph at lines 42758--42763
[]\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 42758--42763
\T1/ptm/m/n/10 to be used for con-struct-ing dim-names for \T1/pcr/m/n/10 array
Ind() \T1/ptm/m/n/10 (and hence,
Underfull \hbox (badness 1533) in paragraph at lines 42758--42763
\T1/pcr/m/n/10 which(*, arr.ind=TRUE)\T1/ptm/m/n/10 ). If [][]\T1/pcr/m/n/10 na
mes[][][](.dimnames) \T1/ptm/m/n/10 is not empty,
Underfull \hbox (badness 6592) in paragraph at lines 42774--42779
[]\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
[622]
Underfull \hbox (badness 1603) in paragraph at lines 42793--42797
[][][]\T1/pcr/m/n/10 Logic[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 which.min[]
[][] \T1/ptm/m/n/10 for the in-dex of the min-i-mum or max-i-mum, and [][]\T1/p
cr/m/n/10 match[][][] \T1/ptm/m/n/10 for the
[623]
Underfull \hbox (badness 10000) in paragraph at lines 42858--42861
[]\T1/ptm/m/n/10 If this ex-tremum is unique (or empty), the re-sults are the s
ame as
Underfull \hbox (badness 10000) in paragraph at lines 42858--42861
\T1/ptm/m/n/10 (but more ef-fi-cient than) \T1/pcr/m/n/10 which(x == min(x, na.
rm = TRUE)) \T1/ptm/m/n/10 or
Underfull \hbox (badness 2818) in paragraph at lines 42864--42870
[]\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
Overfull \hbox (15.18042pt too wide) in paragraph at lines 42899--42899
[]\T1/pcr/m/n/9 ## Find the first occurrence, i.e. the first TRUE, if there is
at least one:[]
[624] [625]
Underfull \hbox (badness 1622) in paragraph at lines 42993--42995
[]\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 .
[626] [627] [628] [629]
Underfull \hbox (badness 10000) in paragraph at lines 43261--43266
[]\T1/ptm/m/n/10 This is a spe-cial case of rank-ing, but as a less gen-eral fu
nc-tion than [][]\T1/pcr/m/n/10 rank[][][]
Underfull \hbox (badness 10000) in paragraph at lines 43261--43266
\T1/ptm/m/n/10 is more suit-able to be made generic. The de-fault method is sim
-i-lar to
Underfull \hbox (badness 10000) in paragraph at lines 43261--43266
\T1/pcr/m/n/10 rank(x, ties.method = "min", na.last = "keep")\T1/ptm/m/n/10
, so \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 val-ues are
[630]
Underfull \hbox (badness 2846) in paragraph at lines 43355--43359
[]\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
[631]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 43395--43395
[]\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char
acter vector[]
Underfull \hbox (badness 3209) in paragraph at lines 43416--43420
[]\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
[632]) (./compiler-pkg.tex
Chapter 2.
[633]
Underfull \hbox (badness 2884) in paragraph at lines 101--115
[]\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 101--115
\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
[634] [635] [636]) (./datasets-pkg.tex
Chapter 3.
Underfull \hbox (badness 10000) in paragraph at lines 12--14
[]\T1/ptm/m/n/10 This pack-age con-tains a va-ri-ety of datasets. For a com-ple
te list, use
[637] [638] [639] [640] [641]
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[] \T1/pcr/m/n/9 plot(ff, data = anscombe, col = "red", pch = 21, bg = "orang
e", cex = 1.2,[]
[642]
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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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[644] [645] [646] [647]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[648] [649]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[650] [651]
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[]\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.
[652] [653]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[654] [655] [656] [657] [658]
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[]\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption
time (sec)")[]
[659] [660]
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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
[661] [662] [663]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[664]
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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)[]
[665] [666]
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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]]))))[]
[667] [668] [669] [670]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[671] [672] [673]
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[674] [675] [676] [677] [678]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[679]
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[680]
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[682]
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[683] [684]
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[685]
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[]\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main =
1.2, pch = ".")[]
[686] [687] [688] [689] [690] [691] [692]
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[] \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t
he monthly one:[]
[693] [694]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[695]
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[696]
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\T1/ptm/m/it/10 Ed-u-ca-tion\T1/ptm/m/n/10 , \T1/ptm/b/n/10 3\T1/ptm/m/n/10 . [
][]$\T1/pcr/m/n/10 https : / / www . amstat . org / publications / jse / v3n3 /
datasets .
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[697]
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[] \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of
supplement")[]
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[]\T1/ptm/m/n/10 Time Se-ries Data Li-brary: [][]$\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 /
[698] [699] [700] [701] [702] [703] [704] [705] [706] [707] [708] [709]
[710] [711]) (./grDevices-pkg.tex [712]
Chapter 4.
[713] [714] [715] [716] [717] [718]
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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/pcr/m/n/10 quantile[][][](x, c(1,3)/4)\T1/ptm/m/n/10 . The hinges equal
the quar-tiles for odd $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 (where
[719]
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[]\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d
.pdf",[]
[720] [721] [722] [723] [724] [725] [726] [727] [728]
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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
[729]
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\T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 make.rgb[][][]\T1/ptm/m/n/10 . Built-in co
lor spaces may be ref-er-enced by strings: \T1/pcr/m/n/10 "XYZ"\T1/ptm/m/n/10 ,
\T1/pcr/m/n/10 "sRGB"\T1/ptm/m/n/10 ,
[730]
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[]\T1/ptm/m/n/10 For the white points [][]$\T1/pcr/m/n/10 http : / / www . efg2
. com / Lab / Graphics / Colors /
[731]
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[]\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab",
scale.in = 255))[]
[732]
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[]\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
[733] [734] [735]
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[]\T1/ptm/m/n/10 character: Which events can be gen-er-ated on
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\T1/ptm/m/n/10 this de-vice? Cur-rently this will be a sub-set of
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\T1/pcr/m/n/10 c("MouseDown", "MouseMove", "MouseUp", "Keybd")\T1/ptm/m/n/10
,
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[]\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 if the de-vice does not sup-port cap-ture,
oth-er-wise a ma-trix of color names (for
[736]
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[]\T1/ptm/m/n/10 logical; if \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion
also re-turns \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 when
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[][]\T1/pcr/m/n/10 .Device[][][] == "null device" \T1/ptm/m/n/10 and [][]\T1/pc
r/m/n/10 getOption[][][]("device") \T1/ptm/m/n/10 is
[737] [738] [739]
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[]\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
[740]
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[]\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res
= 72,[]
[741]
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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 ,
[742]
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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
[743] [744]
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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
[745] [746]
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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
[747] [748]
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[]\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r"
, yaxs = "r") {[]
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[750] [751] [752] [753] [754]
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[756] [757] [758] [759] [760]
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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))[]
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[]\T1/ptm/m/n/10 A length two in-te-ger vec-tor \T1/pcr/m/n/10 nr, nc \T1/ptm/m
/n/10 giv-ing the num-ber of rows and columns, ful-fill-ing
[761]
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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
[762] [763] [764]
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[]\T1/pcr/m/n/10 rainbow(n, s = 1, v = 1, start = 0, end = max(1, n - 1)/n, al
pha = 1)
[765]
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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 C in-te-ger for-mat such as
[766]
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[]\T1/ptm/m/n/10 title string to em-bed as the `\T1/pcr/m/n/10 /Title\T1/ptm/m/
n/10 ' field in the file. De-faults to
[767] [768] [769] [770]
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[]\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 ,
[771] [772] [773] [774] [775]
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\T1/pcr/m/n/10 / / www . adobe . com / products / postscript / pdfs / PLRM . pd
f$[][] \T1/ptm/m/n/10 or PDF [][]$\T1/pcr/m/n/10 https : / /
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\T1/pcr/m/n/10 www . adobe . com / devnet / acrobat / pdfs / pdf _ reference _
1-[]7 . pdf$[][] \T1/ptm/m/n/10 and in dec-i-
[776]
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[] \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz
w+p", "zip+p"),[]
[778]
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[]\T1/ptm/m/n/10 for \T1/pcr/m/n/10 type = "cairo"\T1/ptm/m/n/10 , giv-ing the
type of anti-aliasing (if any) to be
[779] [780]
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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
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[][][]\T1/pcr/m/n/10 capabilities[][][] \T1/ptm/m/n/10 to see if these de-vices
are sup-ported by this build of \T1/phv/m/n/10 R\T1/ptm/m/n/10 , and if
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[]\T1/pcr/m/n/9 ## Not run: dev.print(png, file = "myplot.png", width = 1024,
height = 768)[]
[781]
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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
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[]\T1/ptm/m/n/10 title string to em-bed as the \T1/pcr/m/n/10 Title \T1/ptm/m/n
/10 com-ment in the file. De-faults to
[782]
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\T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/pcr/
m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as
[783]
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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
[784] [785]
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[]\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
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[][][]\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
[786] [787]
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\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
[788]
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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
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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 /
[789] [790]
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[]\T1/pcr/m/n/9 ## time ranges in diverse scales:% also in ../../../../tests/r
eg-tests-1c.R[]
[791]
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[]\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100
, ...)[]
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[]\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on
ly), de-fault
[792] [793]
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[]\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
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[]\T1/ptm/m/n/10 A fairly com-mon Mac prob-lem is no text ap-pear-ing on plots
due to cor-rupted or du-pli-
[794] [795] [796] [797] [798]
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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
[799] [800] [801] [802] [803] [804] [805]
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[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
[806]
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[]\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK
lan-guages and
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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
[807]
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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
[808]
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[] \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height
= 6, xpos = 0,[]
[809]
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[]\T1/ptm/m/n/10 These func-tions ap-ply only to an [][]\T1/pcr/m/n/10 X11[][][
] \T1/ptm/m/n/10 de-vice with \T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 --
[810]
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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 /
[811] [812] [813]
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\T1/ptm/m/n/10 ity of co-or-di-nates. These are com-pared af-ter round-ing them
via
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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
[814] [815] [816]) (./graphics-pkg.tex
Chapter 5.
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[]\T1/ptm/m/n/10 For a com-plete list of func-tions with in-di-vid-ual help pag
es, use
[817] [818] [819] [820]
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[]\T1/ptm/m/n/10 Friendly, M. (1992), Graph-i-cal meth-ods for cat-e-gor-i-cal
data. \T1/ptm/m/it/10 SAS User Group In-ter-na-
[821] [822] [823]
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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
[824] [825] [826]
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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
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[]\T1/pcr/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p
tm/m/n/10 in-ter-face to the C func-tion \T1/pcr/m/n/10 CreateAtVector() \T1/pt
m/m/n/10 in
[827]
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[] \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n
intLog = 5))[]
[828] [829]
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[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , the lines whic
h di-vide ad-ja-cent (non-stacked!) bars
[830] [831] [832] [833] [834] [835] [836]
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[] \T1/pcr/m/n/10 horizontal = FALSE, add = FALSE, at = NULL, show.names =
NULL,[]
[837]
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\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 width, point char-ac-ter, point size ex-pan-sion, color, and bac
k-ground
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\T1/ptm/m/n/10 color. The de-fault \T1/pcr/m/n/10 medpch = NA \T1/ptm/m/n/10 su
p-presses the point, and
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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 ),
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[]\T1/ptm/m/n/10 When \T1/pcr/m/n/10 add = FALSE\T1/ptm/m/n/10 , \T1/pcr/m/n/10
xlim \T1/ptm/m/n/10 now de-faults to \T1/pcr/m/n/10 xlim = range(at, *) +
c(-0.5, 0.5)\T1/ptm/m/n/10 .
[838]
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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",[]
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[] \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl
ty = 1, outpch = NA)[]
[839] [840] [841] [842] [843]
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[][][]\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
[844]
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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 = "")[]
[845]
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[]\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col
umns,
[846] [847]
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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))[]
[848] [849] [850] [851]
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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
[852] [853] [854] [855] [856] [857]
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[]\T1/pcr/m/n/9 ## maybe change the desired number of tick marks: par(lab = c
(mx, my, 7))[]
[858] [859]
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\T1/ptm/m/n/10 they are the rel-a-tive fre-quen-cies \T1/pcr/m/n/10 counts/n \T
1/ptm/m/n/10 and in gen-eral sat-isfy
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[]\T1/ptm/m/n/10 Typical plots with ver-ti-cal bars are \T1/ptm/m/it/10 not \T1
/ptm/m/n/10 his-tograms. Con-sider [][]\T1/pcr/m/n/10 barplot[][][] \T1/ptm/m/n
/10 or
[860]
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[]\T1/pcr/m/n/9 ## Extreme outliers; the "FD" rule would take very large numbe
r of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 breaks\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[]
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[]\T1/pcr/m/n/9 length(hh$breaks) ## typically 1 million -- though 1e6 was "a
suggestion only"[]
[861]
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[][][]\T1/ptm/m/n/10 graphical pa-ram-e-ters[][][], or ar-gu-ments to [][]\T1/p
cr/m/n/10 hist.default[][][] \T1/ptm/m/n/10 such as
[862] [863] [864]
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[]\T1/pcr/m/n/9 identifyPch <- function(x, y = NULL, n = length(x), plot = FAL
SE, pch = 19, ...)[]
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[] \T1/pcr/m/n/9 ans <- identify(x[!sel], y[!sel], labels = which(!sel)
, n = 1, plot = plot, ...)[]
[865]
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[]\T1/ptm/m/n/10 a list of col-ors such as that gen-er-ated by [][]\T1/pcr/m/n/
10 rainbow[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 heat.colors[][][]\T1/ptm/m/
n/10 ,
[866]
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 useRaster \T1/ptm/m/n/10 is not spec-i-fied,
raster im-ages are used when the
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[][]\T1/pcr/m/n/10 getOption[][][]("preferRaster") \T1/ptm/m/n/10 is true, the
grid is reg-u-lar and ei-ther
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[][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage \T1/ptm/m/
n/10 is \T1/pcr/m/n/10 "yes" \T1/ptm/m/n/10 or it is
[867] [868] [869]
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[]\T1/pcr/m/n/9 barplot(yhist$counts, axes = FALSE, xlim = c(0, top), space =
0, horiz = TRUE)[]
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[] \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col =
par("fg"),[]
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[] \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace =
FALSE,[]
[870] [871] [872]
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[] \T1/pcr/m/n/9 text (1, y.leg[i] - 0.1, paste("cex=", formatC(cexv[i])), c
ex = 0.8, adj = 0)[]
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[] \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce
x = cexv[i])[]
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[] \T1/pcr/m/n/9 "text(c(3,3),2:3,\"c(rect(...)\")"), adj
= c(0, 0.3))[]
Underfull \vbox (badness 10000) has occurred while \output is active [873]
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[]\T1/pcr/m/n/9 legend(.4,1, "sin(c x)", pch = 21, pt.bg = "white", lty = 1, c
ol = "blue")[]
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[]\T1/pcr/m/n/9 legend("topleft", "(x,y)", pch=1, title= "topleft, inset =
.05", inset = .05)[]
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[]\T1/pcr/m/n/9 legend("topright", "(x,y)", pch=1, title= "topright, inset
= .02",inset = .02)[]
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[] \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste
("text.font =",i))[]
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[][][]\T1/pcr/m/n/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
[875] [876]
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[] \T1/pcr/m/n/10 log = "", ..., add = FALSE, verbose = getOption("verb
ose"))[]
[877]
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[]\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol
s given by
[878] [879]
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[]\T1/ptm/m/n/10 The mag-ni-fi-ca-tion to be used for axis an-no-ta-tion, as a
mul-ti-ple of
[880] [881] [882] [883]
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[]\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat
a con-tain
[884]
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\T1/ptm/m/n/10 which draws the ti-tle. You may want to spec-ify \T1/pcr/m/n/10
oma \T1/ptm/m/n/10 when chang-ing
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[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are
to be used, see
[885] [886]
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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))[]
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[]\T1/pcr/m/n/9 pairs(swiss, panel = panel.smooth, lwd = 2, cex = 1.5, col = "
blue") # hmm...[]
[887]
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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 ,
[888] [889]
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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.
[890] [891]
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[892 </usr/src/RPM/BUILD/R-3.5.3/library/graphics/help/figures/mai.pdf>]
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[893 </usr/src/RPM/BUILD/R-3.5.3/library/graphics/help/figures/oma.pdf>]
[894]
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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
[895]
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[]\T1/pcr/m/n/9 c(prof.pilots = 16, lawyers = 11, farmers = 10, salesmen = 9,
physicians = 9,[]
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[] \T1/pcr/m/n/9 mechanics = 6, policemen = 6, managers = 6, engineers = 5, t
eachers = 4,[]
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[897]
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[]\T1/ptm/m/n/10 a ex-pan-sion fac-tor ap-plied to the \T1/pcr/m/n/10 z \T1/ptm
/m/n/10 co-or-di-nates. Of-ten used with
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\T1/ptm/m/n/10 are con-trolled by graph-ics pa-ram-e-ters \T1/pcr/m/n/10 "cex.l
ab"\T1/ptm/m/n/10 /\T1/pcr/m/n/10 "font.lab" \T1/ptm/m/n/10 and
[898] [899] [900] [901]
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[]\T1/pcr/m/n/9 pie(c(Sky = 78, "Sunny side of pyramid" = 17, "Shady side of p
yramid" = 5),[]
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[] \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow
3"), border = FALSE)[]
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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.,
Underfull \hbox (badness 1024) in paragraph at lines 5641--5645
\T1/pcr/m/n/10 type = "punkte" \T1/ptm/m/n/10 be-ing equiv-a-lent to \T1/pcr/m/
n/10 type = "p" \T1/ptm/m/n/10 for S com-
[902] [903] [904] [905] [906] [907] [908]
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[]\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth) # numeric v
ector ~ factor[]
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[]\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes") # ext
remely silly[]
[909] [910] [911] [912] [913] [914]
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[]\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see
[915] [916]
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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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[][]
[917 </usr/src/RPM/BUILD/R-3.5.3/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,[]
[918]
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[] \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes = FALSE, xlab = "", ylab =
"", main = main)[]
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[920]
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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)))))[]
[921]
Underfull \hbox (badness 2600) in paragraph at lines 6978--6980
[]\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
[922] [923] [924]
Underfull \hbox (badness 1881) in paragraph at lines 7167--7172
[]\T1/ptm/m/n/10 color for rect-an-gle bor-der(s). The de-fault means \T1/pcr/m
/n/10 par("fg")\T1/ptm/m/n/10 . Use
[925]
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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))[]
[926] [927] [928] [929] [930] [931]
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[]\T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), sp
ace = "Lab")[]
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[]\T1/pcr/m/n/9 ## label the 20 very lowest-density points,the "outliers" (wit
h obs.number):[]
[932]
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[]\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0
, add = TRUE),[]
[933] [934] [935] [936] [937]
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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,[]
[938]
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[] \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10
, key.loc = 0:1,[]
[939] [940]
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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, ...)[]
[941] [942]
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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
[943] [944]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 8364--8364
[]\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),[]
[945] [946]
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[]\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll
apse = ","),[]
[947] [948] [949]
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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...")[]
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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
[950]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit
s}) has been already used, duplicate ignored
<to be read again>
\relax
l.8805 \HeaderA{units}{Graphical Units}{units}
[951]
Underfull \hbox (badness 1205) in paragraph at lines 8870--8872
[]\T1/ptm/m/n/10 vectors con-tain-ing the co-or-di-nates of the ver-tices of th
e poly-gon. See
[952] [953]
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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)[]
[954]) (./grid-pkg.tex
Chapter 6.
[955] [956] [957] [958] [959] [960]
Underfull \hbox (badness 10000) in paragraph at lines 385--391
\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
[961] [962] [963] [964] [965] [966] [967] [968] [969] [970]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1025--1025
[] \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")),[]
Underfull \hbox (badness 1430) in paragraph at lines 1074--1079
[]\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-
[971] [972] [973] [974]
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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
[975] [976] [977] [978] [979] [980]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1675--1675
[] \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75)
, list(...)))[]
[981] [982] [983]
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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")[]
[984]
Underfull \hbox (badness 2961) in paragraph at lines 1926--1931
[]\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 ,
[985]
Underfull \hbox (badness 1430) in paragraph at lines 1985--1990
[]\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
[986] [987] [988]
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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
[989] [990] [991]
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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-
[992] [993] [994]
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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)[]
[995] [996] [997] [998]
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[] \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1
, "inches"),[]
[999] [1000] [1001] [1002]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3179--3179
[] \T1/pcr/m/n/9 children=vpList(viewpor
t(name="vp2"))))[]
[1003] [1004]
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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")))[]
[1005]
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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
[1006]
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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,[]
[1007] [1008] [1009]
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[] \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant
i-clockwise")[]
[1010]
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[] \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other
anti-clockwise")[]
[1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021]
[1022]
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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
[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-
[1024] [1025] [1026]
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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
[1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035]
Underfull \hbox (badness 10000) in paragraph at lines 5189--5191
[]\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
[1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045]
Underfull \hbox (badness 3449) in paragraph at lines 5877--5883
\T1/ptm/m/n/10 to add and sub-tract unit ob-jects (e.g., \T1/pcr/m/n/10 unit(1,
"npc") - unit(1, "inches")\T1/ptm/m/n/10 ),
Underfull \hbox (badness 10000) in paragraph at lines 5877--5883
\T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob-
jects (e.g.,
[1046] [1047] [1048] [1049] [1050]
Underfull \hbox (badness 1867) in paragraph at lines 6187--6189
[]\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
[1051]
Underfull \hbox (badness 10000) in paragraph at lines 6224--6230
[][][]\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 ,
[1052] [1053]
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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
[1054] [1055] [1056]
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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"))))[]
[1057]) (./methods-pkg.tex [1058]
Chapter 7.
[1059] [1060]
Underfull \hbox (badness 1688) in paragraph at lines 166--171
\T1/ptm/m/n/10 func-tion. See that doc-u-men-ta-tion also for de-tails of how c
o-erce meth-ods work. Use
[1061] [1062] [1063]
Underfull \hbox (badness 1348) in paragraph at lines 392--395
[][][]\T1/pcr/m/n/10 GroupGenericFunctions[][][] \T1/ptm/m/n/10 for other in-fo
r-ma-tion about group generic func-tions; [][]Meth-
[1064] [1065]
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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[]
[1066]
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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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[1069]
Underfull \hbox (badness 1546) in paragraph at lines 791--797
[]\T1/ptm/m/n/10 A ma-trix (or ma-trix like ob-ject) com-bin-ing the columns (o
r rows) of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y\T1/ptm/m/n/10 .
Note
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\T1/ptm/m/n/10 that meth-ods must con-struct [][]\T1/pcr/m/n/10 colnames[][][]
\T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 rownames[][][] \T1/ptm/m/n/10 from the co
r-re-spond-ing col-
Underfull \hbox (badness 1789) in paragraph at lines 791--797
\T1/ptm/m/n/10 umn and row names of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr
/m/n/10 y \T1/ptm/m/n/10 (but not from de-pars-ing ar-gu-ment names such as in
[1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080]
[1081] [1082]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1794--1794
[]\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[]
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[]\T1/pcr/m/n/10 signature(from = "ANY", to = "environment")\T1/ptm/m/n/10 : ca
lls
[1083] [1084]
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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
[1085] [1086] [1087]
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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 =
[1088] [1089]
Underfull \hbox (badness 10000) in paragraph at lines 2328--2332
[]\T1/ptm/m/n/10 To see the ac-tual ta-ble (an en-vi-ron-ment) used for meth-od
s dis-patch, call
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2360--2360
[]\T1/pcr/m/n/10 ## Deprecated in 2010 and defunct in 2015 for \code{table = F
ALSE}:[]
[1090] [1091] [1092]
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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
[1093]
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[]\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin
g(where))[]
[1094] [1095] [1096]
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[]\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers
ions visible:[]
[1097] [1098] [1099] [1100] [1101] [1102] [1103]
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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
[1104] [1105]
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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
[1106]
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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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[]
[1107] [1108]
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[] \T1/pcr/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric",
longitude = "numeric", altitude = "numeric"))
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[]\T1/pcr/m/n/10 setMethod("plot", c("Pos", "missing"), function(x, y, ...) {
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[]\T1/pcr/m/n/10 GPS <- setClass("GPS", slots = c(time = "POSIXt"), contains =
"Pos")
[1109]
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[]\T1/pcr/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character")
, contains = "numeric")
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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
[1110] [1111] [1112]
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[]\T1/pcr/m/n/10 signature(from = "ANY", to = "call")\T1/ptm/m/n/10 . A method
ex-ists for
[1113] [1114]
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\T1/pcr/m/n/10 x$ensureLocal() \T1/ptm/m/n/10 on the ob-ject. The other way is
to mod-ify a field ex-plic-itly by
[1115]
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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,[]
[1116]
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[]\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w
here)
[1117] [1118]
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\T1/ptm/m/n/10 se-lect-ing class \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/10 for \T
1/pcr/m/n/10 y \T1/ptm/m/n/10 would pro-duce a method as-so-ci-ated with the si
g-na-ture
[1119]
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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 ,
[1120] [1121] [1122]
Underfull \hbox (badness 10000) in paragraph at lines 4811--4820
[]\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
[1123] [1124] [1125] [1126]
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[]\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate
inheritance[]
[1127]
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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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[1129]
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[]\T1/pcr/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...)
[1130]
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[]\T1/pcr/m/n/10 signature(method = "MethodWithNext")\T1/ptm/m/n/10 : used in-t
er-nally by
[1131]
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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
[1132] [1133] [1134]
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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
[1135]
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
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\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1136]
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
Underfull \hbox (badness 10000) in paragraph at lines 5848--5852
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1137] [1138] [1139] [1140]
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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
[1141] [1142]
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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
[1143]
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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
[1144]
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[]\T1/ptm/m/n/10 Establish a traced ver-sion of method
[1145]
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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
Underfull \hbox (badness 1436) in paragraph at lines 6647--6656
[][]\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
[1146]
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[1148] [1149]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}
[1150]
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[]\T1/pcr/m/n/10 ## Create a new object from the class or use the replacement
version of as().[]
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\T1/ptm/m/n/10 i-nat-ing all the for-mally de-fined slots and turn-ing off the
S4 bit of the ob-ject. With
[1151] [1152]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 7200--7200
[]\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")[]
[1153]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}
pdfTeX warning (ext4): destination wi
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
[1154]
Underfull \hbox (badness 6708) in paragraph at lines 7309--7321
[]\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 ,
[1155] [1156]
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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
[1157] [1158]
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[]\T1/ptm/m/n/10 If no sub-class/superclass re-la-tion-ship pro-vides a method,
\T1/pcr/m/n/10 as \T1/ptm/m/n/10 looks for an in-her-
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\T1/ptm/m/n/10 ited method, but ap-ply-ing, in-her-i-tance for the ar-gu-ment \
T1/pcr/m/n/10 from \T1/ptm/m/n/10 only, not for the
Underfull \hbox (badness 10000) in paragraph at lines 7663--7670
\T1/ptm/m/n/10 ar-gu-ment \T1/pcr/m/n/10 to \T1/ptm/m/n/10 (if you think about
it, you'll prob-a-bly agree that you wouldn't
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\T1/ptm/m/n/10 want the re-sult to be from some class other than the \T1/pcr/m/
n/10 Class \T1/ptm/m/n/10 spec-i-fied). Thus,
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\T1/pcr/m/n/10 selectMethod("coerce", sig, useInherited= c(from=TRUE, to= FALSE
))
[1159] [1160] [1161] [1162] [1163] [1164] [1165] [1166] [1167] [1168] [1169]
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
[1170]
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[]\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact
er(),
[1171]
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[] \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class
Def =,[]
[1172] [1173] [1174] [1175]
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[]\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col
umn matrices[]
[1176] [1177] [1178]
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[] \T1/pcr/m/n/9 setLoadAction(function(ns) assign("myCount", 0, envir = ns),
"setCount")[]
[1179] [1180]
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[]\T1/pcr/m/n/9 ## Using a short form for the signature, which matches like fo
rmal arguments[]
[1182] [1183] [1184] [1185]
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[]\T1/pcr/m/n/9 ## Define a new generic function to compute the residual degre
es of freedom[]
[1186]
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[]\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][]
[1187]
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[]\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][]
[1188] [1189] [1190] [1191] [1192] [1193] [1194] [1195] [1196]
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[]\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
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[]\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl
ass, from the data part; e.g.,
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\T1/pcr/m/n/10 "functionWithTrace" \T1/ptm/m/n/10 ex-tends \T1/pcr/m/n/10 "func
tion"\T1/ptm/m/n/10 . Each of the spe-cific classes ex-tends
[1197] [1198] [1199] [1200]) (./parallel-pkg.tex
Chapter 8.
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[]\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
[1201]
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[]\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
[1202] [1203]
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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
[1204]
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[]\T1/ptm/m/n/10 On Sparc So-laris \T1/pcr/m/n/10 logical = FALSE \T1/ptm/m/n/1
0 re-turns the num-ber of phys-i-cal cores and
[1205] [1206]
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[]\T1/ptm/m/n/10 Character vec-tor of ad-di-tional ar-gu-ments for \T1/pcr/m/n/
10 Rscript \T1/ptm/m/n/10 such as
[1207] [1208] [1209] [1210]
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[]\T1/pcr/m/n/10 mcfork \T1/ptm/m/n/10 re-turns an ob-ject of the class \T1/pcr
/m/n/10 "childProcess" \T1/ptm/m/n/10 to the mas-ter and of class
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\T1/pcr/m/n/10 "masterProcess" \T1/ptm/m/n/10 to the child: both the classes in
-herit from class \T1/pcr/m/n/10 "process"\T1/ptm/m/n/10 . If
[1211] [1212]
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[] \T1/pcr/m/n/10 mc.cleanup = TRUE, mc.allow.recursive = TRUE, affini
ty.list = NULL)[]
[1213]
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[]\T1/pcr/m/n/10 mclapply \T1/ptm/m/n/10 is a par-al-lelized ver-sion of [][]\T
1/pcr/m/n/10 lapply[][][]\T1/ptm/m/n/10 , pro-vided \T1/pcr/m/n/10 mc.cores > 1
\T1/ptm/m/n/10 : for
[1214]
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[]\T1/pcr/m/n/9 mclapply(list(A, A, A), first, mc.preschedule = FALSE, affinit
y.list = affL)[]
[1215]
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[]\T1/pcr/m/n/9 # To optimize the overall execution time elements of X are sch
eduled to suitable CPUs[]
[1216]
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[]\T1/pcr/m/n/10 mcparallel \T1/ptm/m/n/10 re-turns an ob-ject of the class \T1
/pcr/m/n/10 "parallelJob" \T1/ptm/m/n/10 which in-her-its from
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[]\T1/ptm/m/n/10 The be-haviour with \T1/pcr/m/n/10 mc.set.seed = TRUE \T1/ptm/
m/n/10 is dif-fer-ent only if
[1217]
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[]\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)[]
[1218] [1219]
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[] \T1/pcr/m/n/9 as.integer(runif(N, 1, 12)), as.integer(runif
(N, 1, 28)))[]
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[]\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct, format =
"%Y-%m-%d")))[]
Underfull \hbox (badness 1577) in paragraph at lines 1339--1342
[]\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
[1220]
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[]\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
[1221] [1222]) (./splines-pkg.tex
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
[1223] [1224] [1225] [1226] [1227] [1228] [1229]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 492--492
[]\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height, women, bSpl
ine = TRUE))[]
[1230] [1231] [1232] [1233]
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[]\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37,
sparse = TRUE)))[]
[1234] [1235] [1236]) (./stats-pkg.tex
Chapter 10.
[1237]
Underfull \hbox (badness 2781) in paragraph at lines 65--68
[]\T1/pcr/m/n/10 .MFclass \T1/ptm/m/n/10 re-turns a char-ac-ter string, one of
\T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ordered"\T1/ptm/m/n/10
, \T1/pcr/m/n/10 "factor"\T1/ptm/m/n/10 ,
[1238] [1239] [1240] [1241] [1242]
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[]\T1/pcr/m/n/9 add1(glm.D93, scope = ~outcome*treatment, test = "Rao") ## Pea
rson Chi-square[]
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[]\T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet =
FALSE)
[1243] [1244] [1245] [1246] [1247] [1248] [1249]
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[]\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
[1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257]
Underfull \hbox (badness 10000) in paragraph at lines 1391--1393
[]\T1/ptm/m/n/10 an es-ti-mate of the ra-tio of scales. (Only present if ar-gu-
ment
[1258]
Underfull \hbox (badness 10000) in paragraph at lines 1508--1512
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("aov", "lm") \T1/ptm/m/n/
10 or for mul-ti-ple re-sponses of class
Underfull \hbox (badness 10000) in paragraph at lines 1508--1512
\T1/pcr/m/n/10 c("maov", "aov", "mlm", "lm") \T1/ptm/m/n/10 or for mul-ti-ple e
r-ror strata of class
Underfull \hbox (badness 1490) in paragraph at lines 1508--1512
\T1/pcr/m/n/10 c("aovlist", "[][]listof[][][]")\T1/ptm/m/n/10 . There are [][]\
T1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 summary[][][] \
T1/ptm/m/n/10 meth-ods avail-able for
[1259] [1260] [1261] [1262]
Underfull \hbox (badness 10000) in paragraph at lines 1773--1777
[]\T1/ptm/m/n/10 function to be called to han-dle miss-ing val-ues. Cur-rently,
via
Underfull \hbox (badness 2197) in paragraph at lines 1773--1777
\T1/pcr/m/n/10 na.action = na.pass\T1/ptm/m/n/10 , only Yule-Walker method can
han-dle miss-
[1263] [1264]
Underfull \hbox (badness 4303) in paragraph at lines 1874--1876
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 x \T1/ptm/m/n/10 con-tains miss-ing val-ues,
see [][]\T1/pcr/m/n/10 NA[][][]\T1/ptm/m/n/10 , also con-sider us-ing [][]\T1/
pcr/m/n/10 arima[][][]()\T1/ptm/m/n/10 , pos-si-bly with
[1265] [1266] [1267]
Underfull \hbox (badness 10000) in paragraph at lines 2096--2101
[]\T1/ptm/m/n/10 logical; if true, the AR pa-ram-e-ters are trans-formed to en-
sure
Underfull \hbox (badness 10000) in paragraph at lines 2096--2101
\T1/ptm/m/n/10 that they re-main in the re-gion of sta-tion-ar-ity. Not used fo
r
Underfull \hbox (badness 1371) in paragraph at lines 2096--2101
\T1/pcr/m/n/10 method = "CSS"\T1/ptm/m/n/10 . For \T1/pcr/m/n/10 method = "ML"\
T1/ptm/m/n/10 , it has been ad-van-ta-geous
Underfull \hbox (badness 1221) in paragraph at lines 2102--2108
[]\T1/ptm/m/n/10 optional nu-meric vec-tor of the same length as the to-tal num
-ber of pa-
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\T1/ptm/m/n/10 ram-e-ters. If sup-plied, only \T1/pcr/m/n/10 NA \T1/ptm/m/n/10
en-tries in \T1/pcr/m/n/10 fixed \T1/ptm/m/n/10 will be var-ied.
[1268] [1269]
Underfull \hbox (badness 3965) in paragraph at lines 2183--2185
[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
[1270] [1271] [1272]
Underfull \hbox (badness 1221) in paragraph at lines 2457--2462
[]\T1/ptm/m/n/10 optional nu-meric vec-tor of the same length as the to-tal num
-ber of pa-
Underfull \hbox (badness 4608) in paragraph at lines 2457--2462
\T1/ptm/m/n/10 ram-e-ters. If sup-plied, only \T1/pcr/m/n/10 NA \T1/ptm/m/n/10
en-tries in \T1/pcr/m/n/10 fixed \T1/ptm/m/n/10 will be var-ied.
[1273]
Underfull \hbox (badness 3965) in paragraph at lines 2534--2536
[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
[1274] [1275]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2679--2679
[]\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F
ALSE)
[1276] [1277] [1278] [1279]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2919--2919
[]\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co
l = "green")[]
[1280] [1281] [1282]
Overfull \hbox (19.88992pt too wide) in paragraph at lines 3128--3130
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Bartlett test of homoge
neity of variances"\T1/ptm/m/n/10 .
[1283]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3176--3176
[]\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 3177--3177
[]\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p =
FALSE)[]
[1284]
Underfull \hbox (badness 2726) in paragraph at lines 3260--3276
\T1/ptm/m/n/10 We have slightly tweaked the orig-i-nal ``TOMS 708'' al-go-rithm
, and en-hanced for
[1285] [1286] [1287] [1288] [1289]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3568--3568
[]\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = "
log density",[]
[1290] [1291] [1292] [1293]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 3846--3846
[]\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit
df = 0)
[1294] [1295] [1296] [1297] [1298]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4135--4135
[]\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 4136--4136
[]\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p
= FALSE)[]
[1299] [1300] [1301]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4374--4374
[]\T1/pcr/m/n/9 chisq.test(x, p = p) # maybe doubtful
, but is ok![]
[1302] [1303] [1304]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4542--4542
[] \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df =
df, ncp = L)),[]
[1305]
Underfull \hbox (badness 3989) in paragraph at lines 4634--4641
[]\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 =
[1306] [1307]
Underfull \hbox (badness 2080) in paragraph at lines 4754--4756
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 "aov" \T1/ptm/m/n/10 method does not re-por
t aliased co-ef-fi-cients (see [][]\T1/pcr/m/n/10 alias[][][]\T1/ptm/m/n/10 ) b
y de-fault where
Underfull \hbox (badness 2050) in paragraph at lines 4757--4763
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 complete \T1/ptm/m/n/10 ar-gu-ment also ex-
ists for com-pat-i-bil-ity with [][]\T1/pcr/m/n/10 vcov[][][] \T1/ptm/m/n/10 me
th-ods, and \T1/pcr/m/n/10 coef
Underfull \hbox (badness 4954) in paragraph at lines 4757--4763
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 aov \T1/ptm/m/n/10 meth-ods for other classes
should typ-i-cally also keep the \T1/pcr/m/n/10 complete = *
Underfull \hbox (badness 4726) in paragraph at lines 4757--4763
\T1/ptm/m/n/10 be-hav-ior in sync. By that, with \T1/pcr/m/n/10 p <- length(coe
f(obj, complete = TF))\T1/ptm/m/n/10 ,
[1308] [1309] [1310] [1311]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5019--5019
[]\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 5021--5021
[]\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))[]
[1312]
Underfull \hbox (badness 7397) in paragraph at lines 5108--5112
[]\T1/ptm/m/n/10 For con-sis-tency, \T1/pcr/m/n/10 sparse \T1/ptm/m/n/10 is an
ar-gu-ment to all these con-trast func-tions, how-ever
Underfull \hbox (badness 7326) in paragraph at lines 5108--5112
\T1/pcr/m/n/10 sparse = TRUE \T1/ptm/m/n/10 for \T1/pcr/m/n/10 contr.poly \T1/p
tm/m/n/10 is typ-i-cally point-less and is rarely use-ful for
[1313] [1314]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5242--5242
[]\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 5260--5260
[]\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil
ter"))
Underfull \hbox (badness 2680) in paragraph at lines 5287--5289
[]\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
[1315]
Underfull \hbox (badness 10000) in paragraph at lines 5292--5294
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 r <- convolve(x, y, type = "open") \T1/ptm/m
/n/10 and \T1/pcr/m/n/10 n <- length(x)\T1/ptm/m/n/10 ,
[1316] [1317]
Underfull \hbox (badness 1436) in paragraph at lines 5470--5475
[]\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 5470--5475
\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 5470--5475
\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 ,
[1318] [1319] [1320]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5668--5668
[] \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE,
...)[]
[1321]
Underfull \hbox (badness 1168) in paragraph at lines 5740--5745
[]\T1/ptm/m/n/10 For Spear-man's test, p-values are com-puted us-ing al-go-rith
m AS 89 for $\OML/cmm/m/it/10 n < \OT1/cmr/m/n/10 1290$ \T1/ptm/m/n/10 and
[1322] [1323]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5835--5835
[]\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center =
TRUE,
[1324] [1325] [1326]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 6020--6020
[]\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter =
NULL)
[1327] [1328]
Underfull \hbox (badness 10000) in paragraph at lines 6183--6188
[]\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
[1329] [1330] [1331]
Underfull \hbox (badness 5954) in paragraph at lines 6379--6381
[]\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn
, see
[1332]
Underfull \hbox (badness 2503) in paragraph at lines 6461--6464
[]\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 6465--6467
[]\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 6468--6473
\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,
[1333]
Underfull \hbox (badness 7238) in paragraph at lines 6504--6507
[][][]\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
[1334]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6539--6539
[]\T1/pcr/m/n/9 plot(dend2$lower[[3]], nodePar = list(col = 4), horiz = TRUE,
type = "tr")[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6554--6554
[]\T1/pcr/m/n/9 ## merge() all parts back (using default \TS1/pcr/m/n/9 '\T1/p
cr/m/n/9 height\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 instead of original one):[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6569--6569
[]\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h
oriz = TRUE)[]
[1335] [1336] [1337] [1338]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6813--6813
[] \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker
n = TRUE))))[]
[1339] [1340]
Underfull \vbox (badness 10000) has occurred while \output is active [1341]
[1342] [1343] [1344]
Underfull \hbox (badness 10000) in paragraph at lines 7211--7215
\T1/pcr/m/n/10 "maximum"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "manhattan"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "canberra"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "binary" \T1/ptm/
m/n/10 or
[1345]
Underfull \hbox (badness 6493) in paragraph at lines 7310--7313
[]\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T
1/pcr/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the
[1346] [1347]
Underfull \hbox (badness 10000) in paragraph at lines 7447--7450
[]\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/pcr/m/n/10 ht
tps : / / CRAN . R-[]project . org / view =
[1348] [1349] [1350] [1351] [1352] [1353]
Underfull \hbox (badness 10000) in paragraph at lines 7857--7862
[]\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 , ...,
[1354] [1355]
Overfull \hbox (33.6622pt too wide) in paragraph at lines 7995--7997
[]\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 (
\OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1
\OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1
/cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/pcr/m/n/10 -pexp(t, r, lower = FALSE, log
= TRUE)\T1/ptm/m/n/10 .
[1356] [1357] [1358]
Underfull \hbox (badness 1210) in paragraph at lines 8212--8214
[]\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
[1359] [1360] [1361] [1362] [1363] [1364] [1365]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 8687--8687
[]\T1/pcr/m/n/9 ## Not run: glm(y ~ x, family = quasi(variance = "mu^3", link
= "log")) # fails[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 8690--8690
[]\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit
"), start = c(0,1))[]
[1366] [1367]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 8828--8828
[]\T1/pcr/m/n/9 quantile(rel.err(qf(2*p - 1, df1 = 1, df2 = df), qt(p, df)^2),
.90) # ~= 7e-9[]
[1368]
Underfull \hbox (badness 1859) in paragraph at lines 8867--8872
\T1/ptm/m/n/10 If \T1/pcr/m/n/10 inverse \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\
T1/ptm/m/n/10 , the (un-nor-mal-ized) in-verse Fourier trans-form is re-turned,
i.e., if
[1369] [1370] [1371]
Underfull \hbox (badness 2865) in paragraph at lines 9113--9122
[]\T1/ptm/m/n/10 For larger than $\OT1/cmr/m/n/10 2 \OMS/cmsy/m/n/10 ^^B \OT1/c
mr/m/n/10 2$ \T1/ptm/m/n/10 ta-bles and \T1/pcr/m/n/10 hybrid = TRUE\T1/ptm/m/n
/10 , asymp-totic chi-squared prob-a-bil-i-
Underfull \hbox (badness 1331) in paragraph at lines 9113--9122
\T1/ptm/m/n/10 ties are only used if the `Cochran con-di-tions' (or mod-i-fied
ver-sion thereof) spec-i-fied by
[1372] [1373]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 9255--9255
[] \T1/pcr/m/n/9 dimnames = list(income = c("< 15k", "15-25k", "25-4
0k", "> 40k"),[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 9256--9256
[] \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Mod
erateS", "VeryS")))[]
[1374] [1375] [1376]
Overfull \hbox (61.88992pt too wide) in paragraph at lines 9435--9437
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Fligner-Killeen test of
homogeneity of variances"\T1/ptm/m/n/10 .
[1377] [1378] [1379] [1380] [1381] [1382] [1383]
Underfull \hbox (badness 2443) in paragraph at lines 9888--9894
[][][]\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);
[1384] [1385] [1386]
Underfull \hbox (badness 3758) in paragraph at lines 10101--10104
[]\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
[1387] [1388] [1389] [1390]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 10337--10337
[] \T1/pcr/m/n/10 x = FALSE, y = TRUE, singular.ok = TRUE, contrasts = NULL
, ...)[]
Underfull \hbox (badness 4518) in paragraph at lines 10363--10368
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1391]
Underfull \hbox (badness 4132) in paragraph at lines 10402--10406
[]\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth
od
[1392]
Underfull \hbox (badness 10000) in paragraph at lines 10507--10510
[]\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
[1393] [1394] [1395]
Underfull \hbox (badness 2142) in paragraph at lines 10711--10714
[]\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 ^^@
[1396]
Underfull \hbox (badness 1708) in paragraph at lines 10792--10796
[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
[1397]
Underfull \hbox (badness 10000) in paragraph at lines 10834--10840
[][][]\T1/pcr/m/n/10 glm[][][] \T1/ptm/m/n/10 for com-put-ing \T1/pcr/m/n/10 gl
m.obj\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 anova.glm[][][]\T1/ptm/m/n/10 ; the co
r-re-spond-ing \T1/ptm/m/it/10 generic \T1/ptm/m/n/10 func-tions,
Underfull \hbox (badness 1418) in paragraph at lines 10872--10877
\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 (=
[1398] [1399]
Underfull \hbox (badness 2635) in paragraph at lines 11005--11008
\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
[1400] [1401] [1402]
Underfull \hbox (badness 1694) in paragraph at lines 11190--11193
[]\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these
de-fault to
Underfull \hbox (badness 1337) in paragraph at lines 11209--11218
[]\T1/ptm/m/n/10 If ei-ther is a vec-tor (of `weights') then the ap-pro-pri-ate
den-dro-gram is re-ordered ac-cord-
Underfull \hbox (badness 3049) in paragraph at lines 11209--11218
\T1/ptm/m/n/10 ing to the sup-plied val-ues sub-ject to the con-straints im-pos
ed by the den-dro-gram, by
[1403]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 11291--11291
[]\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col
SideColors = cc,[]
[1404]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11324--11324
[] \T1/pcr/m/n/10 optim.start = c(alpha = 0.3, beta = 0.1, gamma =
0.1),[]
Underfull \hbox (badness 10000) in paragraph at lines 11337--11341
[]\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
[1405] [1406] [1407]
Underfull \hbox (badness 7379) in paragraph at lines 11517--11520
[]\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds
[][]\T1/pcr/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq
uiv-a-lent of
[1408] [1409]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11656--11656
[]\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4)
, DEV.FUN = nD)[]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has
been already used, duplicate ignored
<to be read again>
\relax
l.11671 \aliasA{hat}{influence.measures}{hat}
[1410]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11724--11724
[]\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA
LSE),[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11736--11736
[]\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE),
...)[]
[1411]
Underfull \hbox (badness 1062) in paragraph at lines 11785--11790
[]\T1/ptm/m/n/10 The op-tional \T1/pcr/m/n/10 infl\T1/ptm/m/n/10 , \T1/pcr/m/n/
10 res \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sd \T1/ptm/m/n/10 ar-gu-ments are ther
e to en-cour-age the use of these di-
Underfull \hbox (badness 1052) in paragraph at lines 11802--11804
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main
ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing
[1412] [1413]
Underfull \hbox (badness 3623) in paragraph at lines 11956--11958
[]\T1/pcr/m/n/10 rel.tol \T1/ptm/m/n/10 can-not be less than \T1/pcr/m/n/10 max
(50*.Machine$double.eps, 0.5e-28) \T1/ptm/m/n/10 if
[1414] [1415]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12052--12052
[] \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend =
TRUE,[]
[1416]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12145--12145
[] \T1/pcr/m/n/9 interaction.plot(agegp, tobgp, ncases/ncontrols, trace.label
= "tobacco",[]
[1417]
Underfull \hbox (badness 10000) in paragraph at lines 12193--12196
[]\T1/ptm/m/n/10 For nor-mally $\OML/cmm/m/it/10 N\OT1/cmr/m/n/10 (\OML/cmm/m/i
t/10 m; \OT1/cmr/m/n/10 1)$ \T1/ptm/m/n/10 dis-tributed $\OML/cmm/m/it/10 X$\T1
/ptm/m/n/10 , the ex-pected value of \T1/pcr/m/n/10 IQR(X) \T1/ptm/m/n/10 is
[1418] [1419] [1420]
Underfull \hbox (badness 4441) in paragraph at lines 12388--12390
[]\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is
fit-ted to
Underfull \hbox (badness 10000) in paragraph at lines 12395--12397
[]\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
[1421]
Underfull \hbox (badness 4739) in paragraph at lines 12418--12420
[]\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
[1422]
Underfull \hbox (badness 2753) in paragraph at lines 12487--12489
[]\T1/ptm/m/n/10 R bug re-port PR#14682 (2011-2013) [][]$\T1/pcr/m/n/10 https :
/ / bugs . r-[]project . org / bugzilla3 /
[1423] [1424]
Underfull \hbox (badness 1292) in paragraph at lines 12612--12616
\T1/ptm/m/n/10 than one, it means the con-vo-lu-tion of ker-nels of di-men-sion
\T1/pcr/m/n/10 m[j]\T1/ptm/m/n/10 , for
[1425]
Underfull \hbox (badness 10000) in paragraph at lines 12725--12727
[]\T1/ptm/m/n/10 an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of class \T1/pcr/m/
n/10 "kmeans"\T1/ptm/m/n/10 , typ-i-cally the re-sult \T1/pcr/m/n/10 ob \T1/ptm
/m/n/10 of
Underfull \hbox (badness 2894) in paragraph at lines 12731--12735
[]\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 12731--12735
\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
[1426] [1427] [1428] [1429] [1430] [1431] [1432] [1433] [1434] [1435] [1436]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13438--13438
[]\T1/pcr/m/n/9 dimnames(cAS) <- list(paste("it =", format(1:10)), c("intercep
t", "slope"))[]
[1437]
Underfull \hbox (badness 4518) in paragraph at lines 13481--13486
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1438] [1439]
Underfull \hbox (badness 10000) in paragraph at lines 13680--13684
[]\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
,
[1440] [1441] [1442]
Underfull \hbox (badness 6995) in paragraph at lines 13865--13867
[][][]\T1/pcr/m/n/10 naresid[][][] \T1/ptm/m/n/10 is ap-plied to the re-sults a
nd so will fill in with \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 s it the fit had
[1443] [1444]
Underfull \hbox (badness 1163) in paragraph at lines 14013--14021
\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 ,
[1445] [1446]
Underfull \hbox (badness 4518) in paragraph at lines 14133--14138
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1447] [1448]
Underfull \hbox (badness 10000) in paragraph at lines 14271--14275
[]\T1/ptm/m/n/10 Only for the (de-fault) case \T1/pcr/m/n/10 (surface =
Underfull \hbox (badness 7133) in paragraph at lines 14271--14275
\T1/pcr/m/n/10 "interpolate", statistics = "approximate")\T1/ptm/m/n/10 : shoul
d the
[1449]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 14319--14319
[]\T1/pcr/m/n/10 plogis(q, location = 0, scale = 1, lower.tail = TRUE, log.p =
FALSE)[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 14320--14320
[]\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p =
FALSE)[]
[1450]
Underfull \hbox (badness 10000) in paragraph at lines 14375--14378
[]\T1/ptm/m/n/10 The dis-tri-bu-tion func-tion is a rescaled hy-per-bolic tan-g
ent,
Underfull \hbox (badness 1715) in paragraph at lines 14375--14378
\T1/pcr/m/n/10 plogis(x) == (1+ [][]tanh[][][](x/2))/2\T1/ptm/m/n/10 , and it i
s called a \T1/ptm/m/it/10 sig-moid func-tion \T1/ptm/m/n/10 in con-texts
[1451] [1452] [1453] [1454]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 14663--14663
[]\T1/pcr/m/n/10 plnorm(q, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p =
FALSE)[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 14664--14664
[]\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p =
FALSE)[]
[1455]
Overfull \hbox (45.6622pt too wide) in paragraph at lines 14714--14716
[]\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 (
\OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1
\OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1
/cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/pcr/m/n/10 -plnorm(t, r, lower = FALSE, l
og = TRUE)\T1/ptm/m/n/10 .
Overfull \hbox (18.78088pt too wide) in paragraph at lines 14757--14757
[]\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra
nge(x)))
[1456] [1457] [1458] [1459] [1460] [1461] [1462]
Underfull \hbox (badness 2726) in paragraph at lines 15164--15167
[]\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 ,
[1463] [1464] [1465] [1466] [1467] [1468] [1469] [1470] [1471] [1472] [1473]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 15879--15879
[]\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc
gp, data = esoph)
[1474] [1475]
Underfull \hbox (badness 1014) in paragraph at lines 16017--16022
\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
[1476]
Underfull \hbox (badness 1648) in paragraph at lines 16083--16085
[]\T1/ptm/m/n/10 a data frame cre-ated with [][]\T1/pcr/m/n/10 model.frame[][][
]\T1/ptm/m/n/10 . If an-other sort of ob-ject,
Underfull \hbox (badness 2591) in paragraph at lines 16097--16106
\T1/ptm/m/n/10 us-ing the data in \T1/pcr/m/n/10 data \T1/ptm/m/n/10 which must
sup-ply vari-ables with the same names as would
Underfull \hbox (badness 3930) in paragraph at lines 16097--16106
\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
[1477]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 16165--16165
[]\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts = list(a = "contr.sum", b
= "contr.poly"))[]
[1478] [1479] [1480] [1481] [1482] [1483] [1484] [1485]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 16719--16719
[]\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[]
[1486] [1487] [1488] [1489]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 16947--16947
[]\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x,
s, prob = 0.4)),[]
[1490] [1491] [1492] [1493] [1494] [1495] [1496] [1497]
Underfull \hbox (badness 2359) in paragraph at lines 17533--17535
[]\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For-
tran code used by
[1498] [1499]
Underfull \vbox (badness 10000) has occurred while \output is active [1500]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 17705--17705
[] \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21
), th = b[1]))[]
[1501]
Underfull \hbox (badness 10000) in paragraph at lines 17785--17789
[]\T1/ptm/m/n/10 Fits the asymp-totic re-gres-sion model, in the form \T1/pcr/m
/n/10 b0 +
[1502] [1503]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17865--17865
[]\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 17912--17912
[]\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[]
[1504]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 17959--17959
[]\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[]
[1505] [1506] [1507] [1508] [1509] [1510] [1511] [1512]
Underfull \hbox (badness 1248) in paragraph at lines 18450--18453
[]\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma
-tion to the gra-di-ent, on
Underfull \hbox (badness 1127) in paragraph at lines 18463--18467
\T1/ptm/m/n/10 value by a fac-tor of \T1/pcr/m/n/10 reltol * (abs(val) + reltol
) \T1/ptm/m/n/10 at a step. De-faults to
[1513]
Underfull \hbox (badness 1478) in paragraph at lines 18471--18475
\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 18529--18531
[]\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
[1514] [1515]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 18635--18635
[] \T1/pcr/m/n/9 lower = rep(2, 25), upper = rep(4, 25)) # par[24] is *no
t* at boundary[]
Underfull \vbox (badness 10000) has occurred while \output is active [1516]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18677--18677
[] \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem",
axes = FALSE)[]
Overfull \hbox (123.1803pt too wide) in paragraph at lines 18695--18695
[]\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 18698--18698
[]\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 18718--18718
[]\T1/pcr/m/n/10 optimize(f, interval, ..., lower = min(interval), upper = max
(interval),
Overfull \hbox (36.78088pt too wide) in paragraph at lines 18721--18721
[]\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max
(interval),[]
[1517]
Underfull \hbox (badness 2564) in paragraph at lines 18756--18767
[]\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 18756--18767
\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
[1518]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18819--18819
[]\T1/pcr/m/n/9 f <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x -
1)), 10), 10)[]
[1519] [1520] [1521]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 19044--19044
[]\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp =
1, lty = 1:6,[]
[1522]
Underfull \hbox (badness 1337) in paragraph at lines 19120--19123
[]\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
[1523] [1524] [1525] [1526] [1527] [1528]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19439--19439
[] \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd =
1.5),[]
[1529]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 19527--19527
[] \T1/pcr/m/n/10 expression("Cook\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s dist
vs Leverage " * h[ii] / (1 - h[ii]))),[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 19530--19530
[] \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact
ive(),[]
[1530]
Underfull \hbox (badness 3049) in paragraph at lines 19609--19613
[]\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
[1531] [1532] [1533] [1534]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19857--19857
[] \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3,
...)[]
Underfull \hbox (badness 4779) in paragraph at lines 19864--19866
[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read
y ex-ist-ing plot. Only valid for
Underfull \hbox (badness 1194) in paragraph at lines 19867--19870
[]\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting
of the con-fi-dence
[1535]
Underfull \hbox (badness 1107) in paragraph at lines 19925--19927
[]\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
[1536]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 19980--19980
[]\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange
") # all colors[]
[1537]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 19987--19987
[]\T1/pcr/m/n/9 legend(2.5, 1.9, paste("f =", c(0, 0.2, 1)), col = 1:3, lty =
1, y.intersp = 1)[]
Underfull \hbox (badness 10000) in paragraph at lines 20037--20040
[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 function(x, col, bg, pch, type, ...) \T1/ptm/
m/n/10 which gives
Underfull \hbox (badness 10000) in paragraph at lines 20037--20040
\T1/ptm/m/n/10 the ac-tion to be car-ried out in each panel of the dis-play for
[1538]
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[]\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma
r..., oma...)")[]
[1539] [1540]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20206--20206
[] \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE) # no
cancellation[]
[1541]
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[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Exact Poisson test" \T1
/ptm/m/n/10 or
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[]\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple =
FALSE)
[1542]
Underfull \hbox (badness 10000) in paragraph at lines 20372--20374
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 poly(*, simple=TRUE)\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 polym(*, coefs=<non-NULL>)\T1/ptm/m/n/10 , and
[1543]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20409--20409
[] \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 20414--20414
[]\T1/pcr/m/n/9 ## poly(<matrix>, df) --- used to fail till July 14 (vive la F
rance!), 2017:[]
[1544] [1545] [1546] [1547] [1548] [1549] [1550] [1551] [1552] [1553] [1554]
[1555] [1556]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 21264--21264
[] \T1/pcr/m/n/9 all.equal(pz3$sdev, pZ$sdev, tol = 1e-15)) # exactly
equal typically[]
[1557]
Underfull \hbox (badness 6859) in paragraph at lines 21331--21338
[][][]\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 21342--21348
[]\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 ,
[1558] [1559] [1560] [1561] [1562] [1563] [1564] [1565] [1566] [1567] [1568]
[1569]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 22080--22080
[] \T1/pcr/m/n/10 subset = rep_len(TRUE, nrow(as.matrix(x))), fix_sign
= TRUE, ...)[]
[1570] [1571] [1572] [1573] [1574]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 22364--22364
[] \T1/pcr/m/n/10 has.Pvalue = nc >= 4L && length(cn <- colnames(x
)) &&[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 22365--22365
[] \T1/pcr/m/n/10 substr(cn[nc], 1L, 3L) %in% c("Pr("
, "p-v"),[]
[1575] [1576] [1577] [1578] [1579]
Underfull \hbox (badness 1337) in paragraph at lines 22689--22695
[]\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
[1580] [1581] [1582] [1583] [1584] [1585] [1586] [1587]
Overfull \hbox (133.98029pt too wide) in paragraph at lines 23251--23251
[] \T1/pcr/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty
p, ...), quantile(x, prob, type=1)))[]
[1588] [1589]
Underfull \hbox (badness 1028) in paragraph at lines 23392--23395
[]\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
[1590] [1591]
Underfull \hbox (badness 10000) in paragraph at lines 23502--23505
[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by
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\T1/pcr/m/n/10 cutree(hclust.obj, k = k)\T1/ptm/m/n/10 , can be spec-i-fied for
ef-fi-ciency if
[1592]
Underfull \hbox (badness 10000) in paragraph at lines 23557--23559
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 23619--23621
[]\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
[1593] [1594]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 23721--23721
[]\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd,
10:1, mean)")[]
[1595] [1596] [1597]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 23941--23941
[]\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide
", v.names = "x")[]
[1598] [1599] [1600]
Underfull \hbox (badness 10000) in paragraph at lines 24087--24090
[]\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
Underfull \hbox (badness 2134) in paragraph at lines 24139--24143
[][][]\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
[1601]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 24152--24152
[]\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi
ans Example")[]
[1602] [1603] [1604] [1605] [1606] [1607] [1608]
Underfull \hbox (badness 6268) in paragraph at lines 24616--24621
[][]\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 ,
[1609]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 24644--24644
[] \T1/pcr/m/n/9 setNames(pars[c(".lin", "xmid", "scal")], nm = mCall[c("As
ym", "xmid", "scal")])[]
[1610] [1611]
Underfull \hbox (badness 1867) in paragraph at lines 24821--24823
[]\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 24834--24838
\T1/ptm/m/n/10 where \T1/pcr/m/n/10 NN <- [][]nobs[][][](object, use.fallback =
use.fallback) \T1/ptm/m/n/10 and
Underfull \hbox (badness 10000) in paragraph at lines 24834--24838
\T1/pcr/m/n/10 PP <- sum(!is.na([][]coef[][][](object))) \T1/ptm/m/n/10 -- wher
e in older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was
[1612]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 24870--24870
[]\T1/pcr/m/n/9 sigma(lm1) # ~= 7.165 = "Residual standard error" printed fr
om summary(lm1)[]
[1613] [1614] [1615]
Underfull \hbox (badness 2495) in paragraph at lines 25060--25069
[]\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 [][]$\T1/pcr/m/n/10 https : / / en .
[1616]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 25142--25142
[] \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends
= FALSE)[]
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[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui
red; de-faults to
[1617]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 25236--25236
[]\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS
S"), smooth(x)))[]
[1618]
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[]\T1/pcr/m/n/10 smooth.spline(x, y = NULL, w = NULL, df, spar = NULL, lambda
= NULL, cv = FALSE,
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[] \T1/pcr/m/n/10 control.spar = list(), tol = 1e-6 * IQR(x), kee
p.stuff = FALSE)[]
[1619]
Underfull \hbox (badness 10000) in paragraph at lines 25306--25311
[]\T1/ptm/m/n/10 integer or [][]\T1/pcr/m/n/10 function[][][] \T1/ptm/m/n/10 gi
v-ing the num-ber of knots to use when
Underfull \hbox (badness 2435) in paragraph at lines 25306--25311
\T1/pcr/m/n/10 all.knots = FALSE\T1/ptm/m/n/10 . If a func-tion (as by de-fault
), the num-ber of
[1620]
Underfull \hbox (badness 2980) in paragraph at lines 25451--25453
[]\T1/ptm/m/n/10 the value of \T1/pcr/m/n/10 spar \T1/ptm/m/n/10 com-puted or g
iven, un-less it has been given as
[1621]
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[] \T1/pcr/m/n/10 nx <- length(x) - sum(duplicated( round((x - mean(x)) /
tol) ))[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 25536--25536
[]\T1/pcr/m/n/9 plot(dist ~ speed, data = cars, main = "data(cars) & smoothi
ng splines")[]
[1622]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 25557--25557
[]\T1/pcr/m/n/9 with(cars.spl$fit, min + range * knot[-c(1:3, nk+1 +1:3)]) # =
= unique(cars$speed)[]
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[1624]
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[]\T1/pcr/m/n/9 legend(1, 470, paste("endrule", c("keep","constant","median"),
sep = " = "),[]
[1625]
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[]\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na.
fail,
[1626] [1627] [1628] [1629] [1630] [1631]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 26107--26107
[] \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC"
, "hyman"),[]
Underfull \hbox (badness 6477) in paragraph at lines 26161--26164
[]\T1/ptm/m/n/10 Method \T1/pcr/m/n/10 "hyman" \T1/ptm/m/n/10 com-putes a \T1/p
tm/m/it/10 mono-tone \T1/ptm/m/n/10 cu-bic spline us-ing Hy-man fil-ter-ing of
an
[1632] [1633]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 26292--26292
[]\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 26293--26293
[]\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman") (x), add = TRUE, c
ol = 4, n = 1001)[]
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Underfull \hbox (badness 2922) in paragraph at lines 26362--26367
[]\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
[1635]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 26399--26399
[] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5.2), xlim
= c(-.3, 5),[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 26402--26402
[] \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 26411--26411
[] \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 26412--26412
[] \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 26416--26416
[] \T1/pcr/m/n/9 axis(2, at = c(1,AR2,5), labels= expression(phi[2], frac(phi
[1]+phi[2],2), phi[1]),[]
[1636]
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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
Underfull \hbox (badness 3240) in paragraph at lines 26470--26473
[][][]\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 26491--26491
[] \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 26494--26494
[] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(-.5,6), xlim
= c(-1, 8),[]
[1637]
Underfull \hbox (badness 2922) in paragraph at lines 26544--26549
[]\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
[1638]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26577--26577
[] \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 26581--26581
[] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5), xlim =
c(-1/4, 5),[]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 26591--26591
[] \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 26596--26596
[] \T1/pcr/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5]
== frac(log(2), e^{phi[2]})}),[]
[1639]
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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
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26654--26654
[]\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 26670--26670
[] \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 =
1.5 * exp(-x)"),[]
[1640] [1641]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 26784--26784
[]\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK
a)*input))
[1642]
Underfull \hbox (badness 2922) in paragraph at lines 26846--26851
[]\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
[1643]
Overfull \hbox (69.18036pt too wide) in paragraph at lines 26884--26884
[] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "A", phi[2] == "B", phi[3] == "xm
id", phi[4] == "scal")))[]
[1644]
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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
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26964--26964
[]\T1/pcr/m/n/9 lines(x, do.call(SSgompertz, c(list(x=x), coef(fm1))), col = "
red", lwd=2)[]
[1645]
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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
Overfull \hbox (25.98041pt too wide) in paragraph at lines 27023--27023
[]\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)[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27047--27047
[] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "Asym", phi[2] == "xmid", phi[3]
== "scal")))[]
[1646]
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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[]
Underfull \hbox (badness 2922) in paragraph at lines 27092--27097
[]\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
[1647]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27114--27114
[]\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt),
digits = 3)[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 27132--27132
[] \T1/pcr/m/n/9 ann = FALSE, axes = FALSE, main = "Parameters in the SS
micmen model")[]
[1648]
Underfull \hbox (badness 6493) in paragraph at lines 27184--27189
[]\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
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27211--27211
[]\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)[]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 27216--27216
[]\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)[]
[1649] [1650] [1651] [1652] [1653] [1654] [1655] [1656]
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[]\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex-
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\T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/pcr/m/n/10 NULL\T1/ptm/m/
n/10 , the de-fault,
[1657] [1658] [1659] [1660] [1661] [1662] [1663]
Underfull \hbox (badness 3396) in paragraph at lines 28143--28145
[]\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
[1664] [1665] [1666]
Underfull \hbox (badness 2237) in paragraph at lines 28320--28322
[]\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
[1667] [1668]
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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
[1669]
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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
[1670]
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[]\T1/pcr/m/n/10 supsmu(x, y, wt =, span = "cv", periodic = FALSE, bass = 0, t
race = FALSE)
[1671] [1672]
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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
[1675] [1676]
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[]\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/
10 ; cur-rently ex-cept for \T1/pcr/m/n/10 rt()\T1/ptm/m/n/10 , only for
[1677] [1678]
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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",[]
[1679]
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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
[1680]
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[]\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s
pan.smth = 1/4)[]
[1681]
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[]\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out =
TRUE,[]
[1682]
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[]\T1/ptm/m/n/10 A [][]\T1/pcr/m/n/10 terms.object[][][] \T1/ptm/m/n/10 ob-ject
is re-turned. The ob-ject it-self is the re-ordered (un-less
[1683]
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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
[1684] [1685] [1686] [1687] [1688] [1689] [1690] [1691]
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[]\T1/pcr/m/n/10 ptukey(q, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
FALSE)
[1692]
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[]\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
FALSE)[]
[1693] [1694] [1695] [1696]
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[]\T1/ptm/m/n/10 Setting \T1/pcr/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/p
cr/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect
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\T1/pcr/m/n/10 interval = c(lower,upper) \T1/ptm/m/n/10 if \T1/pcr/m/n/10 sign(
f(x)) \T1/ptm/m/n/10 does not sat-isfy the re-quire-ments at
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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)[]
[1697] [1698]
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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:[]
[1699] [1700] [1701] [1702]
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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
[1703] [1704] [1705] [1706] [1707] [1708] [1709] [1710]
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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
[1711]
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[]\T1/ptm/m/n/10 When \T1/pcr/m/n/10 x \T1/ptm/m/n/10 (and \T1/pcr/m/n/10 y \T1
/ptm/m/n/10 if ap-pli-ca-ble) are valid, the func-tion now al-ways re-turns, al
so in the
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[]\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if
ar-gu-ment
[1712] [1713] [1714] [1715] [1716]
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[]\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F
ALSE,
[1717]
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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
[1718]
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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 "")[]
[1719]) (./stats4-pkg.tex [1720]
Chapter 11.
[1721] [1722] [1723]
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[] \T1/pcr/m/n/9 -sum(stats::dpois(y, lambda = exp(lymax)/(1+x/exp(lxhalf))
, log = TRUE))[]
[1724] [1725] [1726]pdfTeX warning (ext4): destination with the same identifier
(name{Rfn.show.Rdash.methods}) has been already used, duplicate ignored
<to be read again>
\relax
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[1727]
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[]\T1/ptm/m/n/10 Generate a sum-mary as an ob-ject of class
[1728] [1729]) (./tcltk-pkg.tex [1730]
Chapter 12.
[1731] [1732] [1733] [1734]
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[]\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all = TRUE) # .Tcl.args put a callback
ref in here[]
[1735] [1736] [1737]
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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/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
[1750]) (./tools-pkg.tex
Chapter 13.
[1751]
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[]\T1/pcr/m/n/9 ## is used for simple print methods in R, and as prototype for
new methods.[]
[1752]
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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
[1753]
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[]\T1/pcr/m/n/9 assertCondition(ff(), "error", "warning") # ok (quietly, catch
ing warning)[]
[1754]
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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 ,
[1755]
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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
[1756] [1757] [1758] [1759] [1760] [1761] [1762]
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[1763] [1764]
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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")[]
[1765] [1766]
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[]\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i
g-nored when
[1767]
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[]\T1/ptm/m/n/10 a named list of char-ac-ter vec-tors with ar-gu-ments to be pa
ssed to
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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-
[1768]
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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
[1769]
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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
[1770] [1771]
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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/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S
up-port func-tion for
[1772] [1773] [1774] [1775] [1776]
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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 .
[1777] [1778] [1779]pdfTeX warning (ext4): destination with the same identifier
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[1780] [1781] [1782]
[1783]
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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}",[]
[1784]
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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
[1785]
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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
[1786]
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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 .
[1787]
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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)[]
[1788] [1789] [1790] [1791]
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[] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macros", "system.
Rd"),[]
[1792]
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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
[1793] [1794] [1795] [1796] [1797]
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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
[1798] [1799] [1800] [1801] [1802]
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[] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macro
s", "system.Rd"))[]
[1803] [1804] [1805] [1806]
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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
[1807] [1808]
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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
[1811]
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[] \T1/pcr/m/n/10 depLevel = c("Depends", "Imports", "Sugg
ests"))[]
[1812]
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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
[1813] [1814] [1815]
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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
[1816]
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 reduce \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE
\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/pcr/m/n/10 De
pendsList
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\T1/ptm/m/n/10 ob-ject such that a min-i-mal set of de-pen-den-cies are spec-i-
fied (for in-stance if
Underfull \hbox (badness 10000) in paragraph at lines 4341--4346
\T1/ptm/m/n/10 there was `\T1/pcr/m/n/10 foo, foo (>= 1.0.0), foo (>= 1.3.0)\T1
/ptm/m/n/10 ', it would only re-turn
[1817] [1818]
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[] \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F
ALSE,[]
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[] \T1/pcr/m/n/10 latestOnly = TRUE, addFiles = FALSE, rds_compr
ess = "xz")[]
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[]\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 ',
[1819]
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\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 ,
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[]\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
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\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 ',
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[]\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
[1820] [1821] [1822]) (./utils-pkg.tex
Chapter 14.
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[]\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 ',
[1823] [1824] [1825]
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[]\T1/pcr/m/n/10 find \T1/ptm/m/n/10 is a dif-fer-ent user in-ter-face for a si
m-i-lar task to \T1/pcr/m/n/10 apropos\T1/ptm/m/n/10 . By de-fault
[1826]
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[]\T1/pcr/m/n/9 find("cor", numeric = TRUE) # numbers with
these names[]
[1827]
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[] \T1/pcr/m/n/10 prompts = getOption("askYesNo", gettext(c("Yes", "No
", "Cancel"))),[]
[1828] [1829] [1830]
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\T1/ptm/m/n/10 28. [][]$\T1/pcr/m/n/10 https : / / journal . r-[]project . org
/ archive / 2011-[]2 / RJournal _ 2011-[]2 _
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[]\T1/pcr/m/n/10 aspell_package_Rd_files(dir, drop = c("\\author", "\\referenc
es"),
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[]\T1/pcr/m/n/10 aspell_package_R_files(dir, ignore = character(), control = l
ist(),[]
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[] \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[]
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[]\T1/pcr/m/n/10 aspell_package_C_files(dir, ignore = character(), control = l
ist(),[]
[1831]
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[] \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[]
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[]\T1/ptm/m/n/10 Functions \T1/pcr/m/n/10 aspell_package_Rd_files\T1/ptm/m/n/10
, \T1/pcr/m/n/10 aspell_package_vignettes\T1/ptm/m/n/10 ,
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\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-
[1832]
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[] \T1/pcr/m/n/10 ignore_repo_cache = FALSE, max_repo_cache
_age,[]
[1833]
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\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
[1834]
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\T1/ptm/m/n/10 ory avail-able and con-trol-ling the load/save pro-cess. If \T1/
pcr/m/n/10 infile \T1/ptm/m/n/10 starts
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\T1/ptm/m/n/10 with a `\T1/pcr/m/n/10 -\T1/ptm/m/n/10 ', use `\T1/pcr/m/n/10 --
\T1/ptm/m/n/10 ' as the fi-nal op-tion. The de-fault op-tions are
[1835]
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[]\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer =
NULL,
[1836]
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\T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f
ault by
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing
[1837] [1838]
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[]\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org
/ wiki / Digital _ Object _
[1839]
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[] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[]
[1840] [1841] [1842] [1843] [1844]
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[]\T1/ptm/m/n/10 For ex-am-ple, sup-pose that on a data set which you know to b
e quite large the com-
[1845] [1846]
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[] \T1/pcr/m/n/9 data = infert, family = b
inomial())))[]
[1847]
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[]\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b
efore$timestamp,[]
[1848]
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[]\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp"
), md5sum=TRUE)[]
[1849]
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[]\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind =
NULL,
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[]\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind =
NULL,
[1850]
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[]\T1/pcr/m/n/10 ind \T1/ptm/m/n/10 chooses a row in the list of cur-rent mir-r
ors, by num-ber. It is best used with
[1851] [1852]
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[]\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the
`\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' file via
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[] \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")[]
[1853]
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[]\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after =
NULL,[]
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[]\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w
hen
[1854]
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[] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[]
[1855]
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[][][]\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;
[1856]
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[]\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/
phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see
Underfull \hbox (badness 1057) in paragraph at lines 2374--2381
\T1/ptm/m/n/10 a [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 ); if FALSE, the
func-tion re-turns a [][]\T1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 . Note that w
hen
[1857] [1858] [1859]
Underfull \hbox (badness 10000) in paragraph at lines 2563--2565
[]\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see
[1860] [1861] [1862] [1863]
Underfull \hbox (badness 10000) in paragraph at lines 2800--2804
[]\T1/ptm/m/n/10 files end-ing `\T1/pcr/m/n/10 .tab\T1/ptm/m/n/10 ', `\T1/pcr/m
/n/10 .txt\T1/ptm/m/n/10 ' or `\T1/pcr/m/n/10 .TXT\T1/ptm/m/n/10 ' are read us-
ing
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[][]\T1/pcr/m/n/10 read.table[][][](..., header = TRUE, as.is=FALSE)\T1/ptm/m/n
/10 , and hence re-sult in a
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[]\T1/ptm/m/n/10 files end-ing `\T1/pcr/m/n/10 .csv\T1/ptm/m/n/10 ' or `\T1/pcr
/m/n/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/pcr/m/n/10 read.table[][][
](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 2854--2857
[]\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
[1864]
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[]\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 '[]
[1865]
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[]\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
[1866] [1867] [1868] [1869] [1870] [1871] [1872]
Underfull \hbox (badness 1072) in paragraph at lines 3499--3507
[]\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
[1873]
Underfull \hbox (badness 1231) in paragraph at lines 3548--3554
[]\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers
via en-vi-ron-ment vari-able
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[]\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 3555--3560
\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
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\T1/pcr/m/n/10 [user:password@]machine[:port] \T1/ptm/m/n/10 where the parts in
brack-ets are op-tional. See
[1874] [1875]
Underfull \hbox (badness 4660) in paragraph at lines 3677--3680
\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 additional ar-gu-ments to be passed to [][]\T1/pcr/m/n/10 down
load.file[][][] \T1/ptm/m/n/10 and
[1876] [1877] [1878]
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[]\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
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[]\T1/ptm/m/n/10 For a data frame, the row names will be taken from the orig-i-
nal ob-ject if
[1879]
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[] \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F
ALSE,[]
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\T1/pcr/m/n/10 setRNG = {RNGkind("default", "default"); set.seed(1)}\T1/ptm/m/n
/10 .
[1880] [1881] [1882] [1883] [1884]
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[]\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o
ne is in the[]
[1885]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for
mat}) has been already used, duplicate ignored
<to be read again>
\relax
l.4395 ...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.4395 ...mat Unordered and Ordered Lists}{format}
[1886] [1887] [1888]
[1889] [1890] [1891] [1892] [1893] [1894] [1895] [1896] [1897] [1898] [1899]
[1900]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5348--5348
[] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h
elp(dgamma):[]
[1901]
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[]\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
[1902]
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[]\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words
'. `Key-
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\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are
listed in file
[1903] [1904]
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[]\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de
x,
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\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
[1905]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion
to search. See
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[]\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
[1906] [1907]
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[]\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
[1908]
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[]\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the
sub-architecture used by
[1909]
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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/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/
ptm/m/n/10 .
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[]\T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 means to use \T1/pcr/m/n/10 c("Depends", "
Imports", "LinkingTo", "Suggests")
[1910]
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[]\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to
be passed
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\T1/ptm/m/n/10 to \T1/pcr/m/n/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pack
-age in-stall. E.g.,
[1911]
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[]\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 ,
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[]\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/pcr/m/n/1
0 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail-
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\T1/ptm/m/n/10 able and cur-rent, oth-er-wise try source'. The ac-tion if there
are source pack-ages
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\T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com
-piled is con-trolled by
[1912]
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[]\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 6251--6256
[][][]\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 ,
[1913]
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[] \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc
lude/udunits2"))[]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to ex-tract from each
pack-age's
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[]\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
[1914]
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[]\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields
= "License")[]
[1915] [1916]
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[]\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
[1917] [1918] [1919]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6648--6648
[]\T1/pcr/m/n/9 ls.str(mode = "list") #- what are the structured objects I h
ave defined?[]
[1920] [1921]
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[]\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F
ALSE)
[1922]
Underfull \hbox (badness 10000) in paragraph at lines 6831--6833
[]\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
[1923] [1924]
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[]\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 6977--6979
[]\T1/ptm/m/n/10 typically the re-sult of \T1/pcr/m/n/10 methods(..)\T1/ptm/m/n
/10 , an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of class
[1925] [1926] [1927]
Underfull \hbox (badness 1859) in paragraph at lines 7200--7203
[]\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br
owser (by
[1928]
Underfull \hbox (badness 1655) in paragraph at lines 7282--7285
[]\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 7293--7293
[]\T1/pcr/m/n/9 db3 <- news(Version == "3.0.1" & grepl("^BUG", Category) & gre
pl("PR#", Text),[]
[1929]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7297--7297
[]\T1/pcr/m/n/9 ## News from a date range (\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 Matri
x\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is there in a regular R installation):[]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 7305--7305
[]\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st
andardize a bit more[]
[1930]
Underfull \hbox (badness 10000) in paragraph at lines 7390--7394
[]\T1/ptm/m/n/10 For all stan-dards, \T1/pcr/m/n/10 unit = "auto" \T1/ptm/m/n/1
0 is also al-lowed. If
[1931] [1932] [1933] [1934]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 7654--7654
[] \T1/pcr/m/n/10 date.fields = c("Date", "Packaged", "Date/Publica
tion", "Built"),[]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 7655--7655
[] \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 7656--7656
[] \T1/pcr/m/n/10 desc = packageDescription(pkg, lib.loc=lib.loc, f
ields=date.fields))[]
[1935]
Underfull \hbox (badness 10000) in paragraph at lines 7684--7686
[]\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 7698--7700
[]\T1/pcr/m/n/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut,
al-low-ing things like
Underfull \hbox (badness 1259) in paragraph at lines 7706--7711
[]\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,
[1936]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7752--7752
[] \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 7753--7753
[] \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[]
[1937] [1938]
Underfull \hbox (badness 10000) in paragraph at lines 7882--7887
[]\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 7882--7887
[][]\T1/pcr/m/n/10 installed.packages[][][] \T1/ptm/m/n/10 plus \T1/pcr/m/n/10
"Status"\T1/ptm/m/n/10 , a fac-tor with lev-els
Underfull \hbox (badness 10000) in paragraph at lines 7889--7892
[]\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 7889--7892
[][]\T1/pcr/m/n/10 available.packages[][][] \T1/ptm/m/n/10 plus \T1/pcr/m/n/10
"Status"\T1/ptm/m/n/10 , a fac-tor with lev-els
[1939]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 8005--8005
[] \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme
nt"),[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 8006--8006
[] \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<",
">"),[]
[1940] [1941] [1942]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8177--8177
[] \T1/pcr/m/n/9 "S original, <http://statwww.epfl.ch/davison/BMA/libr
ary.html>"),[]
[1943]
Underfull \hbox (badness 1789) in paragraph at lines 8300--8302
[]\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
[1944]
Underfull \hbox (badness 10000) in paragraph at lines 8358--8362
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
Underfull \hbox (badness 10000) in paragraph at lines 8358--8362
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1945] [1946]
Underfull \hbox (badness 10000) in paragraph at lines 8473--8477
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
Underfull \hbox (badness 10000) in paragraph at lines 8473--8477
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1947]
Underfull \hbox (badness 10000) in paragraph at lines 8538--8542
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
Underfull \hbox (badness 10000) in paragraph at lines 8538--8542
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1948] [1949] [1950] [1951]
Underfull \hbox (badness 5203) in paragraph at lines 8869--8872
[]\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
[1952] [1953] [1954]
Underfull \hbox (badness 1776) in paragraph at lines 9095--9102
[]\T1/ptm/m/n/10 If you are un-com-fort-able with un-so-licited eval-u-a-tion o
f pieces of code, you should set
[1955]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 9119--9119
[] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "
no.loss"),[]
[1956] [1957]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 9280--9280
[]\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr
anspose = TRUE)[]
[1958] [1959]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9461--9461
[]\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[]
[1960] [1961]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 9547--9547
[] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss",
"no.loss"),[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 9550--9550
[] \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines.
skip,[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 9555--9555
[] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski
pNul = FALSE)[]
[1962]
Underfull \hbox (badness 1077) in paragraph at lines 9627--9630
[]\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
[1963] [1964] [1965] [1966] [1967] [1968]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10067--10067
[] \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c
(1, 0)))
[1969]
Underfull \hbox (badness 10000) in paragraph at lines 10154--10156
[]\T1/ptm/m/n/10 To re-move from the li-brary tree \T1/ptm/m/sl/10 lib \T1/ptm/
m/n/10 in-stead of the de-fault one, use
[1970] [1971]
Underfull \hbox (badness 2181) in paragraph at lines 10277--10281
[]\T1/pcr/m/n/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/pcr/m/n
/10 "roman" \T1/ptm/m/n/10 which are in-ter-nally rep-re-sented as in-te-
Underfull \hbox (badness 2269) in paragraph at lines 10277--10281
\T1/ptm/m/n/10 gers, and have suit-able meth-ods for print-ing, for-mat-ting, s
ub-set-ting, co-er-cion, etc, see
Underfull \hbox (badness 10000) in paragraph at lines 10289--10293
\T1/pcr/m/n/10 en . wikipedia . org / w / index . php ? title = Roman _ numeral
s & oldid = 78252134$[][]\T1/ptm/m/n/10 .
[1972]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 10307--10307
[]\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 10311--10311
[]\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in
{1,2,..,3899} :[]
[1973] [1974]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 10443--10443
[]\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold
= 0)
[1975]
Underfull \hbox (badness 1917) in paragraph at lines 10566--10569
[]\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 10566--10569
\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
[1976]
Overfull \hbox (106.98032pt too wide) in paragraph at lines 10589--10589
[]\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 '[]
[1977]
Underfull \hbox (badness 8075) in paragraph at lines 10652--10654
[]\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
[1978]
Underfull \hbox (badness 6725) in paragraph at lines 10702--10711
\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 10702--10711
\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 10702--10711
\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 10702--10711
\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
[1979]
Underfull \hbox (badness 3646) in paragraph at lines 10828--10830
[][][]$\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 /
[1980]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 10866--10866
[] \T1/pcr/m/n/10 split = FALSE, quiet = FALSE, drop.evalFALSE = F
ALSE, ...)[]
[1981] [1982] [1983]
Underfull \hbox (badness 10000) in paragraph at lines 11047--11051
[]\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 11078--11084
[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
[1984]
Underfull \hbox (badness 2012) in paragraph at lines 11173--11179
\T1/ptm/m/n/10 and `\T1/pcr/m/n/10 \includegraphics\T1/ptm/m/n/10 ' state-ments
for fig-ures should be auto-generated. Use
[1985]
Underfull \hbox (badness 2096) in paragraph at lines 11186--11188
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w
hether EPS fig-ures should be gen-er-ated. Ig-nored if
Underfull \hbox (badness 2698) in paragraph at lines 11189--11191
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ), in-di-cat-ing wh
ether PDF fig-ures should be gen-er-ated. Ig-nored if
Underfull \hbox (badness 1527) in paragraph at lines 11196--11199
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w
hether PNG fig-ures should be gen-er-ated. Ig-nored if
Underfull \hbox (badness 1067) in paragraph at lines 11200--11203
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w
hether JPEG fig-ures should be gen-er-ated. Ig-nored if
Overfull \hbox (6.78088pt too wide) in paragraph at lines 11254--11254
[] \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa
rent")[]
[1986]
Underfull \hbox (badness 1009) in paragraph at lines 11272--11283
[]\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
[1987]
Underfull \hbox (badness 2846) in paragraph at lines 11359--11369
\T1/ptm/m/n/10 con-trols the num-ber of lines that are saved (de-fault 512), an
d \T1/pcr/m/n/10 R_HISTFILE \T1/ptm/m/n/10 (de-fault
[1988] [1989]
Underfull \hbox (badness 10000) in paragraph at lines 11498--11501
[]\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the plat-form \T1/phv/m/n/10
R \T1/ptm/m/n/10 was built un-
Underfull \hbox (badness 10000) in paragraph at lines 11498--11501
\T1/ptm/m/n/10 der. Where sub-architectures are in use this is of the form
Underfull \hbox (badness 10000) in paragraph at lines 11515--11518
[]\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in
g
[1990]
Underfull \hbox (badness 2158) in paragraph at lines 11594--11597
[]\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
[1991] [1992] [1993]
Underfull \hbox (badness 3333) in paragraph at lines 11774--11776
[]\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-
[1994] [1995]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 11939--11939
[] \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing =
TRUE, ...))[]
[1996]
Underfull \hbox (badness 5970) in paragraph at lines 11972--11975
[]\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 11972--11975
[][]\T1/pcr/m/n/10 options[][][]("width")\T1/ptm/m/n/10 ; note that this has on
ly a weak ef-fect, un-less
Underfull \hbox (badness 1052) in paragraph at lines 11983--11992
\T1/ptm/m/n/10 (see [][]\T1/pcr/m/n/10 options[][][]\T1/ptm/m/n/10 ) which de-f
aults to \T1/pcr/m/n/10 "no" \T1/ptm/m/n/10 for back com-pat-i-bil-ity rea-sons
;
[1997]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 12027--12027
[]\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification
of binary numbers[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 12058--12058
[]\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 12065--12065
[]\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 12067--12067
[]\T1/pcr/m/n/9 invisible(lapply(60:66, function(N) str( ch , nchar.max = N)))
# "1 is 1" here[]
[1998] [1999] [2000]
Underfull \hbox (badness 10000) in paragraph at lines 12235--12237
[]\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
[2001] [2002]
Underfull \hbox (badness 4492) in paragraph at lines 12392--12399
[]\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 12392--12399
\T1/ptm/m/n/10 turn, and se-lected if their \T1/pcr/m/n/10 extension \T1/ptm/m/
n/10 com-po-nent matches (as a reg-exp) the file
Underfull \hbox (badness 2452) in paragraph at lines 12392--12399
\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$"\T1/ptm/m/n/10 ) and
[2003] [2004] [2005]
Underfull \hbox (badness 2020) in paragraph at lines 12555--12571
\T1/ptm/m/n/10 si-bly use-ful val-ues in-clude `\T1/pcr/m/n/10 -h\T1/ptm/m/n/10
' (fol-low sym-bolic links, also `\T1/pcr/m/n/10 -L\T1/ptm/m/n/10 ' on some pl
at-forms),
Underfull \hbox (badness 1194) in paragraph at lines 12555--12571
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 --acls\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclud
e-backups\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclude-vcs\T1/ptm/m/n/10 ' (and s
im-i-lar) and on Win-dows
[2006]
Underfull \hbox (badness 2809) in paragraph at lines 12675--12679
[]\T1/ptm/m/n/10 NetBSD prior to 8.0 used flag `\T1/pcr/m/n/10 --xz\T1/ptm/m/n/
10 ' rather than `\T1/pcr/m/n/10 -J\T1/ptm/m/n/10 ', so this should be used \T1
/ptm/m/it/10 via
Underfull \hbox (badness 1596) in paragraph at lines 12675--12679
\T1/pcr/m/n/10 extra_flags = "--xz" \T1/ptm/m/n/10 rather than \T1/pcr/m/n/10 c
ompression = "xz"\T1/ptm/m/n/10 . The com-mands from
Underfull \hbox (badness 5022) in paragraph at lines 12690--12694
[]\T1/ptm/m/n/10 When ar-gu-ment \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 is set to th
e com-mand \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-abl
e
Underfull \hbox (badness 10000) in paragraph at lines 12697--12700
[][][]$\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 12697--12700
\T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht
ml # tag _ 20 _
[2007] [2008] [2009]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 12862--12862
[] \T1/pcr/m/n/10 numerals = c("allow.loss", "warn.loss", "no.loss
"), ...)[]
[2010] [2011] [2012] [2013] [2014] [2015]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 13246--13246
[] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc,
...),[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 13252--13252
[] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc,
...),[]
Underfull \hbox (badness 4467) in paragraph at lines 13273--13275
[]\T1/ptm/m/n/10 Download method, see [][]\T1/pcr/m/n/10 download.file[][][]\T1
/ptm/m/n/10 . Un-used if a non-\T1/pcr/m/n/10 NULL
Underfull \hbox (badness 4660) in paragraph at lines 13286--13290
\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 = lib.loc)\T1/ptm/m/n/10 .
Underfull \hbox (badness 10000) in paragraph at lines 13306--13311
[]\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 13306--13311
\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 13306--13311
\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[][][]
[2016]
Underfull \hbox (badness 1052) in paragraph at lines 13312--13314
[]\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and
in-stall. See
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[]\T1/ptm/m/n/10 For how the list of suit-able avail-able pack-ages is de-ter-m
ined see
Underfull \hbox (badness 10000) in paragraph at lines 13342--13347
[][]\T1/pcr/m/n/10 available.packages[][][]\T1/ptm/m/n/10 . \T1/pcr/m/n/10 avai
lable = NULL \T1/ptm/m/n/10 make a call to
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\T1/pcr/m/n/10 available.packages(contriburl = contriburl, method = method) \T1
/ptm/m/n/10 and
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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 13371--13374
[][][]\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 ,
[2017]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13425--13425
[]\T1/pcr/m/n/9 ## Not run: url.show("http://www.stats.ox.ac.uk/pub/datasets/c
sb/ch3a.txt")
[2018] [2019] [2020]
Underfull \hbox (badness 10000) in paragraph at lines 13613--13616
[][][]\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/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:[]
[2021]
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[] \T1/pcr/m/n/9 lm(weight ~ (Time + I(Time^2)) * Diet, d
ata = DAT)))[]
[2022]
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[] \T1/pcr/m/n/9 nls(weight ~ SSlogis(Time, Asym, xmid, scal),
data = DD)))[]
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[]\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep =
" ",
[2023]
Underfull \hbox (badness 1454) in paragraph at lines 13764--13768
[]\T1/ptm/m/n/10 the char-ac-ter(s) to print at the end of each line (row). For
ex-am-ple,
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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 13834--13836
[]\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec-
tion
[2024]
Underfull \hbox (badness 3271) in paragraph at lines 13846--13850
\T1/ptm/m/n/10 set \T1/pcr/m/n/10 sep \T1/ptm/m/n/10 and \T1/pcr/m/n/10 dec \T1
/ptm/m/n/10 (see be-low), \T1/pcr/m/n/10 qmethod = "double"\T1/ptm/m/n/10 , and
\T1/pcr/m/n/10 col.names \T1/ptm/m/n/10 to \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 if
[2025] [2026]) [2027] [2028] (./KernSmooth-pkg.tex
Chapter 15.
[2029]
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[]\T1/pcr/m/n/10 bkde2D(x, bandwidth, gridsize = c(51L, 51L), range.x, truncat
e = TRUE)
[2030] [2031] [2032] [2033] [2034]
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,
[2035] [2036] [2037] [2038]) (./MASS-pkg.tex
Chapter 16.
[2039] [2040] [2041] [2042] [2043] [2044] [2045] [2046] [2047] [2048] [2049]
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))[]
[2050] [2051] [2052] [2053] [2054] [2055] [2056] [2057] [2058] [2059] [2060]
[2061]
Underfull \hbox (badness 7256) in paragraph at lines 1604--1606
[]\T1/ptm/m/n/10 logical. If true and the re-sult would be sparse (only true fo
r
[2062] [2063] [2064] [2065] [2066] [2067] [2068] [2069] [2070] [2071] [2072]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2412--2412
[]\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq",
"F"),[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2416--2416
[]\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq",
"F"),[]
[2073] [2074] [2075] [2076]
Underfull \hbox (badness 6559) in paragraph at lines 2694--2697
[]\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
[2077] [2078] [2079]
Underfull \hbox (badness 10000) in paragraph at lines 2864--2869
\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 8189) in paragraph at lines 2864--2869
\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 ,
Underfull \hbox (badness 3557) in paragraph at lines 2900--2908
[]\T1/ptm/m/n/10 For the fol-low-ing named dis-tri-bu-tions, rea-son-able start
-ing val-ues will be com-puted if
Underfull \hbox (badness 3118) in paragraph at lines 2900--2908
\T1/pcr/m/n/10 start \T1/ptm/m/n/10 is omit-ted or only par-tially spec-i-fied:
\T1/pcr/m/n/10 "cauchy"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 ,
\T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 ,
[2080] [2081]
Underfull \hbox (badness 4686) in paragraph at lines 3032--3034
[]\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i-
na-tor ex-ceeds
Underfull \hbox (badness 1515) in paragraph at lines 3046--3050
[]\T1/ptm/m/n/10 where \T1/pcr/m/n/10 p1\T1/ptm/m/n/10 , \T1/pcr/m/n/10 p2\T1/p
tm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/pcr/m/n
/10 cycles \T1/ptm/m/n/10 terms or when a
[2082] [2083] [2084]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3227--3227
[] \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL
SE, ...)[]
Underfull \hbox (badness 5817) in paragraph at lines 3234--3236
[]\T1/ptm/m/n/10 Fitted model ob-ject from a \T1/pcr/m/n/10 Gamma \T1/ptm/m/n/1
0 fam-ily or \T1/pcr/m/n/10 quasi \T1/ptm/m/n/10 fam-ily with
[2085]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3357--3357
[]\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist =
"exponential")[]
[2086] [2087] [2088] [2089] [2090] [2091] [2092] [2093] [2094] [2095] [2096]
[2097]
Underfull \hbox (badness 1845) in paragraph at lines 4143--4145
[]\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
[2098] [2099] [2100] [2101] [2102] [2103] [2104]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4639--4639
[] \T1/pcr/m/n/10 col = 5, xlab = deparse(substitute(data)), bty = "n",
...)[]
[2105] [2106]
Underfull \hbox (badness 10000) in paragraph at lines 4791--4794
[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[2107]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4861--4861
[]\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model
= FALSE,
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[2108] [2109] [2110] [2111] [2112]
Underfull \hbox (badness 5681) in paragraph at lines 5269--5271
[]\T1/ptm/m/n/10 the quan-tile to be used: see \T1/pcr/m/n/10 Details\T1/ptm/m/
n/10 . This is over-ridden if
Underfull \hbox (badness 5022) in paragraph at lines 5273--5276
[]\T1/ptm/m/n/10 the cut-off / tun-ing con-stant used for $\OML/cmm/m/it/10 ^^_
\OT1/cmr/m/n/10 ()$ \T1/ptm/m/n/10 and $\OML/cmm/m/it/10 \OT1/cmr/m/n/10 ()$ \
T1/ptm/m/n/10 func-tions when
[2113]
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[]\T1/ptm/m/n/10 the value of the cri-te-rion for the best so-lu-tion found, in
the case of
[2114] [2115] [2116] [2117] [2118] [2119] [2120] [2121]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 5908--5908
[]\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP
ACK = FALSE)
[2122]
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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")
[2123] [2124]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.npk}) has been already used, duplicate ignored
<to be read again>
\relax
l.6111 ...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.6111 ...sical N, P, K Factorial Experiment}{npk}
[2125]
Underfull \hbox (badness 1783) in paragraph at lines 6229--6233
[]\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
[2126] [2127] [2128] [2129]
Underfull \vbox (badness 10000) has occurred while \output is active [2130]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6527--6527
[] \T1/pcr/m/n/9 start = list(fixed=c(L75=c(48.7, -0.03), lsc=0.24)), verb
ose = TRUE)))[]
[2131]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 6615--6615
[] \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr
ellis"))[]
[2132] [2133] [2134] [2135] [2136] [2137]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7054--7054
[]\T1/pcr/m/n/9 nlmod <- nls(y ~ Const + A * exp(B * x), start=list(Const=100
, A=10, B=1))[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 7071--7071
[] \T1/pcr/m/n/10 method = c("logistic", "probit", "loglog", "cloglog", "c
auchit"))[]
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[2138]
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[]\T1/ptm/m/n/10 initial val-ues for the pa-ram-e-ters. This is in the for-mat
Underfull \hbox (badness 3138) in paragraph at lines 7149--7155
[]\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 ) =
[2139]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7219--7219
[]\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da
ta = housing)[]
[2140] [2141]
Underfull \hbox (badness 5091) in paragraph at lines 7328--7331
\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
[2142] [2143]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7458--7458
[]\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam
p = "exact")[]
[2144]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 7523--7523
[] \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC
V"), ...)[]
[2145] [2146] [2147] [2148] [2149] [2150]
Underfull \hbox (badness 4686) in paragraph at lines 7961--7963
[]\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i-
na-tor ex-ceeds
Underfull \hbox (badness 1515) in paragraph at lines 7977--7981
[]\T1/ptm/m/n/10 where \T1/pcr/m/n/10 p1\T1/ptm/m/n/10 , \T1/pcr/m/n/10 p2\T1/p
tm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/pcr/m/n
/10 cycles \T1/ptm/m/n/10 terms or when a
[2151] [2152]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 8080--8080
[] \T1/pcr/m/n/10 maxit = 20, acc = 1e-4, test.vec = "resid", lqs.control =
NULL)[]
Underfull \hbox (badness 1590) in paragraph at lines 8104--8108
[]\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
[2153] [2154] [2155] [2156] [2157] [2158] [2159] [2160] [2161] [2162] [2163]
[2164] [2165] [2166] [2167] [2168] [2169] [2170] [2171] [2172]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 9483--9483
[]\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS
E, ...)[]
[2173]
Underfull \hbox (badness 1158) in paragraph at lines 9610--9613
[]\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),
[2174]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 9692--9692
[]\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 9694--9694
[]\T1/pcr/m/n/10 theta.ml(y, mu, n, weights, limit = 10, eps = .Machine$double
.eps^0.25,[]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 9697--9697
[]\T1/pcr/m/n/10 theta.mm(y, mu, dfr, weights, limit = 10, eps = .Machine$doub
le.eps^0.25)[]
[2175] [2176] [2177] [2178] [2179] [2180] [2181] [2182] [2183] [2184] [2185]
[2186] [2187]) (./Matrix-pkg.tex [2188]
Chapter 17.
Underfull \hbox (badness 10000) in paragraph at lines 41--44
[]\T1/ptm/m/n/10 Note that the cur-rent im-ple-men-ta-tion de-tails are sub-jec
t to change, and if you
Underfull \hbox (badness 10000) in paragraph at lines 41--44
\T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack-
age main-tain-ers
[2189]
Underfull \hbox (badness 1769) in paragraph at lines 95--98
[]\T1/ptm/m/n/10 This is cur-rently ex-per-i-men-tal and not yet used for our o
wn code. Please con-tact us
[2190]
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
[2191]
Underfull \hbox (badness 10000) in paragraph at lines 257--260
[]\T1/ptm/m/n/10 these three meth-ods are sim-ply us-ing
Underfull \hbox (badness 10000) in paragraph at lines 263--265
[]\T1/ptm/m/n/10 There are more meth-ods, no-tably also for \T1/pcr/m/n/10 "[][
]sparseVector[][][]"\T1/ptm/m/n/10 's, see
[2192] [2193]
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
[2194]
Underfull \hbox (badness 5119) in paragraph at lines 508--512
[]\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in
g from class
Underfull \hbox (badness 4621) in paragraph at lines 512--516
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m
/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a
Overfull \hbox (4.38043pt too wide) in paragraph at lines 535--535
[]\T1/pcr/m/n/9 s1 <- bandSparse(13, k = -c(0:2, 6), diag = c(diags, diags[2])
, symm=TRUE)[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 537--537
[]\T1/pcr/m/n/9 s2 <- bandSparse(13, k = c(0:2, 6), diag = c(diags, diags[2])
, symm=TRUE)[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 546--546
[]\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20,1), rpois(20,3))[c(
1:3,2:3,3:2)],[]
[2195] [2196]
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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 '[]
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?[]
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[] \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)[]
[2197]
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 .
[2198] [2199] [2200]
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[]\T1/pcr/m/n/10 ## solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D
","P","Pt"), ...)[]
[2201]
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[]\T1/pcr/m/n/10 signature(from = "CHMfactor", to = "sparseMatrix") \T1/ptm/m/n
/10 (or equiv-a-
Underfull \hbox (badness 10000) in paragraph at lines 1045--1050
[]\T1/pcr/m/n/10 signature(x = "CHMfactor"): \T1/ptm/m/n/10 Plot the im-age of
the lower tri-
Underfull \hbox (badness 10000) in paragraph at lines 1045--1050
\T1/ptm/m/n/10 an-gu-lar fac-tor, $\OML/cmm/m/it/10 L$\T1/ptm/m/n/10 , from the
de-com-po-si-tion. This method is equiv-a-lent to
Underfull \hbox (badness 1092) in paragraph at lines 1045--1050
\T1/pcr/m/n/10 image(as(x, "sparseMatrix")) \T1/ptm/m/n/10 so the com-ments in
the above de-scrip-tion of
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[]\T1/pcr/m/n/10 signature(x = "CHMfactor", logarithm = "logical")
[2202]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cho
l}) 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}
[2203pdfTeX 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'
] [2204]
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[]\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur
e & factorization[]
[2205]
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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 1388--1391
[]\T1/ptm/m/n/10 This is a generic func-tion with spe-cial meth-ods for dif-fer
-ent types of ma-tri-ces. Use
[2206]
Underfull \hbox (badness 1609) in paragraph at lines 1435--1439
[]\T1/ptm/m/n/10 Class def-i-ni-tions [][]\T1/pcr/m/n/10 CHMfactor[][][] \T1/pt
m/m/n/10 and [][]\T1/pcr/m/n/10 dsCMatrix[][][] \T1/ptm/m/n/10 and func-tion []
[]\T1/pcr/m/n/10 expand[][][]\T1/ptm/m/n/10 . Note the ex-tra
[2207]
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[]\T1/pcr/m/n/9 ## hence, the identical() check *should* work, but fails on so
me GOTOblas:[]
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[]\T1/pcr/m/n/9 dq <- function(ch) paste(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/p
cr/m/n/9 '\T1/pcr/m/n/9 ,ch,\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/pcr/m/n/9 '\T1/
pcr/m/n/9 , sep="") ## dQuote(<UTF-8>) gives bad plots[]
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[]\T1/pcr/m/n/9 (opts <- expand.grid(perm = c(TRUE,FALSE), LDL = c(TRUE,FALSE)
, super = c(FALSE,TRUE)))[]
[2208]
Underfull \hbox (badness 6445) in paragraph at lines 1531--1538
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("Cholesky", ...) \T1/ptm/m/n/10 or
Underfull \hbox (badness 3861) in paragraph at lines 1531--1538
\T1/pcr/m/n/10 new("BunchKaufman", ...)\T1/ptm/m/n/10 , etc, or rather by calls
of the form [][]\T1/pcr/m/n/10 chol[][][](pm) \T1/ptm/m/n/10 or
Underfull \hbox (badness 1783) in paragraph at lines 1566--1570
[]\T1/ptm/m/n/10 Both these fac-tor-iza-tions can \T1/ptm/m/it/10 di-rectly \T1
/ptm/m/n/10 be treated as (tri-an-gu-lar) ma-tri-ces, as they ex-tend
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\T1/ptm/m/n/10 ply an $\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10
n$ \T1/ptm/m/n/10 nu-meric [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 . Hen
ce, for com-pat-i-bil-ity, the \T1/pcr/m/n/10 "Cholesky" \T1/ptm/m/n/10 and
[2209]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col
Sums}) has been already used, duplicate ignored
<to be read again>
\relax
l.1623 ... Row and Column Sums and Means}{colSums}
pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.colSums.1}) has been already used, dup
licate ignored
<to be read again>
\relax
l.1623 ... Row and Column Sums and Means}{colSums}
pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.colMeans}) has been already used, dupl
icate ignored
<to be read again>
\relax
l.1624 \aliasA{colMeans}{colSums}{colMeans}
pdfTeX warning (ext4): destination w
ith the same identifier (name{Rfn.rowMeans}) has been already used, duplicate i
gnored
<to be read again>
\relax
l.1645 \aliasA{rowMeans}{colSums}{rowMeans}
pdfTeX warning (ext4): destination w
ith the same identifier (name{Rfn.rowSums}) has been already used, duplicate ig
nored
<to be read again>
\relax
l.1656 \aliasA{rowSums}{colSums}{rowSums}
[2210]
Underfull \hbox (badness 2922) in paragraph at lines 1710--1714
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sparse, i.e., i
n-her-it-ing from
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\T1/ptm/m/n/10 class [][]\T1/pcr/m/n/10 sparseVector[][][]\T1/ptm/m/n/10 . Only
ap-pli-ca-ble when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is in-her-it-ing from a
Underfull \hbox (badness 1237) in paragraph at lines 1721--1724
[][][]\T1/pcr/m/n/10 dimnames[][][](x) \T1/ptm/m/n/10 are only kept (as [][]\T1
/pcr/m/n/10 names[][][](v)\T1/ptm/m/n/10 ) when the re-sult-ing \T1/pcr/m/n/10
v \T1/ptm/m/n/10 is [][]\T1/pcr/m/n/10 numeric[][][]\T1/ptm/m/n/10 , since
[2211]
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[]\T1/pcr/m/n/10 signature(x = "compMatrix", value = "list")\T1/ptm/m/n/10 : se
t the
[2212]
Underfull \hbox (badness 3547) in paragraph at lines 1875--1878
[]\T1/ptm/m/n/10 a num-ber $\OML/cmm/m/it/10 > \OT1/cmr/m/n/10 0$\T1/ptm/m/n/10
, the es-ti-mated (1-norm) con-di-tion num-ber $[]$; when
[2213] [2214] [2215]
Underfull \hbox (badness 10000) in paragraph at lines 2112--2114
[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "ddenseMatrix
", where =
[2216] [2217]
Underfull \hbox (badness 10000) in paragraph at lines 2234--2236
[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "denseMatrix"
, where =
Underfull \hbox (badness 3068) in paragraph at lines 2295--2299
\T1/ptm/m/n/10 i-cally via \T1/pcr/m/n/10 as(*, "CsparseMatrix") \T1/ptm/m/n/10
or sim-i-lar. Of-ten how-ever, more eas-ily via
[2218]
Underfull \hbox (badness 4713) in paragraph at lines 2330--2332
[]\T1/pcr/m/n/10 signature(x = "dgCMatrix")\T1/ptm/m/n/10 : com-putes the LU de
-com-po-si-tion of a square
[2219]
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[]\T1/pcr/m/n/10 signature(x = "dgeMatrix", norm = "character") \T1/ptm/m/n/10
or
[2220]
Underfull \hbox (badness 10000) in paragraph at lines 2549--2553
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("dgTMatrix", ...)\T1/ptm/m/n/10 ,
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\T1/ptm/m/n/10 but more typ-i-cally via \T1/pcr/m/n/10 as(*, "dgTMatrix")\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 spMatrix[][][]()\T1/ptm/m/n/10 , or
[2221]
Underfull \hbox (badness 2707) in paragraph at lines 2605--2609
[]\T1/ptm/m/n/10 Note that both \T1/pcr/m/n/10 new(.) \T1/ptm/m/n/10 and [][]\T
1/pcr/m/n/10 spMatrix[][][] \T1/ptm/m/n/10 con-struc-tors for \T1/pcr/m/n/10 "d
gTMatrix" \T1/ptm/m/n/10 (and other
Underfull \hbox (badness 2368) in paragraph at lines 2610--2614
[]\T1/ptm/m/n/10 However this means that a ma-trix typ-i-cally can tbe stored i
n more than one pos-si-ble
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[]\T1/ptm/m/n/10 Class [][]\T1/pcr/m/n/10 dgCMatrix[][][] \T1/ptm/m/n/10 or the
su-per-classes [][]\T1/pcr/m/n/10 dsparseMatrix[][][] \T1/ptm/m/n/10 and [][]\
T1/pcr/m/n/10 TsparseMatrix[][][]\T1/ptm/m/n/10 ;
[2222]
Underfull \hbox (badness 2689) in paragraph at lines 2673--2675
[]\T1/ptm/m/n/10 integer spec-i-fy-ing the di-men-sion of the (square) ma-trix.
If miss-ing,
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[]\T1/ptm/m/n/10 for \T1/pcr/m/n/10 .symDiagonal \T1/ptm/m/n/10 (\T1/pcr/m/n/10
.trDiagonal\T1/ptm/m/n/10 ), the re-sult-ing sparse
Underfull \hbox (badness 3482) in paragraph at lines 2677--2682
[][]\T1/pcr/m/n/10 symmetricMatrix[][][] \T1/ptm/m/n/10 (or [][]\T1/pcr/m/n/10
triangularMatrix[][][]\T1/ptm/m/n/10 ) will have slot \T1/pcr/m/n/10 uplo
[2223]
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[]\T1/pcr/m/n/10 Diagonal() \T1/ptm/m/n/10 re-turns an ob-ject of class [][]\T1
/pcr/m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 ldiMatrix[][][
] \T1/ptm/m/n/10 (with ``su-per-class''
Underfull \hbox (badness 1142) in paragraph at lines 2713--2718
[][]\T1/pcr/m/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 (the re-sult-ing class de
-pend-ing on \T1/pcr/m/n/10 shape \T1/ptm/m/n/10 and \T1/pcr/m/n/10 kind\T1/ptm
/m/n/10 ) rep-re-sen-ta-tion of
[2224]
Underfull \hbox (badness 3646) in paragraph at lines 2951--2954
[]\T1/ptm/m/n/10 the [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , a [][]\T
1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 , see the [][]\T1/pcr/m/n/10 Matrix[][][]
\T1/ptm/m/n/10 class de-scrip-tion. Typ-i-cally
Underfull \hbox (badness 10000) in paragraph at lines 2973--2974
[]\T1/pcr/m/n/10 signature(from = "diagonalMatrix", to = "triangularMatrix")\T1
/ptm/m/n/10 :
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[]\T1/pcr/m/n/10 signature(a = "diagonalMatrix", b, ...)\T1/ptm/m/n/10 : is tri
v-ially im-ple-mented, of
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[]\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
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[]\T1/pcr/m/n/10 signature(x = "diagonalMatrix")\T1/ptm/m/n/10 : all these grou
p meth-ods re-turn a
[2225]
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[]\T1/pcr/m/n/10 signature(e1 = "ddiMatrix", e2="denseMatrix")\T1/ptm/m/n/10 :
the re-sult is from class
Underfull \hbox (badness 10000) in paragraph at lines 3002--3006
[]\T1/pcr/m/n/10 (object = "diagonalMatrix")\T1/ptm/m/n/10 : Re-turns an ob-jec
t of S3 class
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[][][]\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
[2226] [2227]
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[]\T1/pcr/m/n/10 signature(x = "dMatrix", digits = "numeric")\T1/ptm/m/n/10 : t
his group con-tains
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[][][]\T1/pcr/m/n/10 drop0[][][](x, tol=1e-10) \T1/ptm/m/n/10 is some-times pre
fer-able to (and more ef-fi-cient than)
[2228]
Underfull \hbox (badness 1168) in paragraph at lines 3363--3366
[]\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
[2229] [2230]
Underfull \hbox (badness 4967) in paragraph at lines 3528--3532
[]\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
[2231]
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[]\T1/ptm/m/n/10 Creation ``from scratch'' most ef-fi-ciently hap-pens via [][]
\T1/pcr/m/n/10 sparseMatrix[][][](*, symmetric=TRUE)\T1/ptm/m/n/10 .
Underfull \hbox (badness 6364) in paragraph at lines 3575--3578
[]\T1/pcr/m/n/10 signature(a = "dsCMatrix", b = "....")\T1/ptm/m/n/10 : \T1/pcr
/m/n/10 x <- solve(a,b) \T1/ptm/m/n/10 solves
[2232] [2233]
Underfull \hbox (badness 10000) in paragraph at lines 3725--3730
[]\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 3725--3730
\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
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[]\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "missing")\T1/ptm/m/n/10 : a
triv-ial
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[]\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "character")\T1/ptm/m/n/10 :
if
[2234]
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[]\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
Underfull \hbox (badness 10000) in paragraph at lines 3852--3855
[]\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")\T1/ptm/m/n/10 ,
or
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\T1/pcr/m/n/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 type = "missing
"\T1/ptm/m/n/10 : Com-putes the ma-trix norm of the
[2235]
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[]\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")\T1/ptm/m/n/10 ,
or
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\T1/pcr/m/n/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 type = "missing
"\T1/ptm/m/n/10 : Com-putes the re-cip-ro-cal con-di-tion
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[]\T1/pcr/m/n/10 signature(a = "dsyMatrix", b = "....")\T1/ptm/m/n/10 : \T1/pcr
/m/n/10 x <- solve(a,b) \T1/ptm/m/n/10 solves
[2236]
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[]\T1/pcr/m/n/10 signature(a = "dtCMatrix", b = "....")\T1/ptm/m/n/10 : sparse
tri-an-gu-lar solve (aka
[2237]
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[]\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim
= c(5L, 5L),[]
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[]\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
[2238]
Underfull \hbox (badness 10000) in paragraph at lines 4100--4103
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix", y = "dgeMatrix")\T1/ptm/m/n/10 : Ma
-
Underfull \hbox (badness 10000) in paragraph at lines 4100--4103
\T1/ptm/m/n/10 trix mul-ti-pli-ca-tion; ditto for sev-eral other sig-na-ture co
m-bi-na-tions, see
Underfull \hbox (badness 10000) in paragraph at lines 4105--4109
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix", logarithm = "logical")\T1/ptm/m/n/1
0 : the
[2239] [2240] [2241] [2242]
Underfull \hbox (badness 10000) in paragraph at lines 4393--4398
[]\T1/ptm/m/n/10 The ex-po-nen-tial of a ma-trix is de-fined as the in-fi-nite
Tay-lor se-ries
[2243] [2244]
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[] \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 4534--4534
[]\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 4537--4537
[]\T1/pcr/m/n/9 file.info(MMfile)[,c("size", "ctime")] # (some confirmation of
the file\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s)[]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 4547--4547
[]\T1/pcr/m/n/9 ## has columns (i, j, x) -> we can use via do.call() as argume
nts to sparseMatrix():[]
[2245] [2246]
Underfull \hbox (badness 10000) in paragraph at lines 4702--4704
[][][]\T1/pcr/m/n/10 symmpart[][][] \T1/ptm/m/n/10 for the sym-met-ric part of
a ma-trix, or the co-er-cions
[2247] [2248]
Underfull \hbox (badness 10000) in paragraph at lines 4849--4854
[]\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 ,
[2249]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4930--4930
[]\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 4932--4932
[] \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 4936--4936
[] \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE,
dimnames=dns))[]
[2250]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4943--4943
[] \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 '[]
[2251]
Underfull \hbox (badness 10000) in paragraph at lines 5068--5073
[]\T1/ptm/m/n/10 color for the bor-der of each rect-an-gle. \T1/pcr/m/n/10 NA \
T1/ptm/m/n/10 means
Underfull \hbox (badness 10000) in paragraph at lines 5068--5073
\T1/ptm/m/n/10 no bor-der is drawn. When \T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 as
by de-fault,
Underfull \hbox (badness 2644) in paragraph at lines 5068--5073
\T1/pcr/m/n/10 border.col <- if(lwd < .01) NA else NULL \T1/ptm/m/n/10 is used.
Con-
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\T1/ptm/m/n/10 sider us-ing an opaque color in-stead of \T1/pcr/m/n/10 NULL \T1
/ptm/m/n/10 which cor-re-sponds to
[2252]
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[]\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 5124--5124
[]\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 5130--5130
[] \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 5131--5131
[] \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 5134--5134
[]\T1/pcr/m/n/9 image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd=3, bor
der.col = adjustcolor("skyblue", 1/2))[]
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[]\T1/pcr/m/n/9 if(doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CH
ECK_EXTRA")) ||[]
[2253]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5143--5143
[]\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[]
[2254]
Underfull \hbox (badness 1817) in paragraph at lines 5235--5244
[]\T1/ptm/m/n/10 While ``row-indexing'' (of more than one row \T1/ptm/m/it/10 o
r \T1/ptm/m/n/10 us-ing \T1/pcr/m/n/10 drop=FALSE\T1/ptm/m/n/10 ) stays within
the
Underfull \hbox (badness 5637) in paragraph at lines 5277--5279
[]\T1/pcr/m/n/10 signature(x = "matrix", y = "indMatrix") \T1/ptm/m/n/10 and ot
her sig-na-tures (use
[2255]
Underfull \hbox (badness 3138) in paragraph at lines 5303--5305
[]\T1/pcr/m/n/10 signature(x = "indMatrix")\T1/ptm/m/n/10 : re-turn the
[2256]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 5370--5370
[] \T1/pcr/m/n/9 if(getRversion() >= "3.2.0") identical(I12, rbind(I1
, I2)) else TRUE,[]
Underfull \hbox (badness 1603) in paragraph at lines 5391--5393
[]\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 p \T1/ptm/m/n/10 con-t
ains val-ues \T1/pcr/m/n/10 0:(n-1) \T1/ptm/m/n/10 or rather (by de-fault,
Underfull \hbox (badness 10000) in paragraph at lines 5399--5404
[]\T1/ptm/m/n/10 an in-te-ger vec-tor of the same length (\T1/pcr/m/n/10 n\T1/p
tm/m/n/10 ) as \T1/pcr/m/n/10 p\T1/ptm/m/n/10 . By de-fault,
Underfull \hbox (badness 10000) in paragraph at lines 5399--5404
\T1/ptm/m/n/10 (\T1/pcr/m/n/10 zero.p = FALSE, zero.res = FALSE\T1/ptm/m/n/10 )
, \T1/pcr/m/n/10 invPerm(p) \T1/ptm/m/n/10 is the same as
Underfull \hbox (badness 10000) in paragraph at lines 5399--5404
[][]\T1/pcr/m/n/10 order[][][](p) \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 sort.lis
t[][][](p) \T1/ptm/m/n/10 and for that case, the func-tion is equiv-a-lent to
[2257] [2258] [2259]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5628--5628
[]\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[]
[2260]
Underfull \hbox (badness 10000) in paragraph at lines 5709--5712
[][][]\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 5720--5720
[]\T1/pcr/m/n/9 isTriangular(as(M, "dgeMatrix")) # still triangular, even if n
ot "formally"[]
[2261]
Underfull \hbox (badness 1622) in paragraph at lines 5757--5762
[]\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 5757--5762
\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
[2262]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5818--5818
[]\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 5819--5819
[] \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 5826--5826
[] \T1/pcr/m/n/9 identical(dimnames(KhatriRao(m, d0, make.dimnames=TRUE)), di
mnames(Kmd)))[]
[2263]
Underfull \hbox (badness 1062) in paragraph at lines 5955--5958
[]\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
[2264]
Underfull \hbox (badness 2809) in paragraph at lines 5984--5987
[]\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
[2265]
Underfull \hbox (badness 2635) in paragraph at lines 6096--6101
[]\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 6096--6101
\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 6104--6107
[]\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.,
[2266]
Underfull \hbox (badness 10000) in paragraph at lines 6214--6224
\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 6214--6224
[][]\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
[2267]
Underfull \hbox (badness 1184) in paragraph at lines 6296--6299
[]\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
[2268]
Underfull \hbox (badness 10000) in paragraph at lines 6394--6397
[]\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.,
[2269]
Underfull \hbox (badness 10000) in paragraph at lines 6469--6472
[]\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 6485--6485
[]\T1/pcr/m/n/9 str(lutp <- as(lutr, "ltpMatrix"))# packed matrix: only 10 = (
4+1)*4/2 entries[]
[2270]
Underfull \hbox (badness 2443) in paragraph at lines 6524--6530
[]\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 6524--6530
[][]\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 6545--6548
[]\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
[2271]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6615--6615
[] \T1/pcr/m/n/9 # q is a 0-based permutation o
f the columns[]
[2272] [2273]
Underfull \hbox (badness 6268) in paragraph at lines 6751--6754
[]\T1/ptm/m/n/10 Note that when the re-sult-ing ma-trix is di-ag-o-nal (``math-
e-mat-i-cally''),
[2274]
Underfull \hbox (badness 5036) in paragraph at lines 6775--6779
[]\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 6775--6779
\T1/pcr/m/n/10 Matrix(0, nrow,ncol) \T1/ptm/m/n/10 di-rectly con-structs an ``e
mpty'' [][]sparse-Ma-trix[][][], as does
[2275]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det
}) has been already used, duplicate ignored
<to be read again>
\relax
l.6868 \aliasA{det}{Matrix-class}{det}
Underfull \hbox (badness 1348) in paragraph at lines 6948--6951
[]\T1/pcr/m/n/10 signature(x = "Matrix")\T1/ptm/m/n/10 : As [][]\T1/pcr/m/n/10
diff[][][]() \T1/ptm/m/n/10 for tra-di-tional ma-tri-ces, i.e., ap-ply-ing
Underfull \hbox (badness 10000) in paragraph at lines 6953--6956
[]\T1/pcr/m/n/10 signature(x = "Matrix", value = "ANY")\T1/ptm/m/n/10 : where \
T1/pcr/m/n/10 value \T1/ptm/m/n/10 is
Underfull \hbox (badness 10000) in paragraph at lines 6953--6956
\T1/ptm/m/n/10 in-te-ger of length 2. Al-lows to \T1/ptm/m/it/10 re-shape \T1/p
tm/m/n/10 Ma-trix ob-jects, but only when
Underfull \hbox (badness 10000) in paragraph at lines 6971--6974
Underfull \hbox (badness 7326) in paragraph at lines 6981--6983
[]\T1/pcr/m/n/10 signature(from = "ANY", to = "Matrix")\T1/ptm/m/n/10 : This re
-lies on a cor-rect
[2276]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.7044 ...*\%}{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.7152 ...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.7252 ...tcrossprod}{matrix-products}{tcrossprod}
[2277]
Underfull \hbox (badness 1881) in paragraph at lines 7350--7356
\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
[2278pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cros
sprod.Rdash.methods}) has been already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox
\fi \fi
l.7412 \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.7412 \end{Details}
]
Underfull \hbox (badness 10000) in paragraph at lines 7423--7426
[]\T1/pcr/m/n/10 signature(x = "dgeMatrix", y = "dgeMatrix")\T1/ptm/m/n/10 : Ma
-
Underfull \hbox (badness 10000) in paragraph at lines 7423--7426
\T1/ptm/m/n/10 trix mul-ti-pli-ca-tion; ditto for sev-eral other sig-na-ture co
m-bi-na-tions, see
Underfull \hbox (badness 5637) in paragraph at lines 7426--7431
[]\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") \T1/ptm/m/n/10 and ot
her sig-na-tures (use
Underfull \hbox (badness 10000) in paragraph at lines 7435--7437
[]\T1/pcr/m/n/10 signature(x = "CsparseMatrix", y = "missing") \T1/ptm/m/n/10 r
e-turns
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[]\T1/pcr/m/n/10 signature(x = "TsparseMatrix", y = "missing") \T1/ptm/m/n/10 r
e-turns
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[]\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") \T1/ptm/m/n/10
and
[2279] [2280]
Underfull \hbox (badness 1062) in paragraph at lines 7622--7625
[]\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
[2281]
Underfull \hbox (badness 2809) in paragraph at lines 7656--7659
[]\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
[2282]
Underfull \hbox (badness 10000) in paragraph at lines 7708--7710
[]\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 X <- (X + t(X))/2 \T1/
ptm/m/n/10 should be done, af-ter
[2283]
Underfull \hbox (badness 1406) in paragraph at lines 7748--7752
[]\T1/ptm/m/n/10 Higham (2002) uses Dyk-stra's cor-rec-tion, but the ver-sion b
y Jens Oehlschlaegel did not
Underfull \hbox (badness 1019) in paragraph at lines 7748--7752
\T1/ptm/m/n/10 use it (ac-ci-den-tally), and has still lead to good re-sults; t
his sim-pli-fi-ca-tion, now only via
[2284]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 7846--7846
[]\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 7911--7916
[]\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 7911--7916
\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 7919--7922
[]\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.,
[2286] [2287]
Underfull \hbox (badness 10000) in paragraph at lines 8113--8115
[]\T1/ptm/m/n/10 fast
[2288]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.nor
m}) has been already used, duplicate ignored
<to be read again>
\relax
l.8153 \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.8153 \HeaderA{norm}{Matrix Norms}{norm}
[2289]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8240--8240
[]\T1/pcr/m/n/9 A <- sparseMatrix(i, j, x = x) ## 8 x 10
"dgCMatrix"[]
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[]\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10
"dsCMatrix"[]
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[]\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10
"dtCMatrix"[]
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[]\T1/ptm/m/n/10 These can be stored in the ``triplet'' form ([][]\T1/pcr/m/n/1
0 TsparseMatrix[][][]\T1/ptm/m/n/10 , sub-classes \T1/pcr/m/n/10 ngTMatrix\T1/p
tm/m/n/10 ,
[2290]
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[]\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
[2291]
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[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,
[2292]
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[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,
[2293]
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[]\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
[2294]
Underfull \hbox (badness 10000) in paragraph at lines 8718--8720
[]\T1/pcr/m/n/10 signature(x = "matrix", y = "pMatrix") \T1/ptm/m/n/10 and othe
r sig-na-tures (use
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[]\T1/pcr/m/n/10 signature(from = "pMatrix", to = "ngTMatrix")\T1/ptm/m/n/10 :
co-er-cion to sparse
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\T1/ptm/m/n/10 ma-trix; note that \T1/pcr/m/n/10 solve(P) \T1/ptm/m/n/10 is ide
n-ti-cal to \T1/pcr/m/n/10 t(P) \T1/ptm/m/n/10 for per-mu-ta-tion ma-tri-ces. S
ee
[2295] [2296]
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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 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[]
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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
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\T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro
m
[2297] [2298]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.qr}) has been already used, duplicate ignored
<to be read again>
\relax
l.8953 \aliasA{qr}{qr-methods}{qr}
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[]\T1/ptm/m/n/10 QR de-com-po-si-tion of a gen-eral sparse double-precision ma-
trix with
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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![]
[2299]
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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[]
[2300]
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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
[2301]
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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"[]
[2302]
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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.9249 ... the Reciprocal Condition Number}{rcond}
[2303]
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[]\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not
have full rank[]
[2304] [2305] [2306]
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[]\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 gets \T1/pcr/m/n/10 x <- rand.x(nnz) \T1/ptm/m/n/10 and calls []
[]\T1/pcr/m/n/10 sparseMatrix[][][](i=i, j=j, x=x, ..)\T1/ptm/m/n/10 . When
[2307] [2308]
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[]\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
[2309]
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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:[]
[2310]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sol
ve}) has been already used, duplicate ignored
<to be read again>
\relax
l.9826 \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[]
[2311]
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 solve \T1/ptm/m/n/10 meth-ods
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[]\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 basically com-putes uses tri-an-gu-lar
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[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list
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\T1/pcr/m/n/10 ( sparse = FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : U
ses the sparse
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[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list
Underfull \hbox (badness 2165) in paragraph at lines 10002--10012
\T1/pcr/m/n/10 ( sparse=FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : Che
cks if \T1/pcr/m/n/10 a \T1/ptm/m/n/10 is sym-
[2312]
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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 , and sim-i-lar \T1/pcr/m/n/10 b\T1/ptm/m/n/10 , in-clud-ing
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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
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10095--10095
[]\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[]
[2313]
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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,
Underfull \hbox (badness 10000) in paragraph at lines 10156--10159
[]\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
[2314]
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[]\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for
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\T1/pcr/m/n/10 sparse.model.matrix \T1/ptm/m/n/10 has been changed to \T1/pcr/m
/n/10 FALSE\T1/ptm/m/n/10 , 2010-07, for
Underfull \hbox (badness 6592) in paragraph at lines 10178--10180
[]\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
[2315]
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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),[]
[2316] [2317]
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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)[]
[2318]
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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
[2319]
Underfull \hbox (badness 10000) in paragraph at lines 10558--10561
[]\T1/ptm/m/n/10 The stan-dard \T1/phv/m/n/10 R [][]\T1/pcr/m/n/10 xtabs[][][](
*, sparse=TRUE)\T1/ptm/m/n/10 , for sparse ta-bles and
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[]\T1/pcr/m/n/9 (A <- sparseMatrix(i, j, x = x)) ## 8 x 10
"dgCMatrix"[]
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[]\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10
"dsCMatrix"[]
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[]\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10
"dtCMatrix"[]
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[]\T1/pcr/m/n/9 (AA <- sparseMatrix(c(1,3:8), c(2,9,6:10), x = 7 * (1:7), dims
= c(10,20)))[]
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[]\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar
e consistent[]
[2320]
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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)[]
[2321]
Underfull \hbox (badness 10000) in paragraph at lines 10730--10738
[]\T1/pcr/m/n/10 (object = "sparseMatrix")\T1/ptm/m/n/10 : Re-turns an ob-ject
of S3 class
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[]\T1/pcr/m/n/10 signature(x = "sparseMatrix", value = "ANY")\T1/ptm/m/n/10 : a
l-lows to \T1/ptm/m/it/10 re-shape \T1/ptm/m/n/10 a
[2322]
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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.10821 \aliasA{qr.Q}{sparseQR-class}{qr.Q}
[2323] [2324]
Underfull \hbox (badness 1430) in paragraph at lines 10951--10953
[]\T1/pcr/m/n/10 signature(a = "sparseQR", b = "ANY")\T1/ptm/m/n/10 : For \T1/p
cr/m/n/10 solve(a,b)\T1/ptm/m/n/10 , sim-ply uses
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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
[2325]
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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 ,
[2326]
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[]\T1/pcr/m/n/10 signature(x = "sparseVector", mode = "character") \T1/ptm/m/n/
10 co-erces
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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
[2327]
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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
[2328] [2329]
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[]\T1/ptm/m/n/10 The ma-trix $\OML/cmm/m/it/10 M$ \T1/ptm/m/n/10 will have \T1/
pcr/m/n/10 M[i[k], j[k]] == x[k]\T1/ptm/m/n/10 , for $\OML/cmm/m/it/10 k \OT1/c
mr/m/n/10 = 1\OML/cmm/m/it/10 ; \OT1/cmr/m/n/10 2\OML/cmm/m/it/10 ; [] ; n$\T1/
ptm/m/n/10 , where
Underfull \hbox (badness 1831) in paragraph at lines 11371--11377
[][][]\T1/pcr/m/n/10 Matrix[][][](*, sparse=TRUE) \T1/ptm/m/n/10 for the more u
sual con-struc-tor of such ma-tri-ces. Then,
[2330]
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[]\T1/pcr/m/n/10 signature(object = "symmetricMatrix")\T1/ptm/m/n/10 : re-turns
\T1/ptm/m/it/10 sym-met-ric
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[][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , even when the \T1/pcr/m/n/10
Dimnames \T1/ptm/m/n/10 slot only has row or col-umn names. This
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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
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\T1/pcr/m/n/10 list(NULL, <character>)\T1/ptm/m/n/10 , e.g., for ef-fi-ciency.
How-ever, [][]\T1/pcr/m/n/10 dimnames[][][]() \T1/ptm/m/n/10 and other
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\T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 triangularMatrix[][][]\T1/ptm/m/n/10
, and, e.g., [][]\T1/pcr/m/n/10 dsyMatrix[][][] \T1/ptm/m/n/10 for nu-meric \T1
/ptm/m/it/10 dense \T1/ptm/m/n/10 ma-tri-ces, or
[2331]
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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.,
[2332] [2333]
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[]\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 11688--11692
\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
[2334]
Underfull \hbox (badness 7649) in paragraph at lines 11795--11797
[]\T1/ptm/m/n/10 a sparse ma-trix stored in triplet form, i.e., in-her-it-ing f
rom class
[2335] [2336] [2337]
Underfull \hbox (badness 7362) in paragraph at lines 11996--11998
[]\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
[2338]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 12034--12034
[]\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)[]
[2339] [2340]
Underfull \hbox (badness 6910) in paragraph at lines 12285--12287
[]\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back
[2341] [2342] [2343]) (./boot-pkg.tex [2344]
Chapter 18.
[2345] [2346] [2347] [2348] [2349] [2350] [2351]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 530--530
[]\T1/pcr/m/n/10 boot(data, statistic, R, sim = "ordinary", stype = c("i", "f"
, "w"),
[2352]
Underfull \hbox (badness 1325) in paragraph at lines 568--575
[]\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sim-u-la-tion r
e-quired. Pos-si-ble
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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-
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\T1/ptm/m/n/10 lems. This may be spec-i-fied for any sim-u-la-tion, but is ig-n
ored when
[2353]
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[]\T1/ptm/m/n/10 logical, only al-lowed to be \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/1
0 for \T1/pcr/m/n/10 sim = "ordinary", stype = "i", n = 0
[2354]
Underfull \hbox (badness 6268) in paragraph at lines 797--807
\T1/ptm/m/n/10 or \T1/pcr/m/n/10 parallel = "snow" \T1/ptm/m/n/10 us-ing the de
-fault clus-ter, a sec-ond ap-proach is used if
[2355]
Underfull \hbox (badness 1881) in paragraph at lines 824--826
[]\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi
-cient boot-strap sim-u-la-tion.
Underfull \hbox (badness 6493) in paragraph at lines 851--855
[][][]\T1/pcr/m/n/10 boot.array[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.c
i[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 censboot[][][]\T1/ptm/m/n/10 , [][]\
T1/pcr/m/n/10 empinf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 tilt.boot[][][]\T1/ptm/m/n/10 ,
[2356]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 885--885
[]\T1/pcr/m/n/9 nuke.lm <- glm(log(cost) ~ date+log(cap)+ne+ct+log(cum.n)+pt,
data = nuke)[]
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[2358]
Underfull \hbox (badness 10000) in paragraph at lines 1066--1070
[]\T1/ptm/m/n/10 A vec-tor of char-ac-ter strings rep-re-sent-ing the type of i
n-ter-
Underfull \hbox (badness 10000) in paragraph at lines 1066--1070
\T1/ptm/m/n/10 vals re-quired. The value should be any sub-set of the val-ues
[2359]
Underfull \hbox (badness 1496) in paragraph at lines 1082--1091
[]\T1/ptm/m/n/10 If sup-plied, a value to be used as an es-ti-mate of the vari-
ance of the
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\T1/ptm/m/n/10 statis-tic for the nor-mal ap-prox-i-ma-tion and stu-den-tized i
n-ter-vals. If it
Underfull \hbox (badness 2343) in paragraph at lines 1082--1091
\T1/ptm/m/n/10 is not sup-plied and \T1/pcr/m/n/10 length(index) \T1/ptm/m/n/10
is 2 then \T1/pcr/m/n/10 var.t0 \T1/ptm/m/n/10 de-faults to
Underfull \hbox (badness 2150) in paragraph at lines 1103--1109
[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa
ult value is
[2360] [2361] [2362] [2363]
Underfull \hbox (badness 1571) in paragraph at lines 1443--1445
[]\T1/ptm/m/n/10 Rawlings, J.O. (1988) \T1/ptm/m/it/10 Ap-plied Re-gres-sion An
al-y-sis\T1/ptm/m/n/10 . Wadsworth and Brooks/Cole Statis-
[2364] [2365] [2366] [2367] [2368]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1735--1735
[]\T1/pcr/m/n/10 censboot(data, statistic, R, F.surv, G.surv, strata = matrix(
1,n,2),
[2369] [2370] [2371]
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Overfull \hbox (31.3804pt too wide) in paragraph at lines 2010--2010
[]\T1/pcr/m/n/9 mel.cox <- coxph(Surv(time, status == 1) ~ ns(thickness, df=4)
+ strata(ulcer),[]
[2373]
Underfull \hbox (badness 6268) in paragraph at lines 2081--2083
[]\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch
an-ning House.
[2374] [2375] [2376]
Underfull \hbox (badness 1565) in paragraph at lines 2335--2340
[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est on the ori
g-i-nal data set
[2377]
Underfull \hbox (badness 4595) in paragraph at lines 2360--2365
\T1/ptm/m/n/10 are passed un-changed ev-ery time \T1/pcr/m/n/10 boot.out$statis
tic \T1/ptm/m/n/10 is called.
Underfull \hbox (badness 1881) in paragraph at lines 2429--2431
[]\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi
-cient boot-strap sim-u-la-tion.
Underfull \hbox (badness 2057) in paragraph at lines 2437--2438
[][][]\T1/pcr/m/n/10 boot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 empinf[][][]
\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 k3.linear[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 linear.approx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 saddle.distn[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smooth.spline[][][]\T1/ptm/m/n/10 ,
[2378] [2379]
Underfull \hbox (badness 1077) in paragraph at lines 2533--2537
[]\T1/ptm/m/n/10 The un-bi-ased es-ti-ma-tor uses a mul-ti-plier of \T1/pcr/m/n
/10 n/((n-1)*(n-2)) \T1/ptm/m/n/10 where \T1/pcr/m/n/10 n \T1/ptm/m/n/10 is the
sam-ple
Underfull \hbox (badness 1112) in paragraph at lines 2533--2537
\T1/ptm/m/n/10 size, if \T1/pcr/m/n/10 unbiased \T1/ptm/m/n/10 is \T1/pcr/m/n/1
0 FALSE \T1/ptm/m/n/10 then a mul-ti-plier of \T1/pcr/m/n/10 1/n \T1/ptm/m/n/10
is used. This is mul-ti-plied by
[2380] [2381] [2382] [2383] [2384]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2892--2892
[]\T1/pcr/m/n/10 EEF.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t
= 25,
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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,[]
[2385] [2386] [2387]
Underfull \hbox (badness 3861) in paragraph at lines 3102--3105
[][][]\T1/pcr/m/n/10 boot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.array[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.ci[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 control[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[][][
]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 linear.approx[][][]\T1/ptm/m/n/10 ,
[2388]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 3155--3155
[]\T1/pcr/m/n/10 envelope(boot.out = NULL, mat = NULL, level = 0.95, index = 1
:ncol(mat))
[2389] [2390] [2391]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3375--3375
[]\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t
he resampling
[2392] [2393] [2394] [2395] [2396] [2397] [2398]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3835--3835
[] \T1/pcr/m/n/10 t = boot.out$t[, index], w = NULL, def = TRUE, q
= NULL)[]
[2399] [2400]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3974--3974
[]\T1/pcr/m/n/9 grav.p <- imp.prob(grav.tilt.boot, w = grav.w, index = 3, t0 =
grav.z0[3])[]
[2401] [2402] [2403]
Underfull \hbox (badness 10000) in paragraph at lines 4187--4189
[]\T1/ptm/m/n/10 The quan-tiles at which the plots are re-quired. The de-fault
is
[2404]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4256--4256
[]\T1/pcr/m/n/9 # To draw the jackknife-after-bootstrap plot for the head siz
e data as in
[2405] [2406]
Underfull \hbox (badness 10000) in paragraph at lines 4359--4361
[]\T1/ptm/m/n/10 The in-dex of the vari-able of in-ter-est within the out-put o
f
Underfull \hbox (badness 1430) in paragraph at lines 4368--4372
\T1/ptm/m/n/10 If \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is sup-plied but nei-ther \T
1/pcr/m/n/10 t \T1/ptm/m/n/10 nor \T1/pcr/m/n/10 L \T1/ptm/m/n/10 are sup-plied
then \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is set to
Underfull \hbox (badness 2269) in paragraph at lines 4386--4389
[]\T1/ptm/m/n/10 The lin-ear ap-prox-i-ma-tion to a boot-strap repli-cate with
fre-quency vec-tor \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is given by
[2407] [2408] [2409] [2410] [2411] [2412] [2413] [2414] [2415]
Underfull \hbox (badness 3000) in paragraph at lines 4956--4959
[]\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put
of a call to
[2416] [2417] [2418] [2419]
Underfull \hbox (badness 2293) in paragraph at lines 5235--5238
[]\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the
boot-strap
Underfull \hbox (badness 1668) in paragraph at lines 5235--5238
\T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl
os-est to
[2420]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5314--5314
[]\T1/pcr/m/n/9 grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w", strat
a = grav1[, 2])[]
[2421] [2422] [2423] [2424] [2425] [2426] [2427] [2428]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5863--5863
[]\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c
ity.sp1$spa[1][]
[2429]
Underfull \hbox (badness 1127) in paragraph at lines 5985--6003
\T1/ptm/m/n/10 etc. un-til a point is found with a cdf ap-prox-i-ma-tion less t
han \T1/pcr/m/n/10 min(alpha)/10\T1/ptm/m/n/10 , then
[2430]
Underfull \hbox (badness 2837) in paragraph at lines 6018--6021
[]\T1/ptm/m/n/10 The re-turned value is an ob-ject of class \T1/pcr/m/n/10 "sad
dle.distn"\T1/ptm/m/n/10 . See the help file for
[2431] [2432] [2433] [2434]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6303--6303
[]\T1/pcr/m/n/9 # This example is taken from Exercise 7.5 of Gill, Murray and
Wright (1991).
[2435] [2436]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6492--6492
[]\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t
he resampling
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6494--6494
[]\T1/pcr/m/n/9 # value of the test statistic 1.84. In the book exponential t
ilting was used[]
[2437] [2438] [2439]
Underfull \hbox (badness 1596) in paragraph at lines 6739--6743
[]\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sec-ond ar-gu-m
ent ex-pected by
[2440] [2441]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6899--6899
[] \T1/pcr/m/n/9 stype = "i", sim = "balanced", alpha =
c(0.05, 0.95),[]
[2442] [2443] [2444] [2445] [2446] [2447] [2448] [2449]) (./class-pkg.tex
[2450]
Chapter 19.
[2451] [2452] [2453] [2454] [2455] [2456] [2457] [2458]
Underfull \hbox (badness 10000) in paragraph at lines 608--610
[]\T1/ptm/m/n/10 the size of the code-book. De-faults to
[2459] [2460] [2461] [2462] [2463] [2464] [2465] [2466]) (./cluster-pkg.tex
Chapter 20.
[2467]
Underfull \hbox (badness 3098) in paragraph at lines 133--142
[]\T1/ptm/b/n/10 Care \T1/ptm/m/n/10 and ex-per-tise is prob-a-bly needed when
us-ing \T1/pcr/m/n/10 method = "flexible" \T1/ptm/m/n/10 par-tic-u-
Underfull \hbox (badness 2253) in paragraph at lines 133--142
\T1/ptm/m/n/10 larly for the case when \T1/pcr/m/n/10 par.method \T1/ptm/m/n/10
is spec-i-fied of longer length than one. Since
Underfull \hbox (badness 3323) in paragraph at lines 133--142
\T1/ptm/b/n/10 clus-ter \T1/ptm/m/n/10 ver-sion 2.0, choices lead-ing to in-val
id \T1/pcr/m/n/10 merge \T1/ptm/m/n/10 struc-tures now sig-nal an er-ror
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\T1/ptm/m/n/10 as \T1/pcr/m/n/10 method="flexible", par.method = 0.5\T1/ptm/m/n
/10 . Fur-ther, \T1/pcr/m/n/10 method= "single"
Underfull \hbox (badness 10000) in paragraph at lines 133--142
\T1/ptm/m/n/10 is equiv-a-lent to \T1/pcr/m/n/10 method="flexible", par.method
= c(.5,.5,0,-.5)\T1/ptm/m/n/10 , and
Overfull \hbox (48.49016pt too wide) in paragraph at lines 133--142
\T1/pcr/m/n/10 method="complete" \T1/ptm/m/n/10 is equiv-a-lent to \T1/pcr/m/n/
10 method="flexible", par.method = c(.5,.5,0,+.5)\T1/ptm/m/n/10 .
[2468]
Underfull \hbox (badness 10000) in paragraph at lines 167--169
[]\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 method = "gaverage", par.method = 0 \
T1/ptm/m/n/10 (or \T1/pcr/m/n/10 par.method =
[2469]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 252--252
[] \T1/pcr/m/n/9 all.equal(a.wgt [iC], agnes(d.vr, method="flexible", par.met
hod = 0.5)[iC]) ,[]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 253--253
[] \T1/pcr/m/n/9 all.equal(a.sing[iC], agnes(d.vr, method="flex", par.method=
c(.5,.5,0, -.5))[iC]),[]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 254--254
[] \T1/pcr/m/n/9 all.equal(a.comp[iC], agnes(d.vr, method="flex", par.method=
c(.5,.5,0, +.5))[iC]))[]
[2470] [2471]
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[2473]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 518--518
[] \T1/pcr/m/n/10 col = c(2, 0), border = 0, axes = TRUE, frame.plot
= axes,[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 522--522
[] \T1/pcr/m/n/10 yaxRight = fromLeft, y.mar = 2.4 + max.strlen/2.5,
...)[]
[2474]
Underfull \hbox (badness 5374) in paragraph at lines 539--541
[]\T1/ptm/m/n/10 logical in-di-cat-ing the ban-ner should be framed; mainly use
d when
[2475]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 637--637
[] \T1/pcr/m/n/10 keep.data = medoids.x, rngR = FALSE, pamLike = FALSE, c
orrect.d = TRUE)[]
[2476]
Underfull \hbox (badness 3078) in paragraph at lines 688--691
[]\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
[2477] [2478]
Underfull \hbox (badness 2941) in paragraph at lines 778--781
[][][]\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 816--816
[]\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo
r this seed):[]
[2479]
Underfull \hbox (badness 10000) in paragraph at lines 863--865
[]\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p
le, see
[2480]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 928--928
[] \T1/pcr/m/n/10 arrowArgs = list(col="red3", length=1/16, angle=90, code
=3), ...)[]
[2481]
Underfull \hbox (badness 4872) in paragraph at lines 974--976
[]\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 988--992
[]\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in
2012,
[2482]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1095--1095
[] \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE.
factor = SEf)))[]
[2483]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 1112--1112
[]\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 1150--1150
[]\T1/pcr/m/n/9 plot(gsP.Z, main = "clusGap(<iid_rnorm_p=3>) ==> k = 1 clust
er is optimal")[]
[2484]
Underfull \hbox (badness 4144) in paragraph at lines 1182--1186
[]\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
[2485]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 1258--1258
[] \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 1264--1264
[] \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin
t variability."),[]
[2486] [2487]
Underfull \hbox (badness 10000) in paragraph at lines 1403--1408
[]\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 1451--1454
[2488]
Underfull \hbox (badness 10000) in paragraph at lines 1468--1472
[][][]\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 1492--1492
[]\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 1502--1502
[] \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i
dent. only points[]
[2489]
Underfull \hbox (badness 5741) in paragraph at lines 1542--1545
[]\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
[2490]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1608--1608
[] \T1/pcr/m/n/10 warnBin = warnType, warnAsym = warnType, warnConst = wa
rnType,[]
[2491]
Underfull \hbox (badness 5008) in paragraph at lines 1725--1733
\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
[2492] [2493]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1816--1816
[]\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 1835--1835
[]\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st
and = FALSE,
[2494] [2495] [2496] [2497]
Underfull \hbox (badness 10000) in paragraph at lines 2143--2145
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the con-verged. This is de-fined as
Underfull \hbox (badness 10000) in paragraph at lines 2154--2157
Underfull \hbox (badness 3179) in paragraph at lines 2168--2174
[][][]\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.
[2498] [2499] [2500]
Underfull \hbox (badness 10000) in paragraph at lines 2326--2329
[][][]\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 ,
[2501]
Underfull \hbox (badness 1292) in paragraph at lines 2394--2397
[]\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 2403--2405
[]\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 2426--2429
[][][]\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 ,
[2502] [2503] [2504] [2505]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2642--2642
[]\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 ):[]
[2506] [2507]
Underfull \hbox (badness 1067) in paragraph at lines 2829--2834
[]\T1/ptm/m/n/10 The de-fault \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 (or in-te-ger
\T1/pcr/m/n/10 0\T1/ptm/m/n/10 ) cor-re-sponds to the orig-i-nal ``swap'' al-g
o-rithm, whereas
[2508]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2888--2888
[]\T1/pcr/m/n/9 ## no _build_ *and* no _swap_ phase: just cluster all obs. aro
und (1, 16):[]
[2509] [2510]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 2991--2991
[]\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co
l.axis = "red")[]
[2511] [2512] [2513]
Overfull \hbox (78.78088pt too wide) in paragraph at lines 3187--3187
[] \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x
$ac, digits = 2)),[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3188--3188
[] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
= TRUE, ...)[]
[2514]
Underfull \hbox (badness 10000) in paragraph at lines 3255--3258
[]\T1/ptm/m/n/10 For the den-dro-gram, more flex-i-bil-ity than via \T1/pcr/m/n
/10 pltree() \T1/ptm/m/n/10 is pro-vided by
[2515]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3305--3305
[] \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc,
digits = 2)),[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3306--3306
[] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
= TRUE, ...)[]
[2516] [2517] [2518]
Underfull \hbox (badness 10000) in paragraph at lines 3491--3494
[]\T1/ptm/m/n/10 when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 does not have a \T1/pcr/m
/n/10 diss \T1/ptm/m/n/10 com-po-nent as for
Underfull \hbox (badness 3471) in paragraph at lines 3491--3494
[][]\T1/pcr/m/n/10 pam[][][](*, keep.diss=FALSE)\T1/ptm/m/n/10 , \T1/pcr/m/n/10
dist \T1/ptm/m/n/10 must be the dis-sim-i-lar-ity if a
[2519]
Underfull \hbox (badness 10000) in paragraph at lines 3554--3559
[][][]\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 ,
[2520]
Underfull \hbox (badness 4621) in paragraph at lines 3616--3621
[]\T1/ptm/m/n/10 Note that cur-rently the method func-tion sim-ply calls \T1/pc
r/m/n/10 plot([][]as.hclust[][][](x), ...)\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1990) in paragraph at lines 3616--3621
\T1/ptm/m/n/10 which dis-patches to [][]\T1/pcr/m/n/10 plot.hclust[][][](..)\T1
/ptm/m/n/10 . If more flex-i-ble plots are needed, con-sider
Underfull \hbox (badness 6268) in paragraph at lines 3628--3631
[][][]\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 ,
[2521] [2522] [2523]
Underfull \hbox (badness 10000) in paragraph at lines 3813--3816
[][][]\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 3844--3847
[][][]\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 ,
[2524]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 3897--3897
[] \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right =
TRUE, ...)[]
Underfull \hbox (badness 2035) in paragraph at lines 3908--3910
[]\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
[2525] [2526] [2527] [2528]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 4101--4101
[] \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 4103--4103
[] \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat
= TRUE, ...)[]
Underfull \hbox (badness 1946) in paragraph at lines 4132--4137
[]\T1/ptm/m/n/10 arguments passed [][]\T1/pcr/m/n/10 barplot[][][]()\T1/ptm/m/n
/10 ; note that the de-fault used to be \T1/pcr/m/n/10 col
[2529]
Underfull \hbox (badness 10000) in paragraph at lines 4199--4207
\T1/pcr/m/n/10 attr(sil, "Ordered") \T1/ptm/m/n/10 is a log-i-cal in-di-cat-ing
if \T1/pcr/m/n/10 sil \T1/ptm/m/it/10 is \T1/ptm/m/n/10 or-dered as by
[2530]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4241--4241
[]\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 4250--4250
[] \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 4252--4252
[] \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 4255--4255
[]\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 4257--4257
[] \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 4264--4264
[]\T1/pcr/m/n/9 str(xc1k <- xclara[ sample(nrow(xclara), size = 1000) ,]) # ro
wnames == indices[]
[2531] [2532] [2533] [2534] [2535] [2536]
Underfull \hbox (badness 10000) in paragraph at lines 4622--4628
[]\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 4638--4640
[]\T1/ptm/m/n/10 Sample data set ac-com-pa-ny-ing the ref-er-ence be-low (file
`\T1/pcr/m/n/10 xclara.dat\T1/ptm/m/n/10 ' in side
Overfull \hbox (52.98038pt too wide) in paragraph at lines 4651--4651
[]\T1/pcr/m/n/9 ## Visualization: Assuming groups are defined as {1:1000}, {10
01:2000}, {2001:3000}
Overfull \hbox (9.78043pt too wide) in paragraph at lines 4653--4653
[]\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)$id.med[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4663--4663
[] \T1/pcr/m/n/9 ## We see 3 + 2 + 2 = 7 clear "outlier"s or "wrong group" o
bservations:[]
[2537]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4667--4667
[] \T1/pcr/m/n/9 ## Apart from these, what are the robust ranges of indices? -
- Robust range:[]
[2538]) (./codetools-pkg.tex
Chapter 21.
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[] \T1/pcr/m/n/10 suppressParamUnused = !all, suppressFundefMismatch
= FALSE,[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 17--17
[] \T1/pcr/m/n/10 suppressLocalUnused = FALSE, suppressNoLocalFun =
!all,[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 18--18
[] \T1/pcr/m/n/10 skipWith = FALSE, suppressUndefined = dfltSuppress
Undefined,[]
[2539]
Underfull \hbox (badness 10000) in paragraph at lines 65--70
[]\T1/pcr/m/n/10 checkUsageEnv \T1/ptm/m/n/10 and \T1/pcr/m/n/10 checkUsagePack
age \T1/ptm/m/n/10 are con-ve-nience func-tions that ap-ply
[2540]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 119--119
[]\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e
nterInternal,[]
[2541] [2542] [2543]) (./foreign-pkg.tex [2544]
Chapter 22.
[2545]
Underfull \hbox (badness 1231) in paragraph at lines 67--70
[]\T1/ptm/m/n/10 a char-ac-ter string with the name of the ARFF file to read fr
om, or a
Underfull \hbox (badness 6708) in paragraph at lines 78--81
[]\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / /
www . cs . waikato . ac . nz / ~ml / weka / arff .
[2546] [2547]
Underfull \hbox (badness 3601) in paragraph at lines 235--243
[]\T1/ptm/m/n/10 A data frame with at-tributes. These will in-clude \T1/pcr/m/n
/10 "datalabel"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "time.stamp"\T1/ptm/m/n/10 ,
[2548]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 296--296
[]\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates =
FALSE,
[2549] [2550] [2551]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 462--462
[] \T1/pcr/m/n/10 trim_values = TRUE, reencode = NA, use.missings = t
o.data.frame,[]
[2552]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 463--463
[] \T1/pcr/m/n/10 sub = ".", add.undeclared.levels = c("sort", "appen
d", "no"),[]
Underfull \hbox (badness 10000) in paragraph at lines 506--515
[]\T1/ptm/m/n/10 character: what to do with du-pli-cated value la-bels for dif-
fer-
Underfull \hbox (badness 6001) in paragraph at lines 506--515
\T1/ptm/m/n/10 ent lev-els. For \T1/pcr/m/n/10 "append" \T1/ptm/m/n/10 (the de-
fault), the first orig-i-nal value
Underfull \hbox (badness 10000) in paragraph at lines 506--515
\T1/ptm/m/n/10 la-bel is kept while fur-ther du-pli-cated la-bels are re-named
to
Underfull \hbox (badness 10000) in paragraph at lines 506--515
\T1/pcr/m/n/10 paste0(label, duplicated.value.labels.infix, level)\T1/ptm/m/n/1
0 ,
Underfull \hbox (badness 10000) in paragraph at lines 516--519
[]\T1/ptm/m/n/10 character: the in-fix used for la-bels of fac-tor lev-els with
du-
Underfull \hbox (badness 10000) in paragraph at lines 516--519
\T1/ptm/m/n/10 pli-cated value la-bels in SPSS (de-fault \T1/pcr/m/n/10 "_dupli
cated_"\T1/ptm/m/n/10 ) if
[2553]
Underfull \hbox (badness 10000) in paragraph at lines 551--559
[]\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 http : / / msdn . microsoft . com / en
-[]us / library / ms776446(VS . 85 ) .aspx$[][]
Underfull \hbox (badness 7613) in paragraph at lines 569--575
[]\T1/ptm/m/n/10 There may be at-tributes \T1/pcr/m/n/10 "label.table" \T1/ptm/
m/n/10 and \T1/pcr/m/n/10 "variable.labels"\T1/ptm/m/n/10 . At-tribute
[2554]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 624--624
[]\T1/pcr/m/n/9 ### hence may need some special treatment with appropriate arg
ument settings.[]
Overfull \hbox (112.38031pt too wide) in paragraph at lines 625--625
[]\T1/pcr/m/n/9 ### Expect lots of warnings as value labels (corresponding to
R factor labels) are uncomplete,[]
[2555]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 658--658
[]\T1/pcr/m/n/9 ## Long Strings (>255 chars) are imported in consecutive separ
ate variables[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 662--662
[]\T1/pcr/m/n/9 cat.long.string <- function(x, w=70) cat(paste(strwrap(x, widt
h=w), "\n"))[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 669--669
[]\T1/pcr/m/n/9 long.string <- apply(x[,c("string_500", "STRIN0")], 1, paste,
collapse="")[]
[2556] [2557]
Underfull \hbox (badness 10000) in paragraph at lines 813--814
Overfull \hbox (4.38043pt too wide) in paragraph at lines 823--823
[]\T1/pcr/m/n/9 iris.s <- read.systat(system.file("files/Iris.syd", package="f
oreign")[1])[]
[2558] [2559]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 899--899
[] \T1/pcr/m/n/10 data.restore(file, print = FALSE, verbose = FALSE, env = .G
lobalEnv)
[2560]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 963--963
[]\T1/pcr/m/n/10 write.arff(x, file, eol = "\n", relation = deparse(substitute
(x)))
Underfull \hbox (badness 6708) in paragraph at lines 989--992
[]\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / /
www . cs . waikato . ac . nz / ~ml / weka / arff .
[2561] [2562]
Underfull \hbox (badness 10000) in paragraph at lines 1073--1074
[][][]$\T1/pcr/m/n/10 http : / / www . clicketyclick . dk / databases / xbase /
format / data _ types .
Overfull \hbox (24.78088pt too wide) in paragraph at lines 1109--1109
[] \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric",
"codes"))[]
[2563]
Underfull \hbox (badness 1286) in paragraph at lines 1194--1198
[]\T1/ptm/m/n/10 Unless dis-abled by ar-gu-ment \T1/pcr/m/n/10 convert.dates =
FALSE\T1/ptm/m/n/10 , \T1/phv/m/n/10 R \T1/ptm/m/n/10 date and date-time ob-jec
ts
[2564]
Underfull \hbox (badness 10000) in paragraph at lines 1267--1273
[]\T1/ptm/m/n/10 The work for this func-tion is done by \T1/pcr/m/n/10 foreign:
::writeForeignStata\T1/ptm/m/n/10 ,
[2565]
Underfull \hbox (badness 6725) in paragraph at lines 1293--1296
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 package="SPSS"\T1/ptm/m/n/10 , as a side ef
-fect, the dec-i-mal in-di-ca-tor is al-ways set by
[2566]) (./lattice-pkg.tex
Chapter 23.
[2567] [2568] [2569]
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"),[]
[2570]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 298--298
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defaul
t.dotplot"),[]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 305--305
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.barchart"),[]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 313--313
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.stripplot"),[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 334--334
[] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 338--338
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.bwplot"),[]
[2571]
Underfull \hbox (badness 4060) in paragraph at lines 357--369
[]\T1/ptm/m/n/10 For the func-tions doc-u-mented here, the for-mula is gen-er-a
lly of the
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\T1/ptm/m/n/10 form \T1/pcr/m/n/10 y ~ x | g1 * g2 * ... \T1/ptm/m/n/10 (or equ
iv-a-lently, \T1/pcr/m/n/10 y ~ x |
Underfull \hbox (badness 1028) in paragraph at lines 397--412
\T1/ptm/m/n/10 This for-mula would be taken to mean that the user wants to plot
both
Underfull \hbox (badness 10000) in paragraph at lines 413--415
[]\T1/ptm/m/n/10 To in-ter-pret \T1/pcr/m/n/10 y1 + y2 \T1/ptm/m/n/10 as a sum,
one can ei-ther set
[2572]
Underfull \hbox (badness 7631) in paragraph at lines 479--484
[]\T1/ptm/m/n/10 A po-ten-tially use-ful com-po-nent of \T1/pcr/m/n/10 scales \
T1/ptm/m/n/10 in this case may be
[2573] [2574]
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
[2575] [2576] [2577] [2578]
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.
[2579]
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
[2580] [2581]
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
[2582] [2583] [2584]
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 ,
[2585]
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 ,
[2586]
Underfull \vbox (badness 10000) has occurred while \output is active [2587]
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
[2588]
Underfull \hbox (badness 6808) in paragraph at lines 1755--1759
[]\T1/ptm/m/n/10 graphical ar-gu-ments, which are pro-cessed and even-tu-ally p
assed to
Underfull \hbox (badness 10000) in paragraph at lines 1772--1775
[]\T1/ptm/m/n/10 style set-tings be-yond the stan-dard \T1/pcr/m/n/10 col\T1/pt
m/m/n/10 , \T1/pcr/m/n/10 lty\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lwd\T1/ptm/m/n/10
, etc; see
[2589]
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
[2590] [2591] [2592]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2071--2071
[] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl
ot"),[]
Underfull \hbox (badness 10000) in paragraph at lines 2086--2093
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 formula \T1/ptm/m/n/10 method, \T1/pcr/
m/n/10 x \T1/ptm/m/n/10 can be a for-mula of the form
Underfull \hbox (badness 1997) in paragraph at lines 2086--2093
\T1/pcr/m/n/10 ~ x | g1 * g2 * ...\T1/ptm/m/n/10 , in-di-cat-ing that his-togra
ms or ker-nel den-sity
[2593]
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
[2594] [2595] [2596]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 2345--2345
[] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 2349--2349
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.qqmath"),[]
Underfull \hbox (badness 4441) in paragraph at lines 2362--2366
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 method, \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 should be a for-mula of the form
[2597] [2598] [2599]
Underfull \hbox (badness 4441) in paragraph at lines 2547--2554
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 method, \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 should be a for-mula of the form
[2600] [2601]
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"),[]
[2602]
Underfull \hbox (badness 10000) in paragraph at lines 2761--2766
[]\T1/ptm/m/n/10 for the \T1/pcr/m/n/10 formula \T1/ptm/m/n/10 method, a for-mu
la of the form \T1/pcr/m/n/10 z ~ x * y
[2603]
Underfull \hbox (badness 2913) in paragraph at lines 2791--2796
[]\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix.
Underfull \hbox (badness 3058) in paragraph at lines 2791--2796
\T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p
tm/m/n/10 must have the same lengths as
Underfull \hbox (badness 6758) in paragraph at lines 2877--2881
[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the col-orkey should be
Underfull \hbox (badness 7576) in paragraph at lines 2877--2881
\T1/ptm/m/n/10 ren-dered as a raster im-age us-ing [][]\T1/pcr/m/n/10 grid.rast
er[][][]\T1/ptm/m/n/10 . See also
Underfull \hbox (badness 10000) in paragraph at lines 2883--2885
[]\T1/ptm/m/n/10 Logical flag, passed to [][]\T1/pcr/m/n/10 rasterGrob[][][] \T
1/ptm/m/n/10 when
[2604]
Underfull \hbox (badness 1609) in paragraph at lines 2935--2941
[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether raster rep-re-sen-ta-ti
ons should be used,
Underfull \hbox (badness 2772) in paragraph at lines 2935--2941
\T1/ptm/m/n/10 both for the false color im-age and the color key (if present).
Ef-
Underfull \hbox (badness 1400) in paragraph at lines 2935--2941
\T1/ptm/m/n/10 fec-tively, set-ting this to \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10
changes the de-fault panel func-tion from
Underfull \hbox (badness 2486) in paragraph at lines 2959--2963
[]\T1/ptm/m/n/10 Other use-ful ar-gu-ments are men-tioned in the help page for
the de-fault panel func-tion
[2605] [2606]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3060--3060
[] \T1/pcr/m/n/10 xlim = if (is.factor(x)) levels(x) else range(x, finite
= TRUE),[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3061--3061
[] \T1/pcr/m/n/10 ylim = if (is.factor(y)) levels(y) else range(y, finite
= TRUE),[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3062--3062
[] \T1/pcr/m/n/10 zlim = if (is.factor(z)) levels(z) else range(z, finite
= TRUE),[]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3073--3073
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
cloud"),[]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 3085--3085
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.wireframe"),[]
[2607]
Underfull \hbox (badness 10000) in paragraph at lines 3110--3118
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 meth-ods, a fo
r-mula of the form \T1/pcr/m/n/10 z ~ x
Underfull \hbox (badness 2913) in paragraph at lines 3143--3150
[]\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix.
Underfull \hbox (badness 3058) in paragraph at lines 3143--3150
\T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p
tm/m/n/10 must have the same lengths as
[2608] [2609] [2610] [2611]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.parallel}) has been already used, duplicate ignored
<to be read again>
\relax
l.3431 \aliasA{parallel}{B\_08\_splom}{parallel}
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3473--3473
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
splom"),[]
[2612]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3496--3496
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.parallel"),[]
[2613] [2614] [2615] [2616] [2617]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3832--3832
[]\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt(
var(x)))
[2618]
Underfull \hbox (badness 10000) in paragraph at lines 3922--3926
\T1/ptm/m/n/10 fy-ing \T1/pcr/m/n/10 lattice.options(default.theme = "col.white
bg")\T1/ptm/m/n/10 .
Underfull \hbox (badness 2435) in paragraph at lines 3922--3926
\T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa
ded) set to
[2619] [2620]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4052--4052
[]\T1/pcr/m/n/10 trellis.par.set(name, value, ..., theme, warn = TRUE, strict
= FALSE)
Underfull \hbox (badness 1173) in paragraph at lines 4061--4065
[]\T1/ptm/m/n/10 A char-ac-ter string giv-ing the name of a com-po-nent. If un-
spec-i-fied in
Underfull \hbox (badness 3219) in paragraph at lines 4088--4090
[]\T1/ptm/m/n/10 A log-i-cal flag, in-di-cat-ing whether a warn-ing should be i
s-sued when
Underfull \hbox (badness 1728) in paragraph at lines 4105--4109
\T1/pcr/m/n/10 theme\T1/ptm/m/n/10 ). These are used to mod-ify the cur-rent se
t-tings (ob-tained by
[2621]
Underfull \hbox (badness 5161) in paragraph at lines 4170--4174
[]\T1/ptm/m/n/10 The ac-tual list of the com-po-nents in \T1/pcr/m/n/10 trellis
.settings \T1/ptm/m/n/10 has not been fi-nal-ized,
Underfull \hbox (badness 4913) in paragraph at lines 4170--4174
\T1/ptm/m/n/10 so I'm not at-tempt-ing to list them here. The cur-rent value ca
n be ob-tained by
[2622] [2623]
Underfull \hbox (badness 1067) in paragraph at lines 4284--4294
[]\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. \T1/pcr/m/n/10 col \T1/ptm/m/n/10 i
s used for com-po-nents \T1/pcr/m/n/10 "plot.symbol"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 4284--4294
\T1/pcr/m/n/10 "plot.line"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "plot.polygon"\T1/ptm
/m/n/10 , \T1/pcr/m/n/10 "superpose.symbol"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1735) in paragraph at lines 4284--4294
\T1/pcr/m/n/10 "superpose.line"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "superpose.p
olygon"\T1/ptm/m/n/10 . \T1/pcr/m/n/10 col.points
Underfull \hbox (badness 10000) in paragraph at lines 4284--4294
\T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col\T1/ptm/m/n/10 , but is used only f
or \T1/pcr/m/n/10 "plot.symbol" \T1/ptm/m/n/10 and
Underfull \hbox (badness 5231) in paragraph at lines 4284--4294
\T1/pcr/m/n/10 "superpose.symbol"\T1/ptm/m/n/10 . Sim-i-larly, \T1/pcr/m/n/10 c
ol.line \T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col \T1/ptm/m/n/10 for
Underfull \hbox (badness 1701) in paragraph at lines 4309--4312
[]\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 plot
.symbol\T1/ptm/m/n/10 , \T1/pcr/m/n/10 plot.polygon\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 4312--4314
[]\T1/ptm/m/n/10 border color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 pl
ot.polygon \T1/ptm/m/n/10 and
[2624] [2625] [2626] [2627] [2628] [2629]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4716--4716
[]\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab
= "Height")[]
[2630] [2631]
Underfull \hbox (badness 10000) in paragraph at lines 4903--4906
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 trellis\T1/ptm/m/n/10 , by
de-fault plot-ted by \T1/pcr/m/n/10 print.trellis\T1/ptm/m/n/10 .
[2632] [2633]
Underfull \hbox (badness 1442) in paragraph at lines 5035--5038
[]\T1/pcr/m/n/10 plot.shingle \T1/ptm/m/n/10 dis-plays the ranges of shin-gles
via rect-an-gles. \T1/pcr/m/n/10 print.shingle \T1/ptm/m/n/10 and
[2634] [2635] [2636] [2637] [2638] [2639]
Underfull \hbox (badness 3646) in paragraph at lines 5367--5370
[][][]\T1/pcr/m/n/10 Lattice[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 draw.key[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 trellis.par.get[][][]\T1/ptm/m/n/10 ,
and [][]\T1/pcr/m/n/10 xyplot[][][]\T1/ptm/m/n/10 , specif-i-cally the en-try f
or
Overfull \hbox (36.78088pt too wide) in paragraph at lines 5397--5397
[] \T1/pcr/m/n/10 bg = trellis.par.get("strip.background")$col[wh
ich.given],[]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 5398--5398
[] \T1/pcr/m/n/10 fg = trellis.par.get("strip.shingle")$col[which
.given],[]
[2640]
Underfull \hbox (badness 10000) in paragraph at lines 5486--5489
[]\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i
-zon-tal.
Underfull \hbox (badness 2103) in paragraph at lines 5486--5489
\T1/pcr/m/n/10 horizontal=FALSE \T1/ptm/m/n/10 is use-ful for strips on the lef
t of pan-els us-ing
Underfull \hbox (badness 6412) in paragraph at lines 5503--5509
[]\T1/ptm/m/n/10 default strip func-tion for trel-lis func-tions. Use-ful mostl
y be-cause of the \T1/pcr/m/n/10 style
Underfull \hbox (badness 10000) in paragraph at lines 5503--5509
\T1/ptm/m/n/10 ar-gu-ment --- non-default styles are of-ten more in-for-ma-tive
, es-pe-cially when
Underfull \hbox (badness 10000) in paragraph at lines 5503--5509
\T1/ptm/m/n/10 the names of the lev-els of the fac-tor \T1/pcr/m/n/10 x \T1/ptm
/m/n/10 are small. Tra-di-tional use is as
Underfull \hbox (badness 10000) in paragraph at lines 5503--5509
\T1/pcr/m/n/10 strip = function(...) strip.default(style=2,...)\T1/ptm/m/n/10 ,
though this can be
[2641]
Underfull \hbox (badness 1635) in paragraph at lines 5512--5517
[]\T1/pcr/m/n/10 strip.default \T1/ptm/m/n/10 is called for its side-effect, wh
ich is to draw a strip ap-pro-pri-ate for
[2642]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5661--5661
[]\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la
bels,[]
[2643]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 5675--5675
[]\T1/pcr/m/n/10 panel.link.splom(threshold = 18, verbose = getOption("verbose
"), ...)[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 5676--5676
[]\T1/pcr/m/n/10 panel.brush.splom(threshold = 18, verbose = getOption("verbos
e"), ...)[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5679--5679
[]\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location"
, "toplevel",[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5682--5682
[] \T1/pcr/m/n/10 "xlab", "ylab", "xlab.top", "ylab.rig
ht", "page"),[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 5684--5684
[] \T1/pcr/m/n/10 side = c("left", "top", "right", "bottom", "in
side"),[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 5690--5690
[] \T1/pcr/m/n/10 which.given = lattice.getStatus("current.whi
ch.given",[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5691--5691
[] \T1/pcr/m/n/10 prefix = pre
fix),[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 5692--5692
[] \T1/pcr/m/n/10 which.panel = lattice.getStatus("current.whi
ch.panel",[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5693--5693
[] \T1/pcr/m/n/10 prefix = pre
fix),[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5694--5694
[] \T1/pcr/m/n/10 column = lattice.getStatus("current.focus.co
lumn",[]
Underfull \hbox (badness 10000) in paragraph at lines 5710--5712
[]\T1/ptm/m/n/10 variables defin-ing the con-tents of the panel. In the case of
[2644]
Underfull \hbox (badness 2376) in paragraph at lines 5721--5723
[]\T1/ptm/m/n/10 an op-tional vec-tor of la-bels as-so-ci-ated with each point.
De-faults to
[2645]
Underfull \hbox (badness 2538) in paragraph at lines 5846--5850
\T1/ptm/m/n/10 For \T1/pcr/m/n/10 trellis.focus\T1/ptm/m/n/10 , the de-fault is
\T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 in in-ter-ac-tive mode, and
Underfull \hbox (badness 4205) in paragraph at lines 5857--5864
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 panel.identify.qqmath\T1/ptm/m/n/10 , ex-tr
a pa-ram-e-ters are passed on to
Underfull \hbox (badness 4792) in paragraph at lines 5857--5864
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 trellis.switchFocus\T1/ptm/m/n/10 , these are
used (in com-bi-na-tion with
[2646] [2647]
Underfull \hbox (badness 10000) in paragraph at lines 6010--6014
[][][]\T1/pcr/m/n/10 identify[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Lattice[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.trellis[][][]\T1/ptm/m/n/10 , []
[]\T1/pcr/m/n/10 trellis.currentLayout[][][]\T1/ptm/m/n/10 ,
[2648] [2649]
Underfull \hbox (badness 4242) in paragraph at lines 6157--6162
[]\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li
s pa-ram-e-
[2650] [2651]
Underfull \hbox (badness 3601) in paragraph at lines 6273--6278
[]\T1/ptm/m/n/10 Creates Box and Whisker plot of \T1/pcr/m/n/10 x \T1/ptm/m/n/1
0 for ev-ery level of \T1/pcr/m/n/10 y \T1/ptm/m/n/10 (or the other way round
Underfull \hbox (badness 2486) in paragraph at lines 6273--6278
\T1/ptm/m/n/10 if \T1/pcr/m/n/10 horizontal=FALSE\T1/ptm/m/n/10 ). By de-fault,
the ac-tual box-plot statis-tics are cal-cu-lated us-ing
[2652] [2653]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 6360--6360
[] \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co
lors")$palette,[]
[2654]
Underfull \hbox (badness 1888) in paragraph at lines 6492--6499
\T1/pcr/m/n/10 at \T1/ptm/m/n/10 can be a nu-meric vec-tor, \T1/pcr/m/n/10 col.
regions \T1/ptm/m/n/10 a vec-tor of col-ors, and
[2655]
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[]\T1/ptm/m/n/10 All three num-bers should be be-tween 0 and 1. The
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\T1/pcr/m/n/10 shade.colors.palette \T1/ptm/m/n/10 func-tion should re-turn a v
alid color. The
[2656]
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\T1/ptm/m/n/10 fer-ent pur-poses. For cloud, the data is un-struc-tured, and \T
1/pcr/m/n/10 x\T1/ptm/m/n/10 , \T1/pcr/m/n/10 y \T1/ptm/m/n/10 and \T1/pcr/m/n/
10 z \T1/ptm/m/n/10 are all passed to
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\T1/ptm/m/n/10 the \T1/pcr/m/n/10 panel.3d.cloud \T1/ptm/m/n/10 func-tion. For
wire-frame, on the other hand, \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/
10 y \T1/ptm/m/n/10 are in-
[2657] [2658] [2659] [2660] [2661]
Underfull \hbox (badness 1320) in paragraph at lines 6955--6962
[]\T1/pcr/m/n/10 panel.levelplot.raster \T1/ptm/m/n/10 is an al-ter-na-tive pan
el func-tion that uses the raster draw-
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\T1/ptm/m/n/10 can only ren-der data on an eq-ui-s-paced grid), but can be more
ef-fi-cient. When us-ing
[2662]
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[] \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels =
NULL,[]
[2663]
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[]\T1/ptm/m/n/10 The panel func-tion used for the di-ag-o-nals. See ar-gu-ments
to
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\T1/pcr/m/n/10 diag.panel.splom \T1/ptm/m/n/10 to know what ar-gu-ments this fu
nc-tion is passed
[2664]
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\T1/ptm/m/n/10 and \T1/pcr/m/n/10 diag.panel \T1/ptm/m/n/10 from \T1/pcr/m/n/10
panel.pairs\T1/ptm/m/n/10 . Cur-rently ig-nored by
[2665] [2666]
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[]\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu
-ally passed on to
[2667]
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[] \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta
ils.n = 50))[]
[2668] [2669]
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\T1/ptm/m/n/10 ig-nores these. For types "r" and "smooth", these are passed on
to
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[]\T1/ptm/m/n/10 Most gen-er-ally, \T1/pcr/m/n/10 grid \T1/ptm/m/n/10 can be a
list of ar-gu-ments to be sup-plied to
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\T1/ptm/m/n/10 which is called with those ar-gu-ments. If spec-i-fied as a (pos
-si-bly
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\T1/ptm/m/n/10 named) nu-meric vec-tor, \T1/pcr/m/n/10 abline \T1/ptm/m/n/10 is
co-erced to a list. This al-lows ar-
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\T1/ptm/m/n/10 gu-ments of the form \T1/pcr/m/n/10 abline = c(0, 1)\T1/ptm/
m/n/10 , which adds the di-
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\T1/ptm/m/n/10 ag-o-nal line, or \T1/pcr/m/n/10 abline = c(h = 0, v = 0)\T1
/ptm/m/n/10 , which adds the
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\T1/ptm/m/n/10 x- and y-axes to the plot. Use the list form for finer con-trol;
e.g.,
[2670]
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[] \T1/pcr/m/n/9 ylab = list(c("horizontal=TRUE", "horizontal=FALSE"), y
= c(1/6, 4/6)),[]
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[] \T1/pcr/m/n/9 scales = list(alternating = c(0, 2), tck = c(0, 0.7), d
raw = FALSE),[]
[2671]
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[] \T1/pcr/m/n/10 font, fontfamily, fontface, cex, ..., identifier, nam
e.type)[]
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[] \T1/pcr/m/n/10 adj = c(0.5, 0.5), pos = NULL, offset = 0.5, ..., ident
ifier, name.type)[]
[2672] [2673] [2674]
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[]\T1/pcr/m/n/10 panel.grid(h=3, v=3, col, col.line, lty, lwd, x, y, ..., iden
tifier = "grid")[]
[2675]
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[]\T1/ptm/m/n/10 A log-i-cal flag de-ter-min-ing whether the de-fault graph-i-c
al pa-ram-e-ters for
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\T1/ptm/m/n/10 tings. The de-fault is to take them from the ``add.line'' set-ti
ngs. The
[2676] [2677] [2678] [2679] [2680] [2681] [2682] [2683]
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[]\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to \T1/pcr/m/n/10 panel.superpo
se
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\T1/ptm/m/n/10 from \T1/pcr/m/n/10 panel.superpose.2\T1/ptm/m/n/10 , and to \T1
/pcr/m/n/10 panel.groups \T1/ptm/m/n/10 from
[2684] [2685]
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[]\T1/pcr/m/n/10 prepanel.default.bwplot(x, y, horizontal, nlevels, origin, st
ack, ...)[]
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[]\T1/pcr/m/n/10 prepanel.default.histogram(x, breaks, equal.widths, type, nin
t, ...)[]
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[]\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr
ipts, ...)[]
[2686]
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[]\T1/ptm/m/n/10 details of his-togram cal-cu-la-tions. \T1/pcr/m/n/10 type \T1
/ptm/m/n/10 has a dif-fer-ent mean-ing in
[2687]
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[]\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti
es. If used with
[2688]
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[]\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr
ibed in
[2689] [2690]
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[] \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b
ottom$labels$labels)[]
[2691] [2692]
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[]\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su
nspot.year)),[]
[2693]
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[]\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
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\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
[2694] [2695] [2696] [2697] [2698] [2699] [2700]
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[]\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 ,
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\T1/pcr/m/n/10 "Velvet"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Peatland"\T1/ptm/m/n/10
, \T1/pcr/m/n/10 "Glabron"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "No. 457"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "Wisconsin No. 38"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 6300) in paragraph at lines 9627--9630
[]\T1/ptm/m/n/10 Factor with 6 lev-els: \T1/pcr/m/n/10 "Grand Rapids"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "Duluth"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "University Farm"
\T1/ptm/m/n/10 ,
[2701] [2702] [2703]pdfTeX warning (ext4): destination with the same identifier
(name{Rfn.melanoma}) has been already used, duplicate ignored
<to be read again>
\relax
l.9853 \aliasA{melanoma}{H\_melanoma}{melanoma}
[2704] [2705] [2706]
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[]\T1/ptm/m/n/10 Cause of death. A fac-tor with lev-els \T1/pcr/m/n/10 Alzheime
rs\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Cancer\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 10015--10020
\T1/pcr/m/n/10 Cerebrovascular diseases\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Diabetes
\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Flu and pneumonia\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 10015--10020
\T1/pcr/m/n/10 Heart disease\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Lower respiratory\T
1/ptm/m/n/10 , \T1/pcr/m/n/10 Nephritis\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Suicide\
T1/ptm/m/n/10 , and
[2707]
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[] \T1/pcr/m/n/9 par.settings = simpleTheme(pch = 16), auto.key = list(
columns = 2),[]
[2708]) (./mgcv-pkg.tex
Chapter 24.
[2709] [2710]
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[]\T1/pcr/m/n/10 bam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL,
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[] \T1/pcr/m/n/10 paraPen=NULL,chunk.size=10000,rho=0,AR.start=NULL,discret
e=FALSE,[]
[2711]
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[] \T1/pcr/m/n/10 coef=NULL,drop.unused.levels=TRUE,G=NULL,fit=TRUE,drop.in
tercept=NULL,...)[]
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
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\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known
scale.
[2712] [2713] [2714] [2715]
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[][][]\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 ,
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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 ,
Underfull \hbox (badness 10000) in paragraph at lines 361--368
[][]\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 ,
[2716]
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[]\T1/pcr/m/n/9 system.time(b2 <- bam(y ~ s(x0,bs=bs,k=k)+s(x1,bs=bs,k=k)+s(x2
,bs=bs,k=k)+[]
[2717] [2718] [2719]
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[]\T1/ptm/m/n/10 The link func-tion: one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/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
[2720] [2721]
Underfull \hbox (badness 10000) in paragraph at lines 697--698
[]\T1/ptm/m/n/10 First con-sider \T1/pcr/m/n/10 choldrop\T1/ptm/m/n/10 . If \T1
/pcr/m/n/10 R \T1/ptm/m/n/10 is up-per tri-an-gu-lar then
[2722]
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[]\T1/ptm/m/n/10 Choosing the ba-sis di-men-sion, and check-ing the choice, whe
n us-ing pe-nal-ized re-gres-sion
[2723]
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[]\T1/ptm/m/n/10 Wood, S.N. (2017) Gen-er-al-ized Ad-di-tive Mod-els: An In-tro
-duc-tion with R (2nd edi-tion).
[2724]
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[2726] [2727] [2728] [2729]
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[]\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h + 2*b$family$data$
q^.5),col=2)[]
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[]\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$
q^.5),col=2)[]
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[]\T1/pcr/m/n/9 bs <- gam(cbind(time,strata)~s(age,by=sex)+sex+s(nodes)+perfor
+rx+obstruct+adhere,[]
[2730]
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[]\T1/pcr/m/n/9 ## create index picking out elements of stored hazard info for
this stratum...[]
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[]\T1/pcr/m/n/9 if (i==1) plot(bs$family$data$tr[ind],exp(-bs$family$data$h[in
d]),type="l",ylim=c(0,1),[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1178--1178
[] \T1/pcr/m/n/9 lines(bs$family$data$tr[ind],exp(-bs$family$data$h[ind])
,lwd=2,col=i)[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1209--1209
[]\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)[]
[2731]
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[] \T1/pcr/m/n/9 if (inter) prg <- txtProgressBar(min = 0, max = length(sid),
initial = 0,[]
[2732]
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[] \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 1315--1315
[]\T1/pcr/m/n/9 pd <- data.frame(lapply(X=di,FUN=app,t=di$day,to=te)) ## inter
polate to te[]
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[2734] [2735] [2736] [2737] [2738] [2739] [2740] [2741]
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[]\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str
ict=FALSE)
[2742] [2743] [2744] [2745] [2746] [2747]
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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,[]
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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
[2748]
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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.
[2749] [2750]
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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
[2751] [2752]
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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 ,
Underfull \hbox (badness 10000) in paragraph at lines 2560--2566
[][]\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 ,
[2753]
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[2757] [2758] [2759] [2760] [2761] [2762] [2763]
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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)),[]
[2764] [2765] [2766] [2767] [2768] [2769]
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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
[2770] [2771]
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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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[2773] [2774]
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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)+[]
[2782] [2783] [2784]
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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,
[2785]
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[]\T1/pcr/m/n/10 niterPQL=20,verbosePQL=TRUE,method="ML",drop.unused.levels=TR
UE,...)[]
[2786]
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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
[2787]
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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 ( []
[]$\T1/pcr/m/n/10 https : / / cran . r-[]project .
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[]\T1/ptm/m/n/10 If `outer' it-er-a-tion has been used to fit the model (see []
[]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 ar-gu-ment
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[]\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic-
tion, used by
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[]\T1/ptm/m/n/10 A pre-fit gam ob-ject, as pro-duced by \T1/pcr/m/n/10 gam(...,
fit=FALSE) \T1/ptm/m/n/10 or
[2801]
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[] \T1/pcr/m/n/9 ## example using a scale location model for the motorcycle d
ata. A simple plotting[]
[2802]
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[] \T1/pcr/m/n/9 } else lines(xg,predict(din,xg)$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[]
[2804] [2805] [2806] [2807] [2808] [2809]
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[]\T1/pcr/m/n/10 jagam(formula,family=gaussian,data=list(),file,weights=NULL,n
a.action,
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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
[2810] [2811] [2812] [2813] [2814] [2815]
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[]\T1/pcr/m/n/10 ldTweedie(y,mu=y,p=1.5,phi=1,rho=NA,theta=NA,a=1.001,b=1.999,
all.derivs=FALSE)
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[]\T1/pcr/m/n/9 "The world is ruled by idiots because only an idiot would want
to rule the world.",[]
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[] \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y),
nthreads=1)[]
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[]\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra
nts EP/K005251/1 and
[2833] [2834]
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[]\T1/pcr/m/n/9 ## Alternative, better scaling example, using the discrete opt
ion with bam...[]
[2835] [2836]
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[]\T1/pcr/m/n/9 for (sim in c(1,7)) { ## cycle over uncorrelated and correlate
d covariates[]
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[] \T1/pcr/m/n/9 dat1[[dname[i]]][dat1[[by.name]]] <- mean(dat1[[dname[i]]]
,na.rm=TRUE)[]
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[2856]
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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 8655--8658
\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 8655--8658
\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 .
[2857]
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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
[2858] [2859] [2860]
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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,[]
[2861] [2862] [2863]
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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
[2864] [2865] [2866] [2867]
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[] \T1/pcr/m/n/10 na.action=na.pass,cluster=NULL,discrete=TRUE,n.thread
s=1,...)[]
[2868] [2869]
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[] \T1/pcr/m/n/10 na.action=na.pass,unconditional=FALSE,iterms.type=NUL
L,...)[]
[2870] [2871] [2872] [2873]
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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[]
[2875]
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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
[2876]
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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
[2877]
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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,
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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,
[2880] [2881] [2882] [2883]
Underfull \hbox (badness 1946) in paragraph at lines 10241--10248
[]\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.
[2884]
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[]\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat
,method="ML")[]
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[]\T1/ptm/m/n/10 the type of resid-u-als wanted. Usu-ally one of \T1/pcr/m/n/10
"deviance"\T1/ptm/m/n/10 ,
[2885] [2886] [2887] [2888] [2889]
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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)
[2890] [2891] [2892] [2893] [2894] [2895]
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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-
[2896]
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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
[2900]
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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 ,
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[][][]\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
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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
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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
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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 "1st order penalties: red tps; blue bs over (0,1); black bs
over (-.5,1.5)")[]
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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[]
[2909]
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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:[]
[2910]
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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
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\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
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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
[2913]
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[]\T1/pcr/m/n/9 b <- gam(y~s(x,z,bs="ds",m=c(1,.5),k=50),data=data) ## first
deriv penalty[]
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[]\T1/pcr/m/n/9 b1 <- gam(y~s(x,z,bs="ds",m=c(2,.5),k=50),data=data) ## modifi
ed 2nd deriv[]
[2914] [2915] [2916]
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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
[2917] [2918] [2919] [2920]
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[]\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m
ethod="REML")[]
[2921]
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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
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[]\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-
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\T1/ptm/m/n/10 ject, usu-ally gen-er-ated by a term \T1/pcr/m/n/10 s(x,...,bs="
re",)\T1/ptm/m/n/10 . For the
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\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"
[2925] [2926]
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[]\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with
2 variances[]
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[]\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a
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\T1/pcr/m/n/10 s(...,bs="so",xt=list(bnd=bnd,...)) \T1/ptm/m/n/10 term in a \T1
/pcr/m/n/10 gam \T1/ptm/m/n/10 for-
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[]\T1/pcr/m/n/9 ## notice NULL element in \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 xt\TS1
/pcr/m/n/9 ' \T1/pcr/m/n/9 list - to indicate no xt object for "cr" basis...[]
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[2932]
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[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths on the
sphere, via terms like
Underfull \hbox (badness 10000) in paragraph at lines 13091--13092
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[2933] [2934] [2935] [2936]
Underfull \hbox (badness 3396) in paragraph at lines 13352--13355
[][][]\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
[2937]
Underfull \hbox (badness 10000) in paragraph at lines 13397--13399
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[2938] [2939] [2940] [2941]
Underfull \hbox (badness 10000) in paragraph at lines 13621--13624
[]\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 13621--13624
\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
[2942]
Underfull \hbox (badness 10000) in paragraph at lines 13654--13658
[][][]\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 13654--13658
[][]\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 13654--13658
[][]\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 ,
[2943] [2944] [2945] [2946] [2947]
Underfull \hbox (badness 2158) in paragraph at lines 13944--13944
[]\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma-
trix from
[2948]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 14023--14023
[]\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0,
centre=FALSE)[]
[2949] [2950]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 14157--14157
[] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars
"),...)[]
[2951] [2952] [2953]
Underfull \hbox (badness 4846) in paragraph at lines 14288--14291
[]\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
[2954] [2955] [2956] [2957] [2958]
Underfull \vbox (badness 10000) has occurred while \output is active [2959]
[2960] [2961] [2962] [2963] [2964] [2965] [2966]
Underfull \hbox (badness 10000) in paragraph at lines 15113--15121
[]\T1/ptm/m/n/10 Suppose that \T1/pcr/m/n/10 m=1 \T1/ptm/m/n/10 and you fill an
ar-ray us-ing code like
Underfull \hbox (badness 10000) in paragraph at lines 15113--15121
\T1/pcr/m/n/10 for(i in 1:K) for(j in i:K) for(k in j:K) for(l in k:K)
[2967] [2968] [2969] [2970] [2971] [2972]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 15477--15477
[]\T1/pcr/m/n/10 vcov(object, freq = FALSE, dispersion = NULL,unconditional=FA
LSE, ...)[]
[2973] [2974] [2975] [2976] [2977]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 15771--15771
[]\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 15772--15772
[]\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 15784--15784
[]\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val
ues, to check we[]
[2978] [2979] [2980]) (./nlme-pkg.tex
Chapter 25.
[2981]
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
[2982]
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
[2983] [2984] [2985] [2986] [2987]
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,[]
[2988] [2989]
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 ---------------------------
---------------[]
[2990] [2991] [2992] [2993] [2994] [2995] [2996] [2997]
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"),[]
[2998]
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
[2999] [3000] [3001] [3002] [3003] [3004] [3005]
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 ,
[3006]
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
[3007] [3008] [3009] [3010] [3011]
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 ,
[3012]
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")[]
[3013]
Underfull \hbox (badness 1132) in paragraph at lines 2144--2146
[]\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac
ted us-ing the
[3014] [3015]
Underfull \hbox (badness 4168) in paragraph at lines 2255--2261
[][][]\T1/pcr/m/n/10 ACF.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corARMA[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T
1/pcr/m/n/10 Dim.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize
.corStruct[][][]\T1/ptm/m/n/10 ,
[3016]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2280--2280
[] \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[]
[3017] [3018] [3019] [3020] [3021] [3022] [3023] [3024]
Underfull \hbox (badness 10000) in paragraph at lines 2843--2847
[][][]\T1/pcr/m/n/10 corFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corMatr
ix.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 recalc.corStruct[][][]\T1
/ptm/m/n/10 ,
[3025] [3026] [3027] [3028] [3029] [3030] [3031] [3032] [3033] [3034] [3035]
[3036]
Underfull \hbox (badness 6493) in paragraph at lines 3579--3587
[][][]\T1/pcr/m/n/10 corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corGaus[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corSpher[][][]\T1/ptm
/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 ,
[3037] [3038] [3039] [3040] [3041] [3042] [3043] [3044] [3045] [3046] [3047]
[3048] [3049] [3050] [3051] [3052] [3053] [3054] [3055] [3056] [3057] [3058]
[3059] [3060]
Underfull \hbox (badness 10000) in paragraph at lines 5159--5163
[][][]\T1/pcr/m/n/10 getCovariate.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m
/n/10 getCovariate.data.frame[][][]\T1/ptm/m/n/10 ,
[3061] [3062] [3063] [3064] [3065]
Underfull \hbox (badness 10000) in paragraph at lines 5476--5480
[]\T1/ptm/m/n/10 Note that as from ver-sion 3.1-102, this only omits rows omit-
ted in the fit if
Underfull \hbox (badness 2671) in paragraph at lines 5476--5480
\T1/pcr/m/n/10 na.action = na.omit\T1/ptm/m/n/10 , and does not omit at all if
\T1/pcr/m/n/10 na.action = na.exclude\T1/ptm/m/n/10 .
[3066] [3067]
Underfull \hbox (badness 10000) in paragraph at lines 5591--5594
[][][]\T1/pcr/m/n/10 getGroupsFormula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10
getGroups.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getGroups.gls[][]
[]\T1/ptm/m/n/10 ,
[3068] [3069] [3070] [3071] [3072] [3073] [3074] [3075] [3076]
Underfull \hbox (badness 2799) in paragraph at lines 6097--6103
\T1/ptm/m/n/10 covariance ma-trix, ei-ther \T1/pcr/m/n/10 "random.effects" \T1/
ptm/m/n/10 for the random-effects
[3077]
Underfull \hbox (badness 7133) in paragraph at lines 6158--6162
[]\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in \
T1/pcr/m/n/10 model\T1/ptm/m/n/10 ,
[3078]
Underfull \hbox (badness 2057) in paragraph at lines 6242--6253
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsCon
trol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsObject[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gls[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gls[][][]\T1/ptm/m/n/10 ,
[3079]
Underfull \hbox (badness 10000) in paragraph at lines 6306--6308
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6338--6338
[]\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[]
[3080] [3081] [3082] [3083]
Underfull \hbox (badness 7133) in paragraph at lines 6556--6560
[]\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in \
T1/pcr/m/n/10 model\T1/ptm/m/n/10 ,
[3084]
Underfull \hbox (badness 10000) in paragraph at lines 6655--6661
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsCo
ntrol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsObject[][][]\T1/ptm/m/n/10 ,
[][]\T1/pcr/m/n/10 gnlsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict
.gnls[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (54.78088pt too wide) in paragraph at lines 6682--6682
[]\T1/pcr/m/n/10 gnlsControl(maxIter = 50, nlsMaxIter = 7, msMaxIter = 50, min
Scale = 0.001,
[3085]
Underfull \hbox (badness 10000) in paragraph at lines 6720--6722
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3086]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6750--6750
[]\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[]
[3087] [3088] [3089]
Underfull \hbox (badness 10000) in paragraph at lines 6993--7000
[][][]\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 ,
[3090]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7010--7010
[] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla
ry fissure" ),[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7018--7018
[]\T1/pcr/m/n/9 fm1 <- lme( Orth.new ) # fixed and groups formulae extracted
from object[]
Underfull \hbox (badness 2875) in paragraph at lines 7040--7042
[]\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
[3091] [3092] [3093]
Underfull \hbox (badness 10000) in paragraph at lines 7255--7260
[][][]\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 ,
[3094] [3095] [3096]
Underfull \hbox (badness 10000) in paragraph at lines 7407--7415
[]\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 7407--7415
\T1/ptm/m/n/10 tion and op-ti-miza-tion al-go-rithms used in \T1/pcr/m/n/10 lme
\T1/ptm/m/n/10 . De-faults to
Underfull \hbox (badness 1817) in paragraph at lines 7407--7415
\T1/pcr/m/n/10 list(niterEM=20, gradHess=TRUE)\T1/ptm/m/n/10 , im-ply-ing that
20 EM it-er-a-
Underfull \hbox (badness 3118) in paragraph at lines 7430--7433
[][][]\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 ,
[3097] [3098] [3099]
Underfull \hbox (badness 3354) in paragraph at lines 7645--7647
[]\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
[3100] [3101] [3102] [3103] [3104] [3105]
Underfull \hbox (badness 1642) in paragraph at lines 8037--8059
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o
f the form
[3106] [3107]
Underfull \hbox (badness 10000) in paragraph at lines 8157--8174
[][][]\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 8157--8174
[][]\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 8200--8200
[] \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data
= TRUE)[]
Underfull \hbox (badness 1642) in paragraph at lines 8209--8231
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o
f the form
[3108] [3109] [3110] [3111] [3112]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 8474--8474
[]\T1/pcr/m/n/10 lmeControl(maxIter = 50, msMaxIter = 50, tolerance = 1e-6, ni
terEM = 25,
Underfull \hbox (badness 10000) in paragraph at lines 8520--8522
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3113]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8558--8558
[]\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.8565 \aliasA{sigma}{lmeObject}{sigma}
[3114] [3115] [3116]
Underfull \hbox (badness 10000) in paragraph at lines 8726--8738
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 lmList\T1/ptm/m/n/10 , ei-ther a lin-ear fo
r-mula ob-ject of the form
[3117] [3118] [3119] [3120] [3121] [3122] [3123] [3124] [3125]
Underfull \hbox (badness 10000) in paragraph at lines 9317--9324
[][][]\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 9328--9328
[]\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me
thod = "ML")
[3126]
Underfull \hbox (badness 6300) in paragraph at lines 9410--9413
[]\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
[3127] [3128] [3129] [3130]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.Matrix}) has been already used, duplicate ignored
<to be read again>
\relax
l.9679 ...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.9679 ...rA{Matrix}{Assign Matrix Values}{Matrix}
[3131]
Underfull \hbox (badness 10000) in paragraph at lines 9699--9702
[]\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 9743--9746
[]\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 9743--9746
\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
[3132] [3133] [3134]
Underfull \hbox (badness 2435) in paragraph at lines 9917--9922
[]\T1/ptm/m/n/10 The model ma-tri-ces for each el-e-ment of \T1/pcr/m/n/10 form
ula(object)\T1/ptm/m/n/10 , cal-cu-lated us-ing \T1/pcr/m/n/10 data\T1/ptm/m/n/
10 ,
[3135] [3136] [3137] [3138] [3139]
Underfull \hbox (badness 7291) in paragraph at lines 10207--10209
[]\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
[3140] [3141] [3142]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10423--10423
[]\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation,
weights,
[3143]
Underfull \hbox (badness 1596) in paragraph at lines 10452--10478
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o
f the form
[3144] [3145] [3146]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10628--10628
[]\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation,
weights,[]
[3147] [3148]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 10779--10779
[] \T1/pcr/m/n/10 opt = c("nlminb", "nlm"), natural = TRUE, sigma =
NULL, ...)[]
Underfull \hbox (badness 2213) in paragraph at lines 10790--10795
[]\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[][][]
[3149]
Underfull \hbox (badness 10000) in paragraph at lines 10812--10816
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 10831--10833
[]\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 10867--10867
[]\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[]
[3150] [3151] [3152] [3153]
Overfull \hbox (96.18033pt too wide) in paragraph at lines 11123--11123
[]\T1/pcr/m/n/9 cfm1 <- confint(fm1) # via profiling each % FIXME: only *one*
message instead of one *each*[]
[3154] [3155] [3156] [3157] [3158] [3159] [3160] [3161] [3162] [3163] [3164]
[3165]
Underfull \hbox (badness 6268) in paragraph at lines 11902--11912
[][][]\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 ,
[3166] [3167] [3168] [3169]
Underfull \hbox (badness 10000) in paragraph at lines 12163--12169
[][][]\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 ,
[3170] [3171] [3172] [3173] [3174]
Underfull \hbox (badness 6876) in paragraph at lines 12485--12487
[]\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
[3175] [3176]
Underfull \hbox (badness 2452) in paragraph at lines 12641--12648
[][][]\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 ,
[3177]
Underfull \hbox (badness 10000) in paragraph at lines 12706--12712
[][][]\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 ,
[3178] [3179] [3180] [3181] [3182] [3183] [3184] [3185] [3186] [3187] [3188]
[3189] [3190] [3191]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13658--13658
[]\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline =
0, id = 0.05)[]
[3192]
Underfull \hbox (badness 10000) in paragraph at lines 13685--13688
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nffGroupedD
ata\T1/ptm/m/n/10 , rep-re-sent-ing a
Underfull \hbox (badness 6016) in paragraph at lines 13713--13716
[]\T1/ptm/m/n/10 an op-tional char-ac-ter string with the la-bel for the hor-i-
zon-tal axis.
Underfull \hbox (badness 2653) in paragraph at lines 13713--13716
\T1/ptm/m/n/10 De-fault is the \T1/pcr/m/n/10 y \T1/ptm/m/n/10 el-e-ments of \T
1/pcr/m/n/10 attr(object, "labels") \T1/ptm/m/n/10 and
Underfull \hbox (badness 1975) in paragraph at lines 13720--13723
[]\T1/ptm/m/n/10 an op-tional func-tion passed as the \T1/pcr/m/n/10 strip \T1/
ptm/m/n/10 ar-gu-ment to the \T1/pcr/m/n/10 dotplot
Underfull \hbox (badness 1838) in paragraph at lines 13728--13735
[]\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 13728--13735
\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
[3193]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 13785--13785
[]\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect,
panel,[]
Underfull \hbox (badness 10000) in paragraph at lines 13792--13795
[]\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 13792--13795
\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
[3194]
Underfull \hbox (badness 4582) in paragraph at lines 13820--13823
[]\T1/ptm/m/n/10 optional char-ac-ter strings with the la-bels for the plot. De
-fault is
Underfull \hbox (badness 2418) in paragraph at lines 13820--13823
\T1/ptm/m/n/10 the cor-re-spond-ing el-e-ments of \T1/pcr/m/n/10 attr(object,
"labels") \T1/ptm/m/n/10 and
Underfull \hbox (badness 2990) in paragraph at lines 13824--13827
[]\T1/ptm/m/n/10 an op-tional func-tion passed as the \T1/pcr/m/n/10 strip \T1/
ptm/m/n/10 ar-gu-ment to the \T1/pcr/m/n/10 xyplot
[3195]
Underfull \hbox (badness 10000) in paragraph at lines 13900--13903
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nmGroupedDa
ta\T1/ptm/m/n/10 , rep-re-sent-ing a
Underfull \hbox (badness 1472) in paragraph at lines 13925--13932
\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 ,
[3196]
Underfull \hbox (badness 10000) in paragraph at lines 13994--13996
[][][]\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 ,
[3197] [3198] [3199] [3200]
Underfull \hbox (badness 1540) in paragraph at lines 14209--14214
\T1/ptm/m/n/10 a \T1/pcr/m/n/10 loess \T1/ptm/m/n/10 smoother is added to the p
lot. If \T1/pcr/m/n/10 showModel = TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n/10 x \T1
/ptm/m/n/10 in-cludes an
Underfull \hbox (badness 1215) in paragraph at lines 14256--14258
[]\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis.
De-faults to
[3201] [3202] [3203] [3204] [3205]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 14500--14500
[]\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female",
"Male","Male"),[]
[3206] [3207] [3208] [3209] [3210] [3211] [3212] [3213] [3214]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.15153 ...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.15153 ...Extract Random Effects}{random.effects}
[3215] [3216] [3217]
[3218] [3219] [3220] [3221] [3222] [3223] [3224]
Underfull \hbox (badness 1009) in paragraph at lines 15810--15819
\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
[3225] [3226] [3227]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 15957--15957
[] \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi
st = FALSE, ...)[]
[3228] [3229] [3230] [3231]
Underfull \hbox (badness 10000) in paragraph at lines 16235--16253
[]\T1/ptm/m/n/10 any of the fol-low-ing: (i) a one-sided for-mula of the form
Underfull \hbox (badness 1708) in paragraph at lines 16235--16253
\T1/pcr/m/n/10 ~x1+...+xn | g1/.../gm\T1/ptm/m/n/10 , with \T1/pcr/m/n/10 x1+..
.+xn \T1/ptm/m/n/10 spec-i-fy-ing the model
[3232]
Underfull \hbox (badness 10000) in paragraph at lines 16292--16298
[][][]\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 ,
[3233]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 16323--16323
[] \T1/pcr/m/n/10 method = c("REML", "ML"), niterEM = c(40, 200), useG
en, ...)[]
[3234] [3235] [3236] [3237] [3238] [3239] [3240]
Underfull \hbox (badness 1728) in paragraph at lines 16812--16815
[]\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou
t-put in the
[3241] [3242] [3243] [3244] [3245]
Underfull \hbox (badness 1867) in paragraph at lines 17147--17156
\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 17147--17156
\T1/pcr/m/n/10 "Compound Symmetry" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdCompSymm
\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Diagonal"
Underfull \hbox (badness 10000) in paragraph at lines 17147--17156
\T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdDiag\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Multip
le of an Identity" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdIdent\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17147--17156
\T1/pcr/m/n/10 "General Positive-Definite, Natural Parametrization"
[3246]
Underfull \hbox (badness 10000) in paragraph at lines 17211--17219
[]\T1/ptm/m/n/10 an op-tional char-ac-ter string with a de-scrip-tion of the
Underfull \hbox (badness 10000) in paragraph at lines 17211--17219
\T1/pcr/m/n/10 varFunc \T1/ptm/m/n/10 class. De-fault de-pends on the method fu
nc-tion:
Underfull \hbox (badness 10000) in paragraph at lines 17211--17219
\T1/pcr/m/n/10 "Combination of variance functions" \T1/ptm/m/n/10 for \T1/pcr/m
/n/10 varComb\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17211--17219
\T1/pcr/m/n/10 "Constant plus power of covariate" \T1/ptm/m/n/10 for \T1/pcr/m/
n/10 varConstPower\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17211--17219
\T1/pcr/m/n/10 "Exponential of variance covariate" \T1/ptm/m/n/10 for \T1/pcr/m
/n/10 varExp\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17211--17219
\T1/pcr/m/n/10 "Different standard deviations per stratum" \T1/ptm/m/n/10 for
Underfull \hbox (badness 10000) in paragraph at lines 17211--17219
\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 ,
[3247] [3248] [3249] [3250]
Underfull \hbox (badness 10000) in paragraph at lines 17458--17465
[][][]\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 ,
[3251] [3252] [3253] [3254] [3255] [3256] [3257] [3258]
Underfull \hbox (badness 10000) in paragraph at lines 17993--18003
[][][]\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 17993--18003
[][]\T1/pcr/m/n/10 Variogram.corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10
Variogram.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corSphe
r[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 3579) in paragraph at lines 18031--18036
\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
[3259]
Underfull \hbox (badness 3579) in paragraph at lines 18095--18100
\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
[3260]
Underfull \hbox (badness 3579) in paragraph at lines 18158--18163
\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
[3261]
Underfull \hbox (badness 1577) in paragraph at lines 18219--18221
[]\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 18221--18226
\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
[3262]
Underfull \hbox (badness 3579) in paragraph at lines 18284--18289
\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
[3263]
Underfull \hbox (badness 10000) in paragraph at lines 18317--18326
[][][]\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 18317--18326
[][]\T1/pcr/m/n/10 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 V
ariogram.corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corRatio[][]
[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 3579) in paragraph at lines 18356--18361
\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
[3264] [3265] [3266]
Underfull \hbox (badness 1009) in paragraph at lines 18505--18514
\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
[3267] [3268]
Underfull \hbox (badness 1009) in paragraph at lines 18639--18648
\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
[3269] [3270] [3271] [3272] [3273] [3274] [3275] [3276]) (./nnet-pkg.tex
Chapter 26.
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.multinom}
) has been already used, duplicate ignored
<to be read again>
\relax
l.47 ...t Multinomial Log-linear Models}{multinom}
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ation with the same identifier (name{Rfn.multinom.1}) has been already used, du
plicate ignored
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\relax
l.47 ...t Multinomial Log-linear Models}{multinom}
[3277]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 70--70
[] \T1/pcr/m/n/10 contrasts = NULL, Hess = FALSE, summ = 0, censored =
FALSE,[]
Underfull \hbox (badness 10000) in paragraph at lines 78--87
[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[3278] [3279] [3280]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 369--369
[]\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size =
2, rang = 0.1,[]
[3281]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 426--426
[]\T1/pcr/m/n/9 targets <- matrix(c(rep(c(1,0,0),50), rep(c(0,1,0),50), rep(c(
0,0,1),50)),[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 429--429
[]\T1/pcr/m/n/9 ir1 <- nnet(ir[samp,], targets[samp,], size=2, rang=0.1, decay
=5e-4, maxit=200)[]
[3282]
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\T1/ptm/m/n/10 the cor-re-spond-ing class (which is prob-a-bly only use-ful if
the net was gen-er-ated by
[3283]
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[]\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size =
2, rang = 0.1,[]
[3284]) (./rpart-pkg.tex
Chapter 27.
[3285] [3286] [3287] [3288]
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[]\T1/pcr/m/n/10 labels(object, digits = 4, minlength = 1L, pretty, collapse =
TRUE, ...)[]
[3289]
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[]\T1/ptm/m/n/10 Vector of split la-bels (\T1/pcr/m/n/10 collapse = TRUE\T1/ptm
/m/n/10 ) or ma-trix of left and right splits
[3290] [3291] [3292]
Underfull \hbox (badness 1442) in paragraph at lines 591--597
[]\T1/ptm/m/n/10 if \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 , the leaf nodes will be
at the hor-i-zon-tal plot co-or-di-nates of
[3293] [3294]
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[] \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep =
""),[]
[3295]
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[]\T1/ptm/m/n/10 a plot of \T1/pcr/m/n/10 rpart \T1/ptm/m/n/10 is cre-ated us-i
ng the \T1/pcr/m/n/10 postscript \T1/ptm/m/n/10 driver, or the cur-rent de-vice
if
[3296]
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[]\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie
s, probabilities[]
[3297]
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[]\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d
igits"), ...)[]
[3298] [3299] [3300]
Underfull \hbox (badness 2310) in paragraph at lines 1113--1116
[]\T1/ptm/m/n/10 For re-gres-sion or \T1/pcr/m/n/10 anova \T1/ptm/m/n/10 trees
all three resid-ual def-i-ni-tions re-duce to
Overfull \hbox (6.78088pt too wide) in paragraph at lines 1163--1163
[]\T1/pcr/m/n/10 rpart(formula, data, weights, subset, na.action = na.rpart, m
ethod,
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1164--1164
[] \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos
t, ...)[]
Underfull \hbox (badness 2837) in paragraph at lines 1187--1196
[]\T1/ptm/m/n/10 one of \T1/pcr/m/n/10 "anova"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "
poisson"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "class" \T1/ptm/m/n/10 or \T1/pcr/m/n/1
0 "exp"\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 method
Underfull \hbox (badness 2088) in paragraph at lines 1187--1196
\T1/ptm/m/n/10 is miss-ing then the rou-tine tries to make an in-tel-li-gent gu
ess. If \T1/pcr/m/n/10 y
Underfull \hbox (badness 1817) in paragraph at lines 1187--1196
\T1/ptm/m/n/10 is a sur-vival ob-ject, then \T1/pcr/m/n/10 method = "exp" \T1/p
tm/m/n/10 is as-sumed, if \T1/pcr/m/n/10 y \T1/ptm/m/n/10 has 2
[3301]
Underfull \hbox (badness 2846) in paragraph at lines 1226--1228
[]\T1/ptm/m/n/10 a list of op-tions that con-trol de-tails of the \T1/pcr/m/n/1
0 rpart \T1/ptm/m/n/10 al-go-rithm. See
[3302]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1270--1270
[]\T1/pcr/m/n/9 par(mfrow = c(1,2), xpd = NA) # otherwise on some devices the
text is clipped[]
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[]\T1/pcr/m/n/10 rpart.control(minsplit = 20, minbucket = round(minsplit/3), c
p = 0.01,
Overfull \hbox (60.78088pt too wide) in paragraph at lines 1287--1287
[] \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate
= 2, xval = 10,[]
[3303] [3304] [3305] [3306] [3307] [3308]
Underfull \hbox (badness 1565) in paragraph at lines 1739--1742
[]\T1/ptm/m/n/10 the ploidy sta-tus of the tu-mor, from flow cy-tom-e-try. Val-
ues are `\T1/pcr/m/n/10 diploid\T1/ptm/m/n/10 ',
[3309] [3310]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1833--1833
[] \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n =
FALSE,[]
[3311] [3312] [3313]) (./spatial-pkg.tex [3314]
Chapter 28.
[3315] [3316] [3317] [3318] [3319] [3320]
Underfull \hbox (badness 10000) in paragraph at lines 423--427
[3321] [3322] [3323] [3324] [3325] [3326] [3327] [3328] [3329] [3330] [3331]
[3332] [3333]) (./survival-pkg.tex [3334]
Chapter 29.
[3335] [3336]
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[]\T1/pcr/m/n/9 aareg(formula = Surv(time, status) ~ age + sex + ph.ecog, data
= lung, nmin = 1[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 190--190
[]\T1/pcr/m/n/9 ## Not run: lines(lfit2[4], col=2) # Nearly the same, until t
he last point[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 193--193
[]\T1/pcr/m/n/9 # Chronic Granuomatous Disease. See section 8.5 of Therneau a
nd Grambsch.[]
[3337] [3338]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}
[3339] [3340]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 423--423
[]\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)[]
[3341]
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[] \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog),
lung)[]
[3342] [3343]
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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"),[]
[3345] [3346]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 805--805
[] \T1/pcr/m/n/9 subcoh = ~subcohort, id=~seqno, stratum=~instit, cohort.siz
e=stratsizes,[]
[3347] [3348] [3349]
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.
Overfull \hbox (4.38043pt too wide) in paragraph at lines 995--995
[]\T1/pcr/m/n/9 ppois(4, 10.24153) #chance of seeing 4 or fewer events wit
h large rate[]
[3350] [3351]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1110--1110
[]\T1/pcr/m/n/9 ## Not run: clogit(case ~ spontaneous + induced + strata(strat
um), data=infert)
[3352]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col
on}) has been already used, duplicate ignored
<to be read again>
\relax
l.1178 ...erapy for Stage B/C colon cancer}{colon}
[3353]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 1271--1271
[] \T1/pcr/m/n/10 cluster, ymin, ymax, timewt= c("n", "S", "S/G", "n/G", "n/G
2", "I"),[]
[3354] [3355] [3356] [3357] [3358] [3359]
Underfull \hbox (badness 1337) in paragraph at lines 1753--1757
[][][]\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 ,
[3360]
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[]\T1/pcr/m/n/10 iter.max = 20, toler.inf = sqrt(eps), outer.max = 10, timefix
=TRUE)[]
[3361] [3362] [3363] [3364] [3365] [3366]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2246--2246
[] \T1/pcr/m/n/9 [1] "extreme" "logistic" "gaussian" "weibull" "
exponential"[]
[3367] [3368] [3369] [3370]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 2495--2495
[]\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t
df = 5,[]
[3371] [3372] [3373] [3374] [3375]
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Overfull \hbox (15.18042pt too wide) in paragraph at lines 2812--2812
[]\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt
y(id), kidney)
Overfull \hbox (36.7804pt too wide) in paragraph at lines 2848--2848
[] \T1/pcr/m/n/9 factor(c(0, 1, 2,1,0,2), 0:2, c("censored", "progre
ssion", "death")))[]
Underfull \hbox (badness 1389) in paragraph at lines 2862--2864
[]\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
[3377]
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[]\T1/ptm/m/n/10 this pa-ram-e-ter is no longer nec-es-sary and is ig-nored. Se
e the note in
[3378]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 2995--2995
[] \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 )))[]
[3379] [3380] [3381] [3382] [3383]
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[]\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential
ly the same.[]
[3384] [3385] [3386] [3387]
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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 )))[]
[3388]
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[3390] [3391] [3392] [3393] [3394]
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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,[]
[3395] [3396]
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[]\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign),
collapse,[]
[3397]
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[]\T1/pcr/m/n/9 mresid <- (lung$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[]
[3398]
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[] \T1/pcr/m/n/9 predict(fit, reference="sample") + sum(coef(fit) * fit$means
, na.rm=TRUE)[]
[3399]
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[]\T1/pcr/m/n/9 pct <- 1:98/100 # The 100th percentile of predicted survival
is at +infinity[]
[3400] [3401]
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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
[3402] [3403]
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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, ...)[]
[3404] [3405] [3406]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 4787--4787
[] \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year=
entry.dt),[]
Underfull \hbox (badness 1540) in paragraph at lines 4842--4845
[]\T1/ptm/m/n/10 an ar-ray con-tain-ing the ex-pected num-ber of events (or per
-son years if
[3407]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 4889--4889
[]\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)) +[]
[3408] [3409] [3410] [3411] [3412]
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[3414]
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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
[3415] [3416] [3417] [3418] [3419]
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[]\T1/pcr/m/n/9 lfit1 <- survreg(Surv(time, status) ~ age + ridge(ph.ecog, the
ta=5), cancer)[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 5700--5700
[]\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.5705 ...ata from a soldering experiment}{solder}
pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.solder.1}) has been already used, dupl
icate ignored
<to be read again>
\relax
l.5705 ...ata from a soldering experiment}{solder}
[3420]
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[]\T1/pcr/m/n/10 statefig(layout, connect, margin = 0.03, box = TRUE, cex = 1,
col = 1,
[3421] [3422] [3423] [3424] [3425] [3426]
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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,[]
[3427] [3428] [3429] [3430]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 6459--6459
[] \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 ),[]
[3431] [3432]
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 length \T1/ptm/m/n/10 of a \T1/pcr/m/n/10 S
urv \T1/ptm/m/n/10 ob-ject is the num-ber of sur-vival times
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\T1/ptm/m/n/10 it con-tains, not the num-ber of items re-quired to en-code it,
e.g.,
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\T1/pcr/m/n/10 x <- Surv(1:4, 5:9, c(1,0,1,0)); length(x) \T1/ptm/m/n/10 has a
value of 4. Like-
Underfull \hbox (badness 1253) in paragraph at lines 6733--6736
[]\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
[3434] [3435]
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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
[3436]
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[] \T1/pcr/m/n/9 rmap= list(age=(accept.dt - birth.dt), sex=1
, year=accept.dt),[]
[3437]
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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
[3438]
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[]\T1/ptm/m/n/10 numeric value to scale the re-sults. If \T1/pcr/m/n/10 ratetab
le \T1/ptm/m/n/10 is in units/day,
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[] \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d
t-entry.dt)),[]
[3439]
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[]\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival
by 1/2 years[]
[3440] [3441] [3442]
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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 ,
[3443]
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[] \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit",
"arcsin"),[]
[3444] [3445]
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[]\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored
(status=3),[]
[3446] [3447]
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[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the er-ror. Pos-si-ble val-
ues are
[3448] [3449]
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[]\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored
(status=3),[]
[3450] [3451] [3452] [3453]
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[]\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit,
survtype,
[3454]
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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
[3455] [3456]
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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 ,
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\T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 ,\T1/pcr/m/n/10 "lognormal" \T1/ptm/m/n
/10 and \T1/pcr/m/n/10 "loglogistic"\T1/ptm/m/n/10 . Oth-er-wise, it is
[3457]
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[]\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi
on. The survreg[]
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[3459] [3460]
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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 )[]
[3461]
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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 )[]
[3462] [3463] [3464] [3465] [3466]
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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)[]
[3467] [3468] [3469] [3470] [3471] [3472]pdfTeX warning (ext4): destination wit
h the same identifier (name{Rfn.xtfrm.Surv}) has been already used, duplicate i
gnored
<to be read again>
\relax
l.9488 ...ting order for Surv objects}{xtfrm.Surv}
[3473]
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[]\T1/pcr/m/n/10 levels, test = c("global", "trend", "pairwise"), predict = "l
inear",[]
[3474] [3475] [3476]) (./fullrefman.ind [3477] [3478] [3479] [3480] [3481]
[3482] [3483] [3484] [3485] [3486] [3487] [3488] [3489] [3490] [3491] [3492]
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[3498] [3499] [3500] [3501] [3502]
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[]| \T1/pcr/m/n/10 smooth.construct.tp.smooth.spec\T1/ptm/m/n/10 ,
[3503] [3504]
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[]| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 ,
[3505] [3506] [3507] [3508] [3509] [3510] [3511] [3512]
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[]\T1/pcr/m/n/10 qr.qty,sparseQR,ddenseMatrix-method
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[]\T1/pcr/m/n/10 qr.qy,sparseQR,ddenseMatrix-method
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[]\T1/pcr/m/n/10 qr.resid,sparseQR,ddenseMatrix-method
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[]\T1/pcr/m/n/10 qr.resid,sparseQR,numeric-method
[3599]
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[]\T1/pcr/m/n/10 R_AVAILABLE_PACKAGES_CACHE_CONTROL_MAX_AGE
[3600]
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[]\T1/pcr/m/n/10 rbind2,atomicVector,ddiMatrix-method
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[]\T1/pcr/m/n/10 rbind2,atomicVector,ldiMatrix-method
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[]\T1/pcr/m/n/10 rbind2,atomicVector,Matrix-method
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[]\T1/pcr/m/n/10 rbind2,ddiMatrix,atomicVector-method
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[]\T1/pcr/m/n/10 rbind2,denseMatrix,denseMatrix-method
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[]\T1/pcr/m/n/10 rbind2,denseMatrix,matrix-method
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[]\T1/pcr/m/n/10 rbind2,diagonalMatrix,sparseMatrix-method
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[]\T1/pcr/m/n/10 rbind2,indMatrix,indMatrix-method
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[]\T1/pcr/m/n/10 rbind2,ldiMatrix,atomicVector-method
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[]\T1/pcr/m/n/10 rbind2,Matrix,atomicVector-method
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[]\T1/pcr/m/n/10 rbind2,matrix,denseMatrix-method
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[]\T1/pcr/m/n/10 rbind2,matrix,sparseMatrix-method
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[]\T1/pcr/m/n/10 rbind2,numeric,denseMatrix-method
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[]\T1/pcr/m/n/10 rbind2,numeric,sparseMatrix-method
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[]\T1/pcr/m/n/10 rbind2,sparseMatrix,denseMatrix-method
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[]\T1/pcr/m/n/10 rcond,ddenseMatrix,character-method
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[]\T1/pcr/m/n/10 rcond,ddenseMatrix,missing-method
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[]\T1/pcr/m/n/10 rcond,denseMatrix,character-method
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[]\T1/pcr/m/n/10 rcond,dgeMatrix,character-method
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[]\T1/pcr/m/n/10 rcond,dpoMatrix,character-method
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[]\T1/pcr/m/n/10 rcond,dppMatrix,character-method
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[]\T1/pcr/m/n/10 rcond,sparseMatrix,character-method
[3602] [3603] [3604] [3605] [3606]
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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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[]\T1/pcr/m/n/10 Schur,generalMatrix,missing-method
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[]\T1/pcr/m/n/10 Schur,symmetricMatrix,logical-method
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[]\T1/pcr/m/n/10 Schur,symmetricMatrix,missing-method
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[]\T1/pcr/m/n/10 Schur,triangularMatrix,logical-method
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[]\T1/pcr/m/n/10 Schur,triangularMatrix,missing-method
[3607] [3608]
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[]\T1/pcr/m/n/10 show,genericFunctionWithTrace-method
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[3609]
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[]\T1/pcr/m/n/10 solve,CHMfactor,ddenseMatrix-method
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[]\T1/pcr/m/n/10 solve,CHMfactor,diagonalMatrix-method
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[]\T1/pcr/m/n/10 solve,dpoMatrix,dgeMatrix-method
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[]\T1/pcr/m/n/10 solve,dppMatrix,dgeMatrix-method
[3611]
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[]\T1/pcr/m/n/10 solve,dsCMatrix,ddenseMatrix-method
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[]\T1/pcr/m/n/10 solve,dtCMatrix,CsparseMatrix-method
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[]\T1/pcr/m/n/10 solve,dtCMatrix,dgeMatrix-method
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[]\T1/pcr/m/n/10 solve,Matrix,diagonalMatrix-method
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[]\T1/pcr/m/n/10 solve,Matrix,sparseVector-method
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[]\T1/pcr/m/n/10 solve,MatrixFactorization,ANY-method
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[]\T1/pcr/m/n/10 solve,MatrixFactorization,missing-method
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[]\T1/pcr/m/n/10 solve,MatrixFactorization,numeric-method
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[]\T1/pcr/m/n/10 solve,TsparseMatrix,missing-method
[3612]
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[3613] [3614]
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[]\T1/pcr/m/n/10 summarize_check_packages_in_dir_depends
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[]\T1/pcr/m/n/10 summarize_check_packages_in_dir_results
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[3615] [3616] [3617] [3618] [3619]
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[]\T1/pcr/m/n/10 tcrossprod,ANY,symmetricMatrix-method
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[3620]
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b>
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+ 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/cluster/libs/cluster.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/class/libs/class.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/rpart/libs/rpart.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/lattice/libs/lattice.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/nnet/libs/nnet.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/spatial/libs/spatial.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/parallel/libs/parallel.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/tcltk/libs/tcltk.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/splines/libs/splines.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/methods/libs/methods.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/stats/libs/stats.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/graphics/libs/graphics.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/grDevices/libs/cairo.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/grDevices/libs/grDevices.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/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.18477
+ umask 022
+ /bin/mkdir -p /usr/src/RPM/BUILD
+ cd /usr/src/RPM/BUILD
+ cd R-3.5.3
+ export TZ=
+ TZ=
+ make check
make: Entering directory '/usr/src/RPM/BUILD/R-3.5.3'
make[1]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/tests'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/tests'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/tests/Examples'
Testing examples for package 'base'
Testing examples for package 'tools'
comparing 'tools-Ex.Rout' to 'tools-Ex.Rout.save' ... OK
Testing examples for package 'utils'
Testing examples for package 'grDevices'
comparing 'grDevices-Ex.Rout' to 'grDevices-Ex.Rout.save' ... OK
Testing examples for package 'graphics'
comparing 'graphics-Ex.Rout' to 'graphics-Ex.Rout.save' ... OK
Testing examples for package 'stats'
comparing 'stats-Ex.Rout' to 'stats-Ex.Rout.save' ... NOTE
6599c6599
< Grand Mean: 291.5937
---
> Grand Mean: 291.5938
15143c15143
< Grand Mean: 291.5937
---
> Grand Mean: 291.5938
17463c17463
< assertCondition: caught "error"
---
> assertCondition: caught 'error'
Testing examples for package 'datasets'
comparing 'datasets-Ex.Rout' to 'datasets-Ex.Rout.save' ... OK
Testing examples for package 'methods'
Testing examples for package 'grid'
comparing 'grid-Ex.Rout' to 'grid-Ex.Rout.save' ... OK
Testing examples for package 'splines'
comparing 'splines-Ex.Rout' to 'splines-Ex.Rout.save' ... OK
Testing examples for package 'stats4'
comparing 'stats4-Ex.Rout' to 'stats4-Ex.Rout.save' ... OK
Testing examples for package 'tcltk'
Testing examples for package 'compiler'
Testing examples for package 'parallel'
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/tests/Examples'
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/tests'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/tests'
running strict specific tests
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/tests'
running code in 'eval-etc.R' ... OK
comparing 'eval-etc.Rout' to './eval-etc.Rout.save' ... OK
running code in 'simple-true.R' ... OK
comparing 'simple-true.Rout' to './simple-true.Rout.save' ... OK
running code in 'arith-true.R' ... OK
comparing 'arith-true.Rout' to './arith-true.Rout.save' ... OK
running code in 'arith.R' ... OK
comparing 'arith.Rout' to './arith.Rout.save' ... OK
running code in 'lm-tests.R' ... OK
comparing 'lm-tests.Rout' to './lm-tests.Rout.save' ... OK
running code in 'ok-errors.R' ... OK
comparing 'ok-errors.Rout' to './ok-errors.Rout.save' ... OK
running code in 'method-dispatch.R' ... OK
comparing 'method-dispatch.Rout' to './method-dispatch.Rout.save' ... OK
running code in 'any-all.R' ... OK
comparing 'any-all.Rout' to './any-all.Rout.save' ... OK
running code in 'd-p-q-r-tests.R' ... OK
comparing 'd-p-q-r-tests.Rout' to './d-p-q-r-tests.Rout.save' ... OK
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/tests'
running sloppy specific tests
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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' ...33c33
< [1] "2040-07-01 12:00:00 GMT"
---
> [1] "2040-07-01 12:00:00 BST"
44c44
< [1] "2040-07-01 12:00:00 EST"
---
> [1] "2040-07-01 12:00:00 EDT"
OK
running code in 'iec60559.R' ... OK
comparing 'iec60559.Rout' to './iec60559.Rout.save' ... OK
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/tests'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/tests'
checking Sys.timezone ...
make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/tests'
running code in 'timezone.R' ...make[4]: *** [Makefile.common:105: timezone.Rout] Error 1
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/tests'
Sys.timezone() appears unknown
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/tests'
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/tests'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/tests'
running regression tests ...
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/tests'
running code in 'array-subset.R' ... OK
running code in 'reg-tests-1a.R' ... OK
running code in 'reg-tests-1b.R' ... OK
running code in 'reg-tests-1c.R' ... OK
running code in 'reg-tests-1d.R' ... OK
running code in 'reg-tests-2.R' ... OK
comparing 'reg-tests-2.Rout' to './reg-tests-2.Rout.save' ... OK
running code in 'reg-examples1.R' ... OK
running code in 'reg-examples2.R' ... OK
running code in 'reg-packages.R' ... OK
running code in 'p-qbeta-strict-tst.R' ... OK
running code in 'r-strict-tst.R' ... OK
running code in 'reg-IO.R' ... OK
comparing 'reg-IO.Rout' to './reg-IO.Rout.save' ... OK
running code in 'reg-IO2.R' ... OK
comparing 'reg-IO2.Rout' to './reg-IO2.Rout.save' ... OK
running code in 'reg-plot.R' ... OK
comparing 'reg-plot.pdf' to './reg-plot.pdf.save' ... OK
running code in 'reg-S4-examples.R' ... OK
running code in 'reg-BLAS.R' ... OK
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/tests'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/tests'
running code in 'reg-tests-3.R' ... OK
comparing 'reg-tests-3.Rout' to './reg-tests-3.Rout.save' ... OK
running code in 'reg-examples3.R' ... OK
comparing 'reg-examples3.Rout' to './reg-examples3.Rout.save' ...340c340
< Achieved convergence tolerance: 9.33e-07
---
> Achieved convergence tolerance: 9.32e-07
407c407
< Achieved convergence tolerance: 2.19e-06
---
> Achieved convergence tolerance: 2.17e-06
OK
running tests of plotting Latin-1
expect failure or some differences if not in a Latin-1 or UTF-8 locale
running code in 'reg-plot-latin1.R' ... FAILED
running code in 'reg-S4.R' ... OK
comparing 'reg-S4.Rout' to './reg-S4.Rout.save' ... OK
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/tests'
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/tests'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/tests'
running tests of Internet functions
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/tests'
running code in 'internet.R' ... OK
comparing 'internet.Rout' to './internet.Rout.save' ...8,10c8,247
< Warning message:
< In nsl("cran.r-project.org") :
< nsl() was unable to resolve host 'cran.r-project.org'
---
> >
> > # test do_download (and "record" #{packages}):
> > ap <- available.packages(contrib.url("http://cran.r-project.org"))
> > ## IGNORE_RDIFF_END
> >
> > # test url connections on http
> > zz <- url("http://cran.r-project.org/")
> > readLines(zz)
> [1] "<!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-3.5.3/tests'
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/tests'
make[1]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/tests'
make: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3'
+ exit 0
Processing files: R-base-3.5.3-alt1
Executing(%doc): /bin/sh -e /usr/src/tmp/rpm-tmp.96798
+ umask 022
+ /bin/mkdir -p /usr/src/RPM/BUILD
+ cd /usr/src/RPM/BUILD
+ cd R-3.5.3
+ DOCDIR=/usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-3.5.3
+ export DOCDIR
+ rm -rf /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-3.5.3
+ /bin/mkdir -p /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-3.5.3
+ cp -prL doc/NEWS README /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-3.5.3
+ chmod -R go-w /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-3.5.3
+ chmod -R a+rX /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-3.5.3
+ exit 0
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Finding Provides (using /usr/lib/rpm/find-provides)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.2ou1e2
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: 1193 symbols, 21 bpp
++ /bin/sed -e '/^libR\.so/{p;s/R/R-2.11/}'
--- find-provides-deps 2019-11-24 04:01:36.928458362 +0000
+++ filter-provides-deps 2019-11-24 04:01:36.930458342 +0000
@@ -1 +1,2 @@
libR.so()(64bit) = set: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
+libR-2.11.so()(64bit) = set:odjvQNYfHFGF6Xo9rSYpedG8BII3EakgydO9cuf3TxqqZyO7yMvQ7wSiUTrcy7nNqGiflliOlRYkEVx3WbfE9EMjzuK8DfBqYQcAifd5xG3BauIcFNL1sZ76iqxUM9hRH43rPONzmSAG7LsxwROHTsK033i8b0gJi5VZjAEWcRCCPuZbOjbw5ZapXarSwbze7OXk9oZitxqybLaksw9aaqOHEnB223TfEVsYBaZxnGEwKdkBoh0ZIRTiaMlYFyDDP9NEVlf0k9nKqTQLgGT84AEkyBhQwfRSwRA0YgRCkFogdJEmuP6RN1espwjZ9zAy0UdgjefE70tytnRStRZEXi0mTOn4e8bbq38e4clbqXZIOCcwWzxBuVc2C8BizZyXUg0lsMgMo7KG8LXMZ6juhZkkPEg9PEW1XNyiZjUYr88T0K4m1VyDBJMZzxU0obgFvsZrcjj2kzEsMVVoTeGyZi2tJk4mSb3VIkEM49lU87j7ZyIddk4Y0aLn19nimTu0LddCZCycnoIBi1r9TC7h8ZmccJLISk6aCoFpqQJ3iFKgSntpZk034k2VOoZ0L8ZHy30mTX4t1ZAsmGCEwS2V8foRvdfffpYq45gGEjgF100a60TrTexlIV4iOJZ9Wo5lC5t2rcS2qunxQqytYaTyPiUPSgdUvaWUpWXtuD72mg20Pa7T45brAXK91D6u5e8eG8IHh30gUCeUqNwVV0Y61vntnZfJvjmpZa4wr0Dbizdh51stjg0hVwQcHxgEE0uVgcZxz1LKkarm5KEtPzv0tDGiUtM6JIZ5jijeePeqEsvdkAuMij9Z3gnAh1y8jkuRTUgjuHRjXrw8pyTG8ihTY1w3ZBbZEoCp9S7TdN6Y8Lc6u2H6hkuTwSgUhl97T1KZxwx7nTZoq20bQuU7FwUbaOh7RVr54iYtw8fMj0q9s0EYGWBxatviZAgKsopVq81j1Z03OTyFJLuw8epTGv9cIjnWTax6Krqq4UuGuYn7V6Ru0Z2gbXMfwqnEs7runz9Xki9HbNJw0QfkEItxFOZ14XCppeiByhS88ANiDOCk60lubLQr8g453AU6RWd91Z5XHSYzA1o1qi2VS3l6wvvWZkngZG4oO4mwooIzBjCyvicnaMsAMdgbh92wsZuZKdylwyHcByxC90X2NCN9cBnQet0YgOjoRHEUWN3xL4zTp2Cik8hFDpDyC1tNeaOq2Ijuba7TcYWkp4pmOo0pkSNfBcy46cixBUFBJZDbl6nFvK3G3yZHV4IhuloZx6DFelZLVkfZ8gZBbSBd4uFpBb6c8BeOMo5NfiwbC7isMKiPiuPmatTNv7wc07q4WiDk8C29wrPbFPqcSgdLqQXm4ylx9eBZqwW9v1B4XGv7nm0Z57bxcsMZIhCpCaUSR8gM0WOoRL9kJVOIsodv0YizyDi4e8gaPIbbm3a0iCg8lDHHkL0Wry3z1lVY4tfY6ZygnmjOXBKaEDs6EV2gFN3TzWOJdZnP8WdufuSantDLrapEMoBmhoUcXisBmwYuBkBkgORF3VOlQhAfC3EkN7v8uN8KwK74s42QxL6m4yhod1xXUcExcU12kXTgRjy2QoSmJtgT61g53urvi0zjG7qO11aooCh2JsOv1S7f8yD4y64MGNY5gnYl1TkkWAn4YcEDNnkO0naPgTpu5taTaZiCroA0Ka94U1WycQhZ2nL9aqclymCa90bPssTagwluO881jZGTro2DWqORfQ5GdGsgP2kDr397h0YF9KCeKE8bcTxbOZzgS0Q0zZKjxHAzp3pBrZjZdCabv42EE112tc2IIYGa39ctTbpHSQoOx4kKcS9ZA7MUN0oZpqnqx2sV4vcBs0zdB5uAQsKeCh9Atc1rRm7Pv4eo1z0leEZufigxYwssXb92bbB7dSpe9deAF0WoJQShuhtLC9yWBGXdSRjwPwY0P0cvziOeQ8DMi2lvXYSfoyFFCZ0xZrV9Xn6IVcZ9WdoaxRLt6khTyoAyR1UHD0Wf3Dwsho05WHTnIdrsAqdvAcMcvIBBpKWFlc0kbCSOKvsUI0QmgsKQpvPRJEfRK3JNv8YDw8kx00Z2wZ8IzieQdsgz6j7ATazLZuX6g2NJhr4aIVyBhOWuLHMIvqZoSk8aw5Fo1U3EQKIT3vC1yulAYPDAcLUUe0NZ7BPX5fegeyXaudMKqduSDIVQGXmvq9NvbjjI9q9KBK1CuUZwNy7MVYqJLYFmlsAyZoVblDOkCED91dtYh288weYAnQZ5jPtZL5IE0OyF9qq5PSD3hw7srebwxZgcO6F9Jh0TZjkU1FCmwLVGcc9K95Mc7Mu5RlZA1viuU4gQGgiepzvZCAZ1UwUoP2UPFPZ6UKSmwQvCas26oMjiW4YcLeR9LIgTjZE9K4u8IzC8kc01uQELl2XoTdaiRVdddyqnjXm6kSZkNIa0JuXUXkMyxrodlCF18PZjkQW0jfpLXdo0vY053
Finding Requires (using /usr/lib/rpm/find-requires)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.t3lP6W
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,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_2.2.5)(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.64()(64bit) >= set:rouin2ooZp9tgudEa9b7dNJZ60, libicuuc.so.64()(64bit) >= set:pmj2RkjF3gfi2hEq1, 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), libopenblas.so.0()(64bit) >= set:rme9dGe009CqZyeEKu0c959bA01WKVsu0KL3f0MzHG9G3SAPMCzdZ2ZyhPe7xLi5vYvWeHEOFls8vqO9WfXluFSG02, libpango-1.0.so.0()(64bit) >= set:miPmiaRgNQ6cD75j31i4ky6SMMCoRQ1, libpangocairo-1.0.so.0()(64bit) >= set:jhWzZgd5, libpcre.so.3()(64bit) >= set:ieELhsZ4oFM1uTpGS8bAqz69j4, 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:nidQ8PMktsCwid18OsyEUS8ifZzElko8gle73YghFZmboE0sZwI3S2Gz6RwZADa29NiWZu0BVGKnVqwyZw4mp, librt.so.1(GLIBC_2.2.5)(64bit), libtiff.so.5()(64bit) >= set:lhyG9VP2iv3ttOWkLJhCwlrr, libz.so.1()(64bit) >= set:kgb6dgb5xDnazO8BhqfiJqdZd6eIL9, rtld(GNU_HASH), sh
Requires(rpmlib): rpmlib(SetVersions)
Finding debuginfo files (using /usr/lib/rpm/find-debuginfo-files)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.cnKE1X
Creating R-base-debuginfo package
Processing files: R-full-3.5.3-alt1
Requires: R-devel = 3.5.3-alt1, R-tcltk = 3.5.3-alt1, R-doc-html = 3.5.3-alt1, gcc-c++, gcc-fortran, liblapack-devel, make
Processing files: R-devel-3.5.3-alt1
Finding Provides (using /usr/lib/rpm/find-provides)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.9jHAc3
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.MmWI1b
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,tcl,typelib)
/usr/src/tmp/R-base-buildroot/usr/include/R/R_ext/GraphicsDevice.h:43:4: error: #error R_ext/GraphicsEngine.h must be included first, and includes this header
# error R_ext/GraphicsEngine.h must be included first, and includes this header
^~~~~
cpp.req: /usr/src/tmp/R-base-buildroot/usr/include/R/R_ext/GraphicsDevice.h: cpp failed, trying c++ mode
/usr/src/tmp/R-base-buildroot/usr/include/R/R_ext/GraphicsDevice.h:43:4: error: #error R_ext/GraphicsEngine.h must be included first, and includes this header
# error R_ext/GraphicsEngine.h must be included first, and includes this header
^~~~~
cpp.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/include/R/R_ext/GraphicsDevice.h: cpp failed
find-requires: FINDPACKAGE-COMMANDS: chmod mkdir rm rmdir
Provides: pkgconfig(libR) = 3.5.3
Requires: /bin/sh, /usr/bin/libtool, /usr/lib64/R/lib/libR.so, /usr/lib64/pkgconfig, coreutils
Requires(pre): R-base = 3.5.3-alt1
Requires(postun): R-base = 3.5.3-alt1
Finding debuginfo files (using /usr/lib/rpm/find-debuginfo-files)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.bEOtIq
Processing files: R-tcltk-3.5.3-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.UjWSAI
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.LlvbE3
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,tcl,typelib)
Provides: tcl(::Utility) = 1.0, tcl(::Utility::dump) = 1.0, tcl(::Utility::expand) = 1.0, tcl(::Utility::number) = 1.0, tcl(::Utility::string) = 1.0, tcl(::Utility::tk) = 1.0, tcl(Hierarchy) = 2.0, tcl(PBar) = 1.0, tcl(Widget) = 2.0
Requires: R-base = 3.5.3-alt1, libR.so()(64bit) >= set:oiZ4ZDvavdS7yJmmEm1yk76RAJNZigoIdZ4rGSanE12warZ61UkMZtzOOW0cQ6tLN8BjJrkKZnL1TEzhiItObZCaSl9pqVwPzwTv35ZmWMAXnz5WOpBZwwMBble1hwYqhmdgOF2MNqAeQO4ABz2QjcXaAt0mBDLIbcof, libc.so.6(GLIBC_2.2.5)(64bit), libc.so.6(GLIBC_2.3.4)(64bit), libc.so.6(GLIBC_2.4)(64bit), libtcl8.6.so()(64bit) >= set:nhgjl7axi5LXwZCwtKzEgR46OGPDdUhperIBMUpAQNxfXAzzCME2ZC3VjYspFcvGIvhP7CaHXaui690CwrRamfbKeqMwV4FNim2oZ0Yf9OWVxM1, libtk8.6.so()(64bit) >= set:mkluxApv1, rtld(GNU_HASH), tcl(Tk)
Requires(rpmlib): rpmlib(SetVersions)
Finding debuginfo files (using /usr/lib/rpm/find-debuginfo-files)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.CjK2Tr
Creating R-tcltk-debuginfo package
Processing files: R-doc-html-3.5.3-alt1
Finding Provides (using /usr/lib/rpm/find-provides)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.LKbJsT
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.KIIKko
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,tcl,typelib)
Requires: R-base = 3.5.3-alt1
Processing files: R-doc-pdf-3.5.3-alt1
Finding Provides (using /usr/lib/rpm/find-provides)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.B6w8xW
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.eZmZwy
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,tcl,typelib)
Conflicts: R-base > 3.5.3, R-base < 3.5.3
Processing files: R-doc-info-3.5.3-alt1
Finding Provides (using /usr/lib/rpm/find-provides)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.vmQQMd
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.OYqTxW
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,tcl,typelib)
Conflicts: R-base > 3.5.3, R-base < 3.5.3
Processing files: R-base-debuginfo-3.5.3-alt1
Finding Provides (using /usr/lib/rpm/find-provides)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.1JbwOI
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.wGboky
find-requires: running scripts (debuginfo)
Provides: debug64(libR.so)
Requires: R-base = 3.5.3-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.64), debug64(libicuuc.so.64), debug64(libjpeg.so.62), debug64(liblapack.so.4), debug64(liblzma.so.5), debug64(libm.so.6), debug64(libopenblas.so.0), debug64(libpango-1.0.so.0), debug64(libpangocairo-1.0.so.0), debug64(libpcre.so.3), debug64(libpng16.so.16), debug64(libpthread.so.0), debug64(libreadline.so.7), debug64(librt.so.1), debug64(libtiff.so.5), debug64(libz.so.1)
Processing files: R-tcltk-debuginfo-3.5.3-alt1
Finding Provides (using /usr/lib/rpm/find-provides)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.V9tt8y
find-provides: running scripts (debuginfo)
Finding Requires (using /usr/lib/rpm/find-requires)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.snWO6C
find-requires: running scripts (debuginfo)
Requires: R-tcltk = 3.5.3-alt1, debug64(libR.so), debug64(libc.so.6), debug64(libtcl8.6.so), debug64(libtk8.6.so)
Adding to R-devel a strict dependency on R-base
Adding to R-tcltk a strict dependency on R-base
Adding to R-doc-html a strict dependency on R-base
Adding to R-base-debuginfo a strict dependency on R-base
Adding to R-full a strict dependency on R-devel
Adding to R-full a strict dependency on R-tcltk
Adding to R-full a strict dependency on R-doc-html
Adding to R-tcltk-debuginfo a strict dependency on R-tcltk
Adding to R-devel a strict dependency on R-base
Adding to R-tcltk-debuginfo a strict dependency on R-base-debuginfo
Removing from R-tcltk-debuginfo 12 sources provided by R-base-debuginfo
also prunning dir /usr/src/debug/R-3.5.3/include/R_ext
also prunning dir /usr/src/debug/R-3.5.3/src/include
also prunning dir /usr/src/debug/R-3.5.3/include
Removing 1 extra deps from R-devel due to dependency on R-base
Removing 1 extra deps from R-tcltk due to dependency on R-base
Removing 1 extra deps from R-tcltk-debuginfo due to dependency on R-base-debuginfo
Removing 2 extra deps from R-devel due to repentancy on R-base
Removing 5 extra deps from R-tcltk due to repentancy on R-base
Removing 1 extra deps from R-tcltk-debuginfo due to repentancy on R-base-debuginfo
warning: Installed (but unpackaged) file(s) found:
/usr/lib64/R/COPYING
/usr/lib64/R/SVN-REVISION
Wrote: /usr/src/RPM/RPMS/x86_64/R-base-3.5.3-alt1.x86_64.rpm
Wrote: /usr/src/RPM/RPMS/noarch/R-full-3.5.3-alt1.noarch.rpm
Wrote: /usr/src/RPM/RPMS/x86_64/R-devel-3.5.3-alt1.x86_64.rpm
Wrote: /usr/src/RPM/RPMS/x86_64/R-tcltk-3.5.3-alt1.x86_64.rpm
Wrote: /usr/src/RPM/RPMS/noarch/R-doc-html-3.5.3-alt1.noarch.rpm
Wrote: /usr/src/RPM/RPMS/noarch/R-doc-pdf-3.5.3-alt1.noarch.rpm
Wrote: /usr/src/RPM/RPMS/noarch/R-doc-info-3.5.3-alt1.noarch.rpm
Wrote: /usr/src/RPM/RPMS/x86_64/R-base-debuginfo-3.5.3-alt1.x86_64.rpm
Wrote: /usr/src/RPM/RPMS/x86_64/R-tcltk-debuginfo-3.5.3-alt1.x86_64.rpm
1064.87user 60.14system 16:33.10elapsed 113%CPU (0avgtext+0avgdata 362900maxresident)k
0inputs+0outputs (0major+20383383minor)pagefaults 0swaps
1195.06user 72.27system 19:53.28elapsed 106%CPU (0avgtext+0avgdata 362900maxresident)k
1285840inputs+0outputs (0major+21883432minor)pagefaults 0swaps