0s autopkgtest [19:23:25]: starting date and time: 2024-03-16 19:23:25+0000 0s autopkgtest [19:23:25]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [19:23:25]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.1l4ucqbv/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:r-base,src:curl,src:glib2.0,src:libpng1.6,src:libpsl,src:libtirpc,src:libxt,src:openssl,src:orthanc-python,src:readline,src:wp2latex --apt-upgrade r-cran-ordinal --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=r-base/4.3.3-2build1 curl/8.5.0-2ubuntu7 glib2.0/2.79.3-3ubuntu5 libpng1.6/1.6.43-3 libpsl/0.21.2-1.1 libtirpc/1.3.4+ds-1.1 libxt/1:1.2.1-1.2 openssl/3.0.13-0ubuntu1 orthanc-python/4.1+ds-2build3 readline/8.2-3.1 wp2latex/4.4~ds-1build1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-25.secgroup --name adt-noble-arm64-r-cran-ordinal-20240316-192325-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 189s autopkgtest [19:26:34]: testbed dpkg architecture: arm64 190s autopkgtest [19:26:35]: testbed apt version: 2.7.12 190s autopkgtest [19:26:35]: @@@@@@@@@@@@@@@@@@@@ test bed setup 190s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 191s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3657 kB] 191s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [474 kB] 191s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 191s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 191s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [646 kB] 191s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 191s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 191s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 191s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4013 kB] 191s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 191s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.5 kB] 191s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 193s Fetched 9065 kB in 2s (5635 kB/s) 193s Reading package lists... 196s Reading package lists... 196s Building dependency tree... 196s Reading state information... 196s Calculating upgrade... 197s The following packages will be REMOVED: 197s libglib2.0-0 libssl3 197s The following NEW packages will be installed: 197s libglib2.0-0t64 libssl3t64 xdg-user-dirs 197s The following packages have been kept back: 197s curl 197s The following packages will be upgraded: 197s gir1.2-glib-2.0 libglib2.0-data libtirpc-common openssl readline-common 197s ubuntu-minimal ubuntu-standard 197s 7 upgraded, 3 newly installed, 2 to remove and 1 not upgraded. 197s Need to get 4613 kB of archives. 197s After this operation, 211 kB of additional disk space will be used. 197s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gir1.2-glib-2.0 arm64 2.79.3-3ubuntu5 [182 kB] 197s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-0t64 arm64 2.79.3-3ubuntu5 [1527 kB] 197s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB] 197s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB] 198s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-data all 2.79.3-3ubuntu5 [46.6 kB] 198s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc-common all 1.3.4+ds-1.1 [8018 B] 198s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 readline-common all 8.2-3.1 [56.4 kB] 198s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-minimal arm64 1.536 [10.7 kB] 198s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-user-dirs arm64 0.18-1 [18.1 kB] 198s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-standard arm64 1.536 [10.7 kB] 198s Fetched 4613 kB in 1s (6253 kB/s) 198s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74758 files and directories currently installed.) 198s Preparing to unpack .../gir1.2-glib-2.0_2.79.3-3ubuntu5_arm64.deb ... 198s Unpacking gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 198s dpkg: libglib2.0-0:arm64: dependency problems, but removing anyway as you requested: 198s udisks2 depends on libglib2.0-0 (>= 2.77.0). 198s shared-mime-info depends on libglib2.0-0 (>= 2.75.3). 198s python3-gi depends on libglib2.0-0 (>= 2.77.0). 198s python3-dbus depends on libglib2.0-0 (>= 2.16.0). 198s netplan.io depends on libglib2.0-0 (>= 2.70.0). 198s netplan-generator depends on libglib2.0-0 (>= 2.70.0). 198s libxmlb2:arm64 depends on libglib2.0-0 (>= 2.54.0). 198s libvolume-key1:arm64 depends on libglib2.0-0 (>= 2.18.0). 198s libudisks2-0:arm64 depends on libglib2.0-0 (>= 2.75.3). 198s libqrtr-glib0:arm64 depends on libglib2.0-0 (>= 2.56). 198s libqmi-proxy depends on libglib2.0-0 (>= 2.30.0). 198s libqmi-glib5:arm64 depends on libglib2.0-0 (>= 2.54.0). 198s libpolkit-gobject-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 198s libpolkit-agent-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 198s libnetplan0:arm64 depends on libglib2.0-0 (>= 2.75.3). 198s libmm-glib0:arm64 depends on libglib2.0-0 (>= 2.62.0). 198s libmbim-proxy depends on libglib2.0-0 (>= 2.56). 198s libmbim-glib4:arm64 depends on libglib2.0-0 (>= 2.56). 198s libjson-glib-1.0-0:arm64 depends on libglib2.0-0 (>= 2.75.3). 198s libjcat1:arm64 depends on libglib2.0-0 (>= 2.75.3). 198s libgusb2:arm64 depends on libglib2.0-0 (>= 2.75.3). 198s libgudev-1.0-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 198s libgirepository-1.0-1:arm64 depends on libglib2.0-0 (>= 2.79.0). 198s libfwupd2:arm64 depends on libglib2.0-0 (>= 2.79.0). 198s libblockdev3:arm64 depends on libglib2.0-0 (>= 2.42.2). 198s libblockdev-utils3:arm64 depends on libglib2.0-0 (>= 2.75.3). 198s libblockdev-swap3:arm64 depends on libglib2.0-0 (>= 2.42.2). 198s libblockdev-part3:arm64 depends on libglib2.0-0 (>= 2.42.2). 198s libblockdev-nvme3:arm64 depends on libglib2.0-0 (>= 2.42.2). 198s libblockdev-mdraid3:arm64 depends on libglib2.0-0 (>= 2.42.2). 198s libblockdev-loop3:arm64 depends on libglib2.0-0 (>= 2.42.2). 198s libblockdev-fs3:arm64 depends on libglib2.0-0 (>= 2.42.2). 198s libblockdev-crypto3:arm64 depends on libglib2.0-0 (>= 2.42.2). 198s fwupd depends on libglib2.0-0 (>= 2.79.0). 198s bolt depends on libglib2.0-0 (>= 2.56.0). 198s 198s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74758 files and directories currently installed.) 198s Removing libglib2.0-0:arm64 (2.79.2-1~ubuntu1) ... 198s Selecting previously unselected package libglib2.0-0t64:arm64. 198s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74733 files and directories currently installed.) 198s Preparing to unpack .../libglib2.0-0t64_2.79.3-3ubuntu5_arm64.deb ... 198s libglib2.0-0t64.preinst: Removing /var/lib/dpkg/info/libglib2.0-0:arm64.postrm to avoid loss of /usr/share/glib-2.0/schemas/gschemas.compiled... 198s removed '/var/lib/dpkg/info/libglib2.0-0:arm64.postrm' 198s Unpacking libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ... 198s Preparing to unpack .../openssl_3.0.13-0ubuntu1_arm64.deb ... 198s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ... 199s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 199s wget depends on libssl3 (>= 3.0.0). 199s u-boot-tools depends on libssl3 (>= 3.0.0). 199s tnftp depends on libssl3 (>= 3.0.0). 199s tcpdump depends on libssl3 (>= 3.0.0). 199s systemd-resolved depends on libssl3 (>= 3.0.0). 199s systemd depends on libssl3 (>= 3.0.0). 199s sudo depends on libssl3 (>= 3.0.0). 199s sbsigntool depends on libssl3 (>= 3.0.0). 199s rsync depends on libssl3 (>= 3.0.0). 199s python3-cryptography depends on libssl3 (>= 3.0.0). 199s openssh-server depends on libssl3 (>= 3.0.10). 199s openssh-client depends on libssl3 (>= 3.0.10). 199s mtd-utils depends on libssl3 (>= 3.0.0). 199s mokutil depends on libssl3 (>= 3.0.0). 199s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 199s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 199s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 199s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 199s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 199s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 199s libnvme1 depends on libssl3 (>= 3.0.0). 199s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 199s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 199s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 199s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 199s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 199s kmod depends on libssl3 (>= 3.0.0). 199s dhcpcd-base depends on libssl3 (>= 3.0.0). 199s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 199s 199s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74758 files and directories currently installed.) 199s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 199s Selecting previously unselected package libssl3t64:arm64. 199s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74747 files and directories currently installed.) 199s Preparing to unpack .../0-libssl3t64_3.0.13-0ubuntu1_arm64.deb ... 199s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ... 199s Preparing to unpack .../1-libglib2.0-data_2.79.3-3ubuntu5_all.deb ... 199s Unpacking libglib2.0-data (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 199s Preparing to unpack .../2-libtirpc-common_1.3.4+ds-1.1_all.deb ... 199s Unpacking libtirpc-common (1.3.4+ds-1.1) over (1.3.4+ds-1build1) ... 199s Preparing to unpack .../3-readline-common_8.2-3.1_all.deb ... 199s Unpacking readline-common (8.2-3.1) over (8.2-3) ... 199s Preparing to unpack .../4-ubuntu-minimal_1.536_arm64.deb ... 199s Unpacking ubuntu-minimal (1.536) over (1.535) ... 199s Selecting previously unselected package xdg-user-dirs. 199s Preparing to unpack .../5-xdg-user-dirs_0.18-1_arm64.deb ... 199s Unpacking xdg-user-dirs (0.18-1) ... 199s Preparing to unpack .../6-ubuntu-standard_1.536_arm64.deb ... 199s Unpacking ubuntu-standard (1.536) over (1.535) ... 199s Setting up ubuntu-minimal (1.536) ... 199s Setting up xdg-user-dirs (0.18-1) ... 199s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ... 199s Setting up libtirpc-common (1.3.4+ds-1.1) ... 199s Setting up ubuntu-standard (1.536) ... 199s Setting up libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ... 199s No schema files found: doing nothing. 199s Setting up libglib2.0-data (2.79.3-3ubuntu5) ... 199s Setting up gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) ... 199s Setting up openssl (3.0.13-0ubuntu1) ... 199s Setting up readline-common (8.2-3.1) ... 199s Processing triggers for man-db (2.12.0-3) ... 200s Processing triggers for install-info (7.1-3) ... 200s Processing triggers for libc-bin (2.39-0ubuntu2) ... 200s Reading package lists... 201s Building dependency tree... 201s Reading state information... 201s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 202s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 202s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 202s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 202s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 203s Reading package lists... 203s Reading package lists... 204s Building dependency tree... 204s Reading state information... 204s Calculating upgrade... 204s The following packages have been kept back: 204s curl 204s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 204s Reading package lists... 205s Building dependency tree... 205s Reading state information... 205s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 208s autopkgtest [19:26:53]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 208s autopkgtest [19:26:53]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-ordinal 210s Get:1 http://ftpmaster.internal/ubuntu noble/universe r-cran-ordinal 2023.12-4-1 (dsc) [2244 B] 210s Get:2 http://ftpmaster.internal/ubuntu noble/universe r-cran-ordinal 2023.12-4-1 (tar) [806 kB] 210s Get:3 http://ftpmaster.internal/ubuntu noble/universe r-cran-ordinal 2023.12-4-1 (diff) [3072 B] 211s gpgv: Signature made Tue Jan 9 07:20:20 2024 UTC 211s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 211s gpgv: issuer "tille@debian.org" 211s gpgv: Can't check signature: No public key 211s dpkg-source: warning: cannot verify inline signature for ./r-cran-ordinal_2023.12-4-1.dsc: no acceptable signature found 211s autopkgtest [19:26:56]: testing package r-cran-ordinal version 2023.12-4-1 211s autopkgtest [19:26:56]: build not needed 212s autopkgtest [19:26:57]: test run-unit-test: preparing testbed 213s Reading package lists... 214s Building dependency tree... 214s Reading state information... 214s Starting pkgProblemResolver with broken count: 0 214s Starting 2 pkgProblemResolver with broken count: 0 214s Done 215s The following additional packages will be installed: 215s curl fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 215s libblas3 libcairo2 libcurl4t64 libdatrie1 libdeflate0 libfontconfig1 215s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libice6 libjbig0 215s libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libnlopt0 libpango-1.0-0 215s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 215s libpng16-16t64 libpsl5t64 libreadline8t64 libsharpyuv0 libsm6 libtcl8.6 215s libthai-data libthai0 libtiff6 libtirpc3t64 libtk8.6 libwebp7 libxcb-render0 215s libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 littler r-base-core 215s r-cran-boot r-cran-brio r-cran-callr r-cran-cli r-cran-crayon r-cran-desc 215s r-cran-diffobj r-cran-digest r-cran-evaluate r-cran-fansi r-cran-fs 215s r-cran-glue r-cran-jsonlite r-cran-lattice r-cran-lifecycle r-cran-littler 215s r-cran-lme4 r-cran-magrittr r-cran-mass r-cran-matrix r-cran-minqa 215s r-cran-nlme r-cran-nloptr r-cran-nnet r-cran-numderiv r-cran-ordinal 215s r-cran-pillar r-cran-pkgbuild r-cran-pkgconfig r-cran-pkgkitten 215s r-cran-pkgload r-cran-praise r-cran-processx r-cran-ps r-cran-r6 r-cran-rcpp 215s r-cran-rcppeigen r-cran-rematch2 r-cran-rlang r-cran-rprojroot 215s r-cran-statmod r-cran-testthat r-cran-tibble r-cran-ucminf r-cran-utf8 215s r-cran-vctrs r-cran-waldo r-cran-withr r-cran-xtable unzip x11-common 215s xdg-utils zip 215s Suggested packages: 215s tcl8.6 tk8.6 elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html 215s r-cran-covr r-cran-spelling r-cran-rstudioapi r-cran-knitr r-cran-rmarkdown 215s r-cran-getopt r-cran-bit64 r-cran-dbi r-cran-dplyr r-cran-formattable 215s r-cran-ggplot2 r-cran-nanotime r-cran-palmerpenguins r-cran-scales 215s r-cran-stringi r-cran-survival r-cran-units r-cran-vdiffr r-cran-inline 215s r-cran-bench r-cran-blob r-cran-here r-cran-hms r-cran-htmltools 215s r-cran-purrr r-cran-tidyr r-cran-plm r-cran-zoo 215s Recommended packages: 215s r-recommended r-base-dev r-doc-html r-cran-covr r-cran-cliapp r-cran-mockery 215s r-cran-htmltools r-cran-htmlwidgets r-cran-knitr r-cran-rmarkdown 215s r-cran-rstudioapi r-cran-whoami r-cran-gh r-cran-spelling r-cran-ggplot2 215s r-cran-unitizer r-cran-dbi r-cran-dplyr r-cran-rsqlite r-cran-httr 215s r-cran-r.rsp r-cran-sf r-cran-lintr r-cran-tidyverse r-cran-lubridate 215s r-cran-cpp11 r-cran-bitops r-cran-mathjaxr r-cran-mockr r-cran-remotes 215s r-cran-codetools r-cran-curl r-cran-webfakes r-cran-pingr r-cran-usethis 215s r-cran-shiny r-cran-xml2 r-cran-data.table r-cran-formattable r-cran-bit64 215s r-cran-generics r-cran-pkgdown r-cran-zeallot libfile-mimeinfo-perl 215s libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils 215s The following packages will be REMOVED: 215s libcurl4 libpng16-16 libpsl5 libreadline8 libtirpc3 215s The following NEW packages will be installed: 215s autopkgtest-satdep fontconfig fontconfig-config fonts-dejavu-core 215s fonts-dejavu-mono libblas3 libcairo2 libcurl4t64 libdatrie1 libdeflate0 215s libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libice6 215s libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libnlopt0 215s libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils 215s libpaper1 libpixman-1-0 libpng16-16t64 libpsl5t64 libreadline8t64 215s libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc3t64 215s libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 215s libxt6t64 littler r-base-core r-cran-boot r-cran-brio r-cran-callr 215s r-cran-cli r-cran-crayon r-cran-desc r-cran-diffobj r-cran-digest 215s r-cran-evaluate r-cran-fansi r-cran-fs r-cran-glue r-cran-jsonlite 215s r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-lme4 r-cran-magrittr 215s r-cran-mass r-cran-matrix r-cran-minqa r-cran-nlme r-cran-nloptr r-cran-nnet 215s r-cran-numderiv r-cran-ordinal r-cran-pillar r-cran-pkgbuild 215s r-cran-pkgconfig r-cran-pkgkitten r-cran-pkgload r-cran-praise 215s r-cran-processx r-cran-ps r-cran-r6 r-cran-rcpp r-cran-rcppeigen 215s r-cran-rematch2 r-cran-rlang r-cran-rprojroot r-cran-statmod r-cran-testthat 215s r-cran-tibble r-cran-ucminf r-cran-utf8 r-cran-vctrs r-cran-waldo 215s r-cran-withr r-cran-xtable unzip x11-common xdg-utils zip 215s The following packages will be upgraded: 215s curl 215s 1 upgraded, 101 newly installed, 5 to remove and 0 not upgraded. 215s Need to get 70.2 MB/70.2 MB of archives. 215s After this operation, 140 MB of additional disk space will be used. 215s Get:1 /tmp/autopkgtest.7IB1w2/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [748 B] 215s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpsl5t64 arm64 0.21.2-1.1 [57.4 kB] 215s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 curl arm64 8.5.0-2ubuntu7 [222 kB] 215s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcurl4t64 arm64 8.5.0-2ubuntu7 [332 kB] 216s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpng16-16t64 arm64 1.6.43-3 [185 kB] 216s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libreadline8t64 arm64 8.2-3.1 [153 kB] 216s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.1 [83.5 kB] 216s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 216s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 216s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 216s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 216s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig arm64 2.15.0-1ubuntu1 [190 kB] 216s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 216s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB] 216s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB] 216s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B] 216s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] 216s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB] 216s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 libdatrie1 arm64 0.2.13-3 [21.7 kB] 216s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 216s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 216s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 216s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 216s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 216s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 216s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 libice6 arm64 2:1.0.10-1build2 [41.7 kB] 216s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 216s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 216s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 216s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] 216s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 libthai-data all 0.1.29-2 [158 kB] 216s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 libthai0 arm64 0.1.29-2 [18.1 kB] 216s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 libpango-1.0-0 arm64 1.51.0+ds-4 [226 kB] 216s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 libpangoft2-1.0-0 arm64 1.51.0+ds-4 [41.2 kB] 216s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libpangocairo-1.0-0 arm64 1.51.0+ds-4 [27.6 kB] 216s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper1 arm64 1.1.29 [13.1 kB] 216s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper-utils arm64 1.1.29 [8480 B] 216s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB] 216s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libsm6 arm64 2:1.2.3-1build2 [16.1 kB] 216s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 libtcl8.6 arm64 8.6.13+dfsg-2 [980 kB] 216s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] 216s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB] 216s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB] 216s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libxft2 arm64 2.3.6-1 [43.3 kB] 216s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 libxss1 arm64 1:1.2.3-1build2 [8252 B] 216s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 libtk8.6 arm64 8.6.13-2 [760 kB] 216s Get:47 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libxt6t64 arm64 1:1.2.1-1.2 [168 kB] 216s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 zip arm64 3.0-13 [172 kB] 216s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 unzip arm64 6.0-28ubuntu3 [171 kB] 216s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 216s Get:51 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 r-base-core arm64 4.3.3-2build1 [26.8 MB] 217s Get:52 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-littler arm64 0.3.19-1 [93.4 kB] 217s Get:53 http://ftpmaster.internal/ubuntu noble/universe arm64 littler all 0.3.19-1 [2472 B] 217s Get:54 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-boot all 1.3-30-1 [619 kB] 217s Get:55 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-brio arm64 1.1.4-1 [37.7 kB] 217s Get:56 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-ps arm64 1.7.6-1 [313 kB] 217s Get:57 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-r6 all 2.5.1-1 [99.0 kB] 217s Get:58 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-processx arm64 3.8.3-1 [345 kB] 217s Get:59 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-callr all 3.7.3-2 [425 kB] 217s Get:60 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-cli arm64 3.6.2-1 [1377 kB] 217s Get:61 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-crayon all 1.5.2-1 [164 kB] 217s Get:62 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-desc all 1.4.3-1 [359 kB] 217s Get:63 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-diffobj arm64 0.3.5-1 [1116 kB] 217s Get:64 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-digest arm64 0.6.34-1 [182 kB] 217s Get:65 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-evaluate all 0.23-1 [90.2 kB] 217s Get:66 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-fansi arm64 1.0.5-1 [616 kB] 217s Get:67 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-fs arm64 1.6.3+dfsg-1 [227 kB] 217s Get:68 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-glue arm64 1.7.0-1 [154 kB] 217s Get:69 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-jsonlite arm64 1.8.8+dfsg-1 [441 kB] 217s Get:70 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lattice arm64 0.22-5-1 [1342 kB] 217s Get:71 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rlang arm64 1.1.3-1 [1663 kB] 217s Get:72 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] 217s Get:73 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-matrix arm64 1.6-5-1 [3776 kB] 218s Get:74 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-mass arm64 7.3-60.0.1-1 [1119 kB] 218s Get:75 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-nlme arm64 3.1.164-1 [2259 kB] 218s Get:76 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pkgkitten all 0.2.3-1 [25.1 kB] 218s Get:77 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rcpp arm64 1.0.12-1 [1971 kB] 218s Get:78 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-minqa arm64 1.2.6-1 [107 kB] 218s Get:79 http://ftpmaster.internal/ubuntu noble/universe arm64 libnlopt0 arm64 2.7.1-5build2 [174 kB] 218s Get:80 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-magrittr arm64 2.0.3-1 [154 kB] 218s Get:81 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pkgbuild all 1.4.3-1 [209 kB] 218s Get:82 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rprojroot all 2.0.4-1 [124 kB] 218s Get:83 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-withr all 2.5.0-1 [225 kB] 218s Get:84 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pkgload all 1.3.4-1 [207 kB] 218s Get:85 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-praise all 1.0.0-4build1 [20.3 kB] 218s Get:86 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-utf8 arm64 1.2.4-1 [140 kB] 218s Get:87 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-vctrs arm64 0.6.5-1 [1327 kB] 218s Get:88 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pillar all 1.9.0+dfsg-1 [464 kB] 218s Get:89 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB] 218s Get:90 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-tibble arm64 3.2.1+dfsg-2 [415 kB] 218s Get:91 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rematch2 all 2.1.2-2build1 [46.5 kB] 218s Get:92 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-waldo all 0.5.2-1build1 [120 kB] 218s Get:93 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-testthat arm64 3.2.1-1 [1678 kB] 218s Get:94 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-nloptr arm64 2.0.3-1 [375 kB] 218s Get:95 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rcppeigen arm64 0.3.3.9.4-1 [1180 kB] 218s Get:96 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-statmod arm64 1.5.0-1 [294 kB] 218s Get:97 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lme4 arm64 1.1-35.1-4 [4116 kB] 218s Get:98 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-nnet arm64 7.3-19-2 [111 kB] 218s Get:99 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-numderiv all 2016.8-1.1-3 [115 kB] 218s Get:100 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-ucminf arm64 1.2.1-1 [34.8 kB] 218s Get:101 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-ordinal arm64 2023.12-4-1 [1263 kB] 218s Get:102 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-xtable all 1:1.8-4-2 [689 kB] 219s Preconfiguring packages ... 219s Fetched 70.2 MB in 3s (21.3 MB/s) 219s dpkg: libpsl5:arm64: dependency problems, but removing anyway as you requested: 219s wget depends on libpsl5 (>= 0.16.0). 219s libcurl4:arm64 depends on libpsl5 (>= 0.16.0). 219s libcurl3-gnutls:arm64 depends on libpsl5 (>= 0.16.0). 219s 219s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74774 files and directories currently installed.) 219s Removing libpsl5:arm64 (0.21.2-1build1) ... 219s Selecting previously unselected package libpsl5t64:arm64. 219s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74769 files and directories currently installed.) 219s Preparing to unpack .../libpsl5t64_0.21.2-1.1_arm64.deb ... 219s Unpacking libpsl5t64:arm64 (0.21.2-1.1) ... 219s Preparing to unpack .../curl_8.5.0-2ubuntu7_arm64.deb ... 219s Unpacking curl (8.5.0-2ubuntu7) over (8.5.0-2ubuntu2) ... 219s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74775 files and directories currently installed.) 219s Removing libcurl4:arm64 (8.5.0-2ubuntu2) ... 219s Selecting previously unselected package libcurl4t64:arm64. 219s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74770 files and directories currently installed.) 219s Preparing to unpack .../libcurl4t64_8.5.0-2ubuntu7_arm64.deb ... 219s Unpacking libcurl4t64:arm64 (8.5.0-2ubuntu7) ... 219s dpkg: libpng16-16:arm64: dependency problems, but removing anyway as you requested: 219s libplymouth5:arm64 depends on libpng16-16 (>= 1.6.2). 219s libfreetype6:arm64 depends on libpng16-16 (>= 1.6.2-1). 219s 219s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74776 files and directories currently installed.) 219s Removing libpng16-16:arm64 (1.6.43-1) ... 219s Selecting previously unselected package libpng16-16t64:arm64. 219s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74766 files and directories currently installed.) 219s Preparing to unpack .../libpng16-16t64_1.6.43-3_arm64.deb ... 219s Unpacking libpng16-16t64:arm64 (1.6.43-3) ... 220s dpkg: libreadline8:arm64: dependency problems, but removing anyway as you requested: 220s parted depends on libreadline8 (>= 6.0). 220s libpython3.12-stdlib:arm64 depends on libreadline8 (>= 7.0~beta). 220s gpgsm depends on libreadline8 (>= 6.0). 220s gpgconf depends on libreadline8 (>= 6.0). 220s gpg depends on libreadline8 (>= 6.0). 220s gawk depends on libreadline8 (>= 6.0). 220s fdisk depends on libreadline8 (>= 6.0). 220s 220s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74777 files and directories currently installed.) 220s Removing libreadline8:arm64 (8.2-3) ... 220s Selecting previously unselected package libreadline8t64:arm64. 220s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74765 files and directories currently installed.) 220s Preparing to unpack .../libreadline8t64_8.2-3.1_arm64.deb ... 220s Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' 220s Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' 220s Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' 220s Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' 220s Unpacking libreadline8t64:arm64 (8.2-3.1) ... 220s dpkg: libtirpc3:arm64: dependency problems, but removing anyway as you requested: 220s lsof depends on libtirpc3 (>= 1.0.2). 220s libpython3.12-stdlib:arm64 depends on libtirpc3 (>= 1.0.2). 220s libnss-nisplus:arm64 depends on libtirpc3 (>= 1.0.2). 220s libnsl2:arm64 depends on libtirpc3 (>= 1.0.2). 220s iproute2 depends on libtirpc3 (>= 1.0.2). 220s 220s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74785 files and directories currently installed.) 220s Removing libtirpc3:arm64 (1.3.4+ds-1build1) ... 220s Selecting previously unselected package libtirpc3t64:arm64. 220s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74779 files and directories currently installed.) 220s Preparing to unpack .../00-libtirpc3t64_1.3.4+ds-1.1_arm64.deb ... 220s Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' 220s Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' 220s Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.1) ... 220s Selecting previously unselected package fonts-dejavu-mono. 220s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 220s Unpacking fonts-dejavu-mono (2.37-8) ... 220s Selecting previously unselected package fonts-dejavu-core. 220s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 220s Unpacking fonts-dejavu-core (2.37-8) ... 220s Selecting previously unselected package fontconfig-config. 220s Preparing to unpack .../03-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 220s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 220s Selecting previously unselected package libfontconfig1:arm64. 220s Preparing to unpack .../04-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 220s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 220s Selecting previously unselected package fontconfig. 220s Preparing to unpack .../05-fontconfig_2.15.0-1ubuntu1_arm64.deb ... 220s Unpacking fontconfig (2.15.0-1ubuntu1) ... 220s Selecting previously unselected package libblas3:arm64. 220s Preparing to unpack .../06-libblas3_3.12.0-3_arm64.deb ... 220s Unpacking libblas3:arm64 (3.12.0-3) ... 220s Selecting previously unselected package libpixman-1-0:arm64. 220s Preparing to unpack .../07-libpixman-1-0_0.42.2-1_arm64.deb ... 220s Unpacking libpixman-1-0:arm64 (0.42.2-1) ... 220s Selecting previously unselected package libxcb-render0:arm64. 220s Preparing to unpack .../08-libxcb-render0_1.15-1_arm64.deb ... 220s Unpacking libxcb-render0:arm64 (1.15-1) ... 220s Selecting previously unselected package libxcb-shm0:arm64. 220s Preparing to unpack .../09-libxcb-shm0_1.15-1_arm64.deb ... 220s Unpacking libxcb-shm0:arm64 (1.15-1) ... 220s Selecting previously unselected package libxrender1:arm64. 220s Preparing to unpack .../10-libxrender1_1%3a0.9.10-1.1_arm64.deb ... 220s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ... 220s Selecting previously unselected package libcairo2:arm64. 220s Preparing to unpack .../11-libcairo2_1.18.0-1_arm64.deb ... 220s Unpacking libcairo2:arm64 (1.18.0-1) ... 220s Selecting previously unselected package libdatrie1:arm64. 220s Preparing to unpack .../12-libdatrie1_0.2.13-3_arm64.deb ... 220s Unpacking libdatrie1:arm64 (0.2.13-3) ... 220s Selecting previously unselected package libdeflate0:arm64. 220s Preparing to unpack .../13-libdeflate0_1.19-1_arm64.deb ... 220s Unpacking libdeflate0:arm64 (1.19-1) ... 220s Selecting previously unselected package libgfortran5:arm64. 220s Preparing to unpack .../14-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 220s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 220s Selecting previously unselected package libgomp1:arm64. 220s Preparing to unpack .../15-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 220s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 220s Selecting previously unselected package libgraphite2-3:arm64. 220s Preparing to unpack .../16-libgraphite2-3_1.3.14-2_arm64.deb ... 220s Unpacking libgraphite2-3:arm64 (1.3.14-2) ... 220s Selecting previously unselected package libharfbuzz0b:arm64. 220s Preparing to unpack .../17-libharfbuzz0b_8.3.0-2_arm64.deb ... 220s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ... 221s Selecting previously unselected package x11-common. 221s Preparing to unpack .../18-x11-common_1%3a7.7+23ubuntu2_all.deb ... 221s Unpacking x11-common (1:7.7+23ubuntu2) ... 221s Selecting previously unselected package libice6:arm64. 221s Preparing to unpack .../19-libice6_2%3a1.0.10-1build2_arm64.deb ... 221s Unpacking libice6:arm64 (2:1.0.10-1build2) ... 221s Selecting previously unselected package libjpeg-turbo8:arm64. 221s Preparing to unpack .../20-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ... 221s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 221s Selecting previously unselected package libjpeg8:arm64. 221s Preparing to unpack .../21-libjpeg8_8c-2ubuntu11_arm64.deb ... 221s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 221s Selecting previously unselected package liblapack3:arm64. 221s Preparing to unpack .../22-liblapack3_3.12.0-3_arm64.deb ... 221s Unpacking liblapack3:arm64 (3.12.0-3) ... 221s Selecting previously unselected package liblerc4:arm64. 221s Preparing to unpack .../23-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ... 221s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 221s Selecting previously unselected package libthai-data. 221s Preparing to unpack .../24-libthai-data_0.1.29-2_all.deb ... 221s Unpacking libthai-data (0.1.29-2) ... 221s Selecting previously unselected package libthai0:arm64. 221s Preparing to unpack .../25-libthai0_0.1.29-2_arm64.deb ... 221s Unpacking libthai0:arm64 (0.1.29-2) ... 221s Selecting previously unselected package libpango-1.0-0:arm64. 221s Preparing to unpack .../26-libpango-1.0-0_1.51.0+ds-4_arm64.deb ... 221s Unpacking libpango-1.0-0:arm64 (1.51.0+ds-4) ... 221s Selecting previously unselected package libpangoft2-1.0-0:arm64. 221s Preparing to unpack .../27-libpangoft2-1.0-0_1.51.0+ds-4_arm64.deb ... 221s Unpacking libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ... 221s Selecting previously unselected package libpangocairo-1.0-0:arm64. 221s Preparing to unpack .../28-libpangocairo-1.0-0_1.51.0+ds-4_arm64.deb ... 221s Unpacking libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ... 221s Selecting previously unselected package libpaper1:arm64. 221s Preparing to unpack .../29-libpaper1_1.1.29_arm64.deb ... 221s Unpacking libpaper1:arm64 (1.1.29) ... 221s Selecting previously unselected package libpaper-utils. 221s Preparing to unpack .../30-libpaper-utils_1.1.29_arm64.deb ... 221s Unpacking libpaper-utils (1.1.29) ... 221s Selecting previously unselected package libsharpyuv0:arm64. 221s Preparing to unpack .../31-libsharpyuv0_1.3.2-0.4_arm64.deb ... 221s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ... 221s Selecting previously unselected package libsm6:arm64. 221s Preparing to unpack .../32-libsm6_2%3a1.2.3-1build2_arm64.deb ... 221s Unpacking libsm6:arm64 (2:1.2.3-1build2) ... 221s Selecting previously unselected package libtcl8.6:arm64. 221s Preparing to unpack .../33-libtcl8.6_8.6.13+dfsg-2_arm64.deb ... 221s Unpacking libtcl8.6:arm64 (8.6.13+dfsg-2) ... 221s Selecting previously unselected package libjbig0:arm64. 221s Preparing to unpack .../34-libjbig0_2.1-6.1ubuntu1_arm64.deb ... 221s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ... 221s Selecting previously unselected package libwebp7:arm64. 221s Preparing to unpack .../35-libwebp7_1.3.2-0.4_arm64.deb ... 221s Unpacking libwebp7:arm64 (1.3.2-0.4) ... 221s Selecting previously unselected package libtiff6:arm64. 221s Preparing to unpack .../36-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ... 221s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 221s Selecting previously unselected package libxft2:arm64. 221s Preparing to unpack .../37-libxft2_2.3.6-1_arm64.deb ... 221s Unpacking libxft2:arm64 (2.3.6-1) ... 221s Selecting previously unselected package libxss1:arm64. 221s Preparing to unpack .../38-libxss1_1%3a1.2.3-1build2_arm64.deb ... 221s Unpacking libxss1:arm64 (1:1.2.3-1build2) ... 221s Selecting previously unselected package libtk8.6:arm64. 221s Preparing to unpack .../39-libtk8.6_8.6.13-2_arm64.deb ... 221s Unpacking libtk8.6:arm64 (8.6.13-2) ... 221s Selecting previously unselected package libxt6t64:arm64. 221s Preparing to unpack .../40-libxt6t64_1%3a1.2.1-1.2_arm64.deb ... 221s Unpacking libxt6t64:arm64 (1:1.2.1-1.2) ... 221s Selecting previously unselected package zip. 221s Preparing to unpack .../41-zip_3.0-13_arm64.deb ... 221s Unpacking zip (3.0-13) ... 221s Selecting previously unselected package unzip. 221s Preparing to unpack .../42-unzip_6.0-28ubuntu3_arm64.deb ... 221s Unpacking unzip (6.0-28ubuntu3) ... 221s Selecting previously unselected package xdg-utils. 221s Preparing to unpack .../43-xdg-utils_1.1.3-4.1ubuntu3_all.deb ... 221s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ... 221s Selecting previously unselected package r-base-core. 221s Preparing to unpack .../44-r-base-core_4.3.3-2build1_arm64.deb ... 221s Unpacking r-base-core (4.3.3-2build1) ... 222s Selecting previously unselected package r-cran-littler. 222s Preparing to unpack .../45-r-cran-littler_0.3.19-1_arm64.deb ... 222s Unpacking r-cran-littler (0.3.19-1) ... 222s Selecting previously unselected package littler. 222s Preparing to unpack .../46-littler_0.3.19-1_all.deb ... 222s Unpacking littler (0.3.19-1) ... 222s Selecting previously unselected package r-cran-boot. 222s Preparing to unpack .../47-r-cran-boot_1.3-30-1_all.deb ... 222s Unpacking r-cran-boot (1.3-30-1) ... 222s Selecting previously unselected package r-cran-brio. 222s Preparing to unpack .../48-r-cran-brio_1.1.4-1_arm64.deb ... 222s Unpacking r-cran-brio (1.1.4-1) ... 222s Selecting previously unselected package r-cran-ps. 222s Preparing to unpack .../49-r-cran-ps_1.7.6-1_arm64.deb ... 222s Unpacking r-cran-ps (1.7.6-1) ... 222s Selecting previously unselected package r-cran-r6. 222s Preparing to unpack .../50-r-cran-r6_2.5.1-1_all.deb ... 222s Unpacking r-cran-r6 (2.5.1-1) ... 222s Selecting previously unselected package r-cran-processx. 222s Preparing to unpack .../51-r-cran-processx_3.8.3-1_arm64.deb ... 222s Unpacking r-cran-processx (3.8.3-1) ... 222s Selecting previously unselected package r-cran-callr. 222s Preparing to unpack .../52-r-cran-callr_3.7.3-2_all.deb ... 222s Unpacking r-cran-callr (3.7.3-2) ... 222s Selecting previously unselected package r-cran-cli. 222s Preparing to unpack .../53-r-cran-cli_3.6.2-1_arm64.deb ... 222s Unpacking r-cran-cli (3.6.2-1) ... 222s Selecting previously unselected package r-cran-crayon. 222s Preparing to unpack .../54-r-cran-crayon_1.5.2-1_all.deb ... 222s Unpacking r-cran-crayon (1.5.2-1) ... 222s Selecting previously unselected package r-cran-desc. 222s Preparing to unpack .../55-r-cran-desc_1.4.3-1_all.deb ... 222s Unpacking r-cran-desc (1.4.3-1) ... 222s Selecting previously unselected package r-cran-diffobj. 222s Preparing to unpack .../56-r-cran-diffobj_0.3.5-1_arm64.deb ... 222s Unpacking r-cran-diffobj (0.3.5-1) ... 222s Selecting previously unselected package r-cran-digest. 222s Preparing to unpack .../57-r-cran-digest_0.6.34-1_arm64.deb ... 222s Unpacking r-cran-digest (0.6.34-1) ... 222s Selecting previously unselected package r-cran-evaluate. 222s Preparing to unpack .../58-r-cran-evaluate_0.23-1_all.deb ... 222s Unpacking r-cran-evaluate (0.23-1) ... 222s Selecting previously unselected package r-cran-fansi. 222s Preparing to unpack .../59-r-cran-fansi_1.0.5-1_arm64.deb ... 222s Unpacking r-cran-fansi (1.0.5-1) ... 223s Selecting previously unselected package r-cran-fs. 223s Preparing to unpack .../60-r-cran-fs_1.6.3+dfsg-1_arm64.deb ... 223s Unpacking r-cran-fs (1.6.3+dfsg-1) ... 223s Selecting previously unselected package r-cran-glue. 223s Preparing to unpack .../61-r-cran-glue_1.7.0-1_arm64.deb ... 223s Unpacking r-cran-glue (1.7.0-1) ... 223s Selecting previously unselected package r-cran-jsonlite. 223s Preparing to unpack .../62-r-cran-jsonlite_1.8.8+dfsg-1_arm64.deb ... 223s Unpacking r-cran-jsonlite (1.8.8+dfsg-1) ... 223s Selecting previously unselected package r-cran-lattice. 223s Preparing to unpack .../63-r-cran-lattice_0.22-5-1_arm64.deb ... 223s Unpacking r-cran-lattice (0.22-5-1) ... 223s Selecting previously unselected package r-cran-rlang. 223s Preparing to unpack .../64-r-cran-rlang_1.1.3-1_arm64.deb ... 223s Unpacking r-cran-rlang (1.1.3-1) ... 223s Selecting previously unselected package r-cran-lifecycle. 223s Preparing to unpack .../65-r-cran-lifecycle_1.0.4+dfsg-1_all.deb ... 223s Unpacking r-cran-lifecycle (1.0.4+dfsg-1) ... 223s Selecting previously unselected package r-cran-matrix. 223s Preparing to unpack .../66-r-cran-matrix_1.6-5-1_arm64.deb ... 223s Unpacking r-cran-matrix (1.6-5-1) ... 223s Selecting previously unselected package r-cran-mass. 223s Preparing to unpack .../67-r-cran-mass_7.3-60.0.1-1_arm64.deb ... 223s Unpacking r-cran-mass (7.3-60.0.1-1) ... 223s Selecting previously unselected package r-cran-nlme. 223s Preparing to unpack .../68-r-cran-nlme_3.1.164-1_arm64.deb ... 223s Unpacking r-cran-nlme (3.1.164-1) ... 223s Selecting previously unselected package r-cran-pkgkitten. 223s Preparing to unpack .../69-r-cran-pkgkitten_0.2.3-1_all.deb ... 223s Unpacking r-cran-pkgkitten (0.2.3-1) ... 223s Selecting previously unselected package r-cran-rcpp. 223s Preparing to unpack .../70-r-cran-rcpp_1.0.12-1_arm64.deb ... 223s Unpacking r-cran-rcpp (1.0.12-1) ... 223s Selecting previously unselected package r-cran-minqa. 223s Preparing to unpack .../71-r-cran-minqa_1.2.6-1_arm64.deb ... 223s Unpacking r-cran-minqa (1.2.6-1) ... 223s Selecting previously unselected package libnlopt0:arm64. 223s Preparing to unpack .../72-libnlopt0_2.7.1-5build2_arm64.deb ... 223s Unpacking libnlopt0:arm64 (2.7.1-5build2) ... 223s Selecting previously unselected package r-cran-magrittr. 223s Preparing to unpack .../73-r-cran-magrittr_2.0.3-1_arm64.deb ... 223s Unpacking r-cran-magrittr (2.0.3-1) ... 223s Selecting previously unselected package r-cran-pkgbuild. 223s Preparing to unpack .../74-r-cran-pkgbuild_1.4.3-1_all.deb ... 223s Unpacking r-cran-pkgbuild (1.4.3-1) ... 223s Selecting previously unselected package r-cran-rprojroot. 223s Preparing to unpack .../75-r-cran-rprojroot_2.0.4-1_all.deb ... 223s Unpacking r-cran-rprojroot (2.0.4-1) ... 223s Selecting previously unselected package r-cran-withr. 223s Preparing to unpack .../76-r-cran-withr_2.5.0-1_all.deb ... 223s Unpacking r-cran-withr (2.5.0-1) ... 223s Selecting previously unselected package r-cran-pkgload. 224s Preparing to unpack .../77-r-cran-pkgload_1.3.4-1_all.deb ... 224s Unpacking r-cran-pkgload (1.3.4-1) ... 224s Selecting previously unselected package r-cran-praise. 224s Preparing to unpack .../78-r-cran-praise_1.0.0-4build1_all.deb ... 224s Unpacking r-cran-praise (1.0.0-4build1) ... 224s Selecting previously unselected package r-cran-utf8. 224s Preparing to unpack .../79-r-cran-utf8_1.2.4-1_arm64.deb ... 224s Unpacking r-cran-utf8 (1.2.4-1) ... 224s Selecting previously unselected package r-cran-vctrs. 224s Preparing to unpack .../80-r-cran-vctrs_0.6.5-1_arm64.deb ... 224s Unpacking r-cran-vctrs (0.6.5-1) ... 224s Selecting previously unselected package r-cran-pillar. 224s Preparing to unpack .../81-r-cran-pillar_1.9.0+dfsg-1_all.deb ... 224s Unpacking r-cran-pillar (1.9.0+dfsg-1) ... 224s Selecting previously unselected package r-cran-pkgconfig. 224s Preparing to unpack .../82-r-cran-pkgconfig_2.0.3-2build1_all.deb ... 224s Unpacking r-cran-pkgconfig (2.0.3-2build1) ... 224s Selecting previously unselected package r-cran-tibble. 224s Preparing to unpack .../83-r-cran-tibble_3.2.1+dfsg-2_arm64.deb ... 224s Unpacking r-cran-tibble (3.2.1+dfsg-2) ... 224s Selecting previously unselected package r-cran-rematch2. 224s Preparing to unpack .../84-r-cran-rematch2_2.1.2-2build1_all.deb ... 224s Unpacking r-cran-rematch2 (2.1.2-2build1) ... 224s Selecting previously unselected package r-cran-waldo. 224s Preparing to unpack .../85-r-cran-waldo_0.5.2-1build1_all.deb ... 224s Unpacking r-cran-waldo (0.5.2-1build1) ... 224s Selecting previously unselected package r-cran-testthat. 224s Preparing to unpack .../86-r-cran-testthat_3.2.1-1_arm64.deb ... 224s Unpacking r-cran-testthat (3.2.1-1) ... 224s Selecting previously unselected package r-cran-nloptr. 224s Preparing to unpack .../87-r-cran-nloptr_2.0.3-1_arm64.deb ... 224s Unpacking r-cran-nloptr (2.0.3-1) ... 224s Selecting previously unselected package r-cran-rcppeigen. 224s Preparing to unpack .../88-r-cran-rcppeigen_0.3.3.9.4-1_arm64.deb ... 224s Unpacking r-cran-rcppeigen (0.3.3.9.4-1) ... 224s Selecting previously unselected package r-cran-statmod. 224s Preparing to unpack .../89-r-cran-statmod_1.5.0-1_arm64.deb ... 224s Unpacking r-cran-statmod (1.5.0-1) ... 224s Selecting previously unselected package r-cran-lme4. 224s Preparing to unpack .../90-r-cran-lme4_1.1-35.1-4_arm64.deb ... 224s Unpacking r-cran-lme4 (1.1-35.1-4) ... 224s Selecting previously unselected package r-cran-nnet. 224s Preparing to unpack .../91-r-cran-nnet_7.3-19-2_arm64.deb ... 224s Unpacking r-cran-nnet (7.3-19-2) ... 224s Selecting previously unselected package r-cran-numderiv. 224s Preparing to unpack .../92-r-cran-numderiv_2016.8-1.1-3_all.deb ... 224s Unpacking r-cran-numderiv (2016.8-1.1-3) ... 224s Selecting previously unselected package r-cran-ucminf. 224s Preparing to unpack .../93-r-cran-ucminf_1.2.1-1_arm64.deb ... 224s Unpacking r-cran-ucminf (1.2.1-1) ... 224s Selecting previously unselected package r-cran-ordinal. 224s Preparing to unpack .../94-r-cran-ordinal_2023.12-4-1_arm64.deb ... 224s Unpacking r-cran-ordinal (2023.12-4-1) ... 224s Selecting previously unselected package r-cran-xtable. 224s Preparing to unpack .../95-r-cran-xtable_1%3a1.8-4-2_all.deb ... 224s Unpacking r-cran-xtable (1:1.8-4-2) ... 224s Selecting previously 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[----------------------- 236s BEGIN TEST anova.R 236s 236s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 236s Copyright (C) 2024 The R Foundation for Statistical Computing 236s Platform: aarch64-unknown-linux-gnu (64-bit) 236s 236s R is free software and comes with ABSOLUTELY NO WARRANTY. 236s You are welcome to redistribute it under certain conditions. 236s Type 'license()' or 'licence()' for distribution details. 236s 236s R is a collaborative project with many contributors. 236s Type 'contributors()' for more information and 236s 'citation()' on how to cite R or R packages in publications. 236s 236s Type 'demo()' for some demos, 'help()' for on-line help, or 236s 'help.start()' for an HTML browser interface to help. 236s Type 'q()' to quit R. 236s 237s > library(ordinal) 238s > data(wine) 238s > 238s > fm1 <- clm(rating ~ temp, data=wine) 238s > fmm1 <- clmm(rating ~ temp + (1|judge), data=wine) 238s > 238s > ## These now give identical printed results: 238s > ## Previously the printed model names were messed up when anova.clmm 238s > ## were called. 238s > anova(fm1, fmm1) 238s Likelihood ratio tests of cumulative link models: 238s 238s formula: link: threshold: 238s fm1 rating ~ temp logit flexible 238s fmm1 rating ~ temp + (1 | judge) logit flexible 238s 238s no.par AIC logLik LR.stat df Pr(>Chisq) 238s fm1 5 194.03 -92.013 238s fmm1 6 189.48 -88.739 6.5492 1 0.01049 * 238s --- 238s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 238s > anova(fmm1, fm1) 238s Likelihood ratio tests of cumulative link models: 238s 238s formula: link: threshold: 238s fm1 rating ~ temp logit flexible 238s fmm1 rating ~ temp + (1 | judge) logit flexible 238s 238s no.par AIC logLik LR.stat df Pr(>Chisq) 238s fm1 5 194.03 -92.013 238s fmm1 6 189.48 -88.739 6.5492 1 0.01049 * 238s --- 238s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 238s > 238s > ## Testing if 'test' and 'type' arguments are ignored properly: 238s > fm1 <- clm(rating ~ temp + contact, data=wine) 238s > fm2 <- clm(rating ~ temp, data=wine) 238s > anova(fm1, fm2, test="Chi") 238s Likelihood ratio tests of cumulative link models: 238s 238s formula: link: threshold: 238s fm2 rating ~ temp logit flexible 238s fm1 rating ~ temp + contact logit flexible 238s 238s no.par AIC logLik LR.stat df Pr(>Chisq) 238s fm2 5 194.03 -92.013 238s fm1 6 184.98 -86.492 11.043 1 0.0008902 *** 238s --- 238s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 238s > anova(fm1, fm2, type="Chi") 238s Likelihood ratio tests of cumulative link models: 238s 238s formula: link: threshold: 238s fm2 rating ~ temp logit flexible 238s fm1 rating ~ temp + contact logit flexible 238s 238s no.par AIC logLik LR.stat df Pr(>Chisq) 238s fm2 5 194.03 -92.013 238s fm1 6 184.98 -86.492 11.043 1 0.0008902 *** 238s --- 238s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 238s > anova(fm1, fm2) 238s Likelihood ratio tests of cumulative link models: 238s 238s formula: link: threshold: 238s fm2 rating ~ temp logit flexible 238s fm1 rating ~ temp + contact logit flexible 238s 238s no.par AIC logLik LR.stat df Pr(>Chisq) 238s fm2 5 194.03 -92.013 238s fm1 6 184.98 -86.492 11.043 1 0.0008902 *** 238s --- 238s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 238s > ## calling anova.clmm 238s > anova(fmm1, fm1, test="Chi") 238s Likelihood ratio tests of cumulative link models: 238s 238s formula: link: threshold: 238s fmm1 rating ~ temp + (1 | judge) logit flexible 238s fm1 rating ~ temp + contact logit flexible 238s 238s 'test' argument ignored in anova.clm 238s 238s 'test' argument ignored in anova.clm 238s 238s no.par AIC logLik LR.stat df Pr(>Chisq) 238s fmm1 6 189.48 -88.739 238s fm1 6 184.98 -86.492 4.4938 0 238s > anova(fmm1, fm1, type="Chi") 238s Likelihood ratio tests of cumulative link models: 238s 238s formula: link: threshold: 238s fmm1 rating ~ temp + (1 | judge) logit flexible 238s fm1 rating ~ temp + contact logit flexible 238s 238s no.par AIC logLik LR.stat df Pr(>Chisq) 238s fmm1 6 189.48 -88.739 238s fm1 6 184.98 -86.492 4.4938 0 238s > 238s > 238s BEGIN TEST clm.fit.R 238s 238s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 238s Copyright (C) 2024 The R Foundation for Statistical Computing 238s Platform: aarch64-unknown-linux-gnu (64-bit) 238s 238s R is free software and comes with ABSOLUTELY NO WARRANTY. 238s You are welcome to redistribute it under certain conditions. 238s Type 'license()' or 'licence()' for distribution details. 238s 238s R is a collaborative project with many contributors. 238s Type 'contributors()' for more information and 238s 'citation()' on how to cite R or R packages in publications. 238s 238s Type 'demo()' for some demos, 'help()' for on-line help, or 238s 'help.start()' for an HTML browser interface to help. 238s Type 'q()' to quit R. 238s 238s > library(ordinal) 239s > data(wine) 239s > 239s > ## clm.fit with nominal and scale effects: 239s > 239s > ## get simple model: 239s > fm1 <- clm(rating ~ temp, scale=~temp, nominal=~ contact, 239s + data=wine, method="design") 239s > str(fm1, give.attr=FALSE) 239s List of 23 239s $ y : Ord.factor w/ 5 levels "1"<"2"<"3"<"4"<..: 2 3 3 4 4 4 5 5 1 2 ... 239s $ y.levels : chr [1:5] "1" "2" "3" "4" ... 239s $ X : num [1:72, 1:2] 1 1 1 1 1 1 1 1 1 1 ... 239s $ offset : num [1:72] 0 0 0 0 0 0 0 0 0 0 ... 239s $ terms :Classes 'terms', 'formula' language rating ~ temp 239s $ contrasts :List of 1 239s ..$ temp: chr "contr.treatment" 239s $ xlevels :List of 1 239s ..$ temp: chr [1:2] "cold" "warm" 239s $ weights : num [1:72] 1 1 1 1 1 1 1 1 1 1 ... 239s $ S : num [1:72, 1:2] 1 1 1 1 1 1 1 1 1 1 ... 239s $ S.terms :Classes 'terms', 'formula' language ~temp 239s $ S.off : num [1:72] 0 0 0 0 0 0 0 0 0 0 ... 239s $ S.contrasts :List of 1 239s ..$ temp: chr "contr.treatment" 239s $ S.xlevels :List of 1 239s ..$ temp: chr [1:2] "cold" "warm" 239s $ NOM : num [1:72, 1:2] 1 1 1 1 1 1 1 1 1 1 ... 239s $ nom.terms :Classes 'terms', 'formula' language ~contact 239s $ nom.contrasts:List of 1 239s ..$ contact: chr "contr.treatment" 239s $ nom.xlevels :List of 1 239s ..$ contact: chr [1:2] "no" "yes" 239s $ doFit : logi TRUE 239s $ control :List of 11 239s ..$ method : chr "design" 239s ..$ sign.location: chr "negative" 239s ..$ sign.nominal : chr "positive" 239s ..$ convergence : chr "warn" 239s ..$ trace : int 0 239s ..$ maxIter : int 100 239s ..$ gradTol : num 1e-06 239s ..$ relTol : num 1e-06 239s ..$ tol : num 1.49e-08 239s ..$ maxLineIter : int 15 239s ..$ maxModIter : int 5 239s $ link : chr "logit" 239s $ threshold : chr "flexible" 239s $ start : NULL 239s $ formulas :List of 4 239s ..$ formula :Class 'formula' language rating ~ temp 239s ..$ scale :Class 'formula' language ~temp 239s ..$ nominal :Class 'formula' language ~contact 239s ..$ fullForm:Class 'formula' language rating ~ temp + temp + contact 239s > fm1$control$method <- "Newton" 239s > res <- clm.fit(fm1) 239s > names(res) 239s [1] "aliased" "alpha" "alpha.mat" "beta" 239s [5] "coefficients" "cond.H" "convergence" "df.residual" 239s [9] "edf" "fitted.values" "gradient" "Hessian" 239s [13] "logLik" "maxGradient" "message" "n" 239s [17] "niter" "nobs" "Theta" "tJac" 239s [21] "vcov" "zeta" 239s > res$Theta 239s contact 1|2 2|3 3|4 4|5 239s 1 no -1.357136 1.2482871 3.839568 5.114111 239s 2 yes -2.969353 -0.2819631 1.959306 3.923477 239s > 239s > ## construct some weights and offsets: 239s > set.seed(1) 239s > off1 <- runif(length(fm1$y)) 239s > set.seed(1) 239s > off2 <- rnorm(length(fm1$y)) 239s > set.seed(1) 239s > wet <- runif(length(fm1$y)) 239s > 239s > ## Fit various models: 239s > fit <- clm.fit(fm1$y, fm1$X, fm1$S, fm1$NOM, weights=wet) 239s > Coef <- 239s + c(-0.905224120279548, 1.31043498891987, 3.34235590523008, 239s + 4.52389661722693, -3.03954652971192, -1.56922389038976, 239s + -1.75662549320839, -1.16845464236365, 2.52988580848393, 239s + -0.0261457032829033) 239s > stopifnot(all.equal(coef(fit), Coef, check.attributes=FALSE, tol=1e-6)) 239s > str(fit) 239s List of 20 239s $ aliased :List of 3 239s ..$ alpha: Named logi [1:8] FALSE FALSE FALSE FALSE FALSE FALSE ... 239s .. ..- attr(*, "names")= chr [1:8] "1|2.(Intercept)" "2|3.(Intercept)" "3|4.(Intercept)" "4|5.(Intercept)" ... 239s ..$ beta :Warning message: 239s Cannot assess if all thresholds are increasing 239s Named logi FALSE 239s .. ..- attr(*, "names")= chr "tempwarm" 239s ..$ zeta : Named logi FALSE 239s .. ..- attr(*, "names")= chr "tempwarm" 239s $ alpha : Named num [1:8] -0.905 1.31 3.342 4.524 -3.04 ... 239s ..- attr(*, "names")= chr [1:8] "1|2.(Intercept)" "2|3.(Intercept)" "3|4.(Intercept)" "4|5.(Intercept)" ... 239s $ beta : Named num 2.53 239s ..- attr(*, "names")= chr "tempwarm" 239s $ coefficients : Named num [1:10] -0.905 1.31 3.342 4.524 -3.04 ... 239s ..- attr(*, "names")= chr [1:10] "1|2.(Intercept)" "2|3.(Intercept)" "3|4.(Intercept)" "4|5.(Intercept)" ... 239s $ cond.H : num 161 239s $ convergence :List of 3 239s ..$ code : int 0 239s ..$ messages : chr "successful convergence" 239s ..$ alg.message: chr "Absolute and relative convergence criteria were met" 239s $ df.residual : num 27 239s $ edf : int 10 239s $ fitted.values: num [1:72] 0.5 0.178 0.394 0.136 0.188 ... 239s $ gradient : Named num [1:10] 7.28e-15 2.70e-13 2.67e-13 -5.17e-13 5.13e-16 ... 239s ..- attr(*, "names")= chr [1:10] "1|2.(Intercept)" "2|3.(Intercept)" "3|4.(Intercept)" "4|5.(Intercept)" ... 239s $ Hessian : num [1:10, 1:10] 2.488 -1.01 0 0 0.207 ... 239s ..- attr(*, "dimnames")=List of 2 239s .. ..$ : chr [1:10] "1|2.(Intercept)" "2|3.(Intercept)" "3|4.(Intercept)" "4|5.(Intercept)" ... 239s .. ..$ : chr [1:10] "1|2.(Intercept)" "2|3.(Intercept)" "3|4.(Intercept)" "4|5.(Intercept)" ... 239s $ logLik : num -44.9 239s $ maxGradient : num 8.93e-13 239s $ message : chr "Absolute and relative convergence criteria were met" 239s $ n : int 72 239s $ niter : Named num [1:2] 9 0 239s ..- attr(*, "names")= chr [1:2] "outer" "inner" 239s $ nobs : num 37 239s $ tJac : num [1:4, 1:4] 1 0 0 0 0 1 0 0 0 0 ... 239s ..- attr(*, "dimnames")=List of 2 239s .. ..$ : chr [1:4] "1|2" "2|3" "3|4" "4|5" 239s .. ..$ : chr [1:4] "1|2" "2|3" "3|4" "4|5" 239s $ vcov : num [1:10, 1:10] 0.5338 0.1835 0.0254 -0.0626 -0.511 ... 239s ..- attr(*, "dimnames")=List of 2 239s .. ..$ : chr [1:10] "1|2.(Intercept)" "2|3.(Intercept)" "3|4.(Intercept)" "4|5.(Intercept)" ... 239s .. ..$ : chr [1:10] "1|2.(Intercept)" "2|3.(Intercept)" "3|4.(Intercept)" "4|5.(Intercept)" ... 239s $ zeta : Named num -0.0261 239s ..- attr(*, "names")= chr "tempwarm" 239s - attr(*, "class")= chr "clm.fit" 239s > 239s > fit <- clm.fit(fm1$y, fm1$X, fm1$S, fm1$NOM, offset=off1) 239s > str(fit) 239s List of 20 239s $ aliased :List of 3 239s ..$ alpha: Named logi [1:8] FALSE FALSE FALSE FALSE FALSE FALSE ... 239s .. ..- attr(*, "names")= chr [1:8] "1|2.(Intercept)" "2|3.(Intercept)" "3|4.(Intercept)" "4|5.(Intercept)" ... 239s ..$ beta : Named logi FALSE 239s .. ..- attr(*, "names")= chr "tempwarm" 239s ..$ zeta : Named logi FALSE 239s .. ..- attr(*, "names")= chr "tempwarm" 239s $ alpha : Named num [1:8] -0.864 1.746 4.342 5.615 -1.567 ... 239s ..- attr(*, "names")= chr [1:8] "1|2.(Intercept)" "2|3.(Intercept)" "3|4.(Intercept)" "4|5.(Intercept)" ... 239s $ beta : Named num 2.7 239s ..- attr(*, "names")= chr "tempwarm" 239s $ coefficients : Named num [1:10] -0.864 1.746 4.342 5.615 -1.567 ... 239s ..- attr(*, "names")= chr [1:10] "1|2.(Intercept)" "2|3.(Intercept)" "3|4.(Intercept)" "4|5.(Intercept)" ... 239s $ cond.H : num 196 239s $ convergence :List of 3 239s ..$ code : int 0 239s ..$ messages : chr "successful convergence" 239s ..$ alg.message: chr "Absolute and relative convergence criteria were met" 239s $ df.residual : num 62 239s $ edf : int 10 239s $ fitted.values: num [1:72] 0.57 0.183 0.452 0.145 0.135 ... 239s $ gradient : Named num [1:10] 2.19e-09 6.14e-08 5.92e-08 -1.23e-07 4.69e-10 ... 239s ..- attr(*, "names")= chr [1:10] "1|2.(Intercept)" "2|3.(Intercept)" "3|4.(Intercept)" "4|5.(Intercept)" ... 239s $ Hessian : num [1:10, 1:10] 4.48 -1.89 0 0 1.02 ... 239s ..- attr(*, "dimnames")=List of 2 239s .. ..$ : chr [1:10] "1|2.(Intercept)" "2|3.(Intercept)" "3|4.(Intercept)" "4|5.(Intercept)" ... 239s .. ..$ : chr [1:10] "1|2.(Intercept)" "2|3.(Intercept)" "3|4.(Intercept)" "4|5.(Intercept)" ... 239s $ logLik : num -86.1 239s $ maxGradient : num 2.17e-07 239s $ message : chr "Absolute and relative convergence criteria were met" 239s $ n : int 72 239s $ niter : Named num [1:2] 8 0 239s ..- attr(*, "names")= chr [1:2] "outer" "inner" 239s $ nobs : num 72 239s $ tJac : num [1:4, 1:4] 1 0 0 0 0 1 0 0 0 0 ... 239s ..- attr(*, "dimnames")=List of 2 239s .. ..$ :Warning message: 239s Cannot assess if all thresholds are increasing 239s chr [1:4] "1|2" "2|3" "3|4" "4|5" 239s .. ..$ : chr [1:4] "1|2" "2|3" "3|4" "4|5" 239s $ vcov : num [1:10, 1:10] 0.33117 0.09074 0.00108 -0.04015 -0.31468 ... 239s ..- attr(*, "dimnames")=List of 2 239s .. ..$ : chr [1:10] "1|2.(Intercept)" "2|3.(Intercept)" "3|4.(Intercept)" "4|5.(Intercept)" ... 239s .. ..$ : chr [1:10] "1|2.(Intercept)" "2|3.(Intercept)" "3|4.(Intercept)" "4|5.(Intercept)" ... 239s $ zeta : Named num 0.114 239s ..- attr(*, "names")= chr "tempwarm" 239s - attr(*, "class")= chr "clm.fit" 239s > 239s > fit <- clm.fit(fm1$y, fm1$X, fm1$S, fm1$NOM, offset=off1, 239s + S.offset=off2) 239s > str(fit) 239s List of 20 239s $ aliased :List of 3 239s ..$ alpha: Named logi [1:8] FALSE FALSE FALSE FALSE FALSE FALSE ... 239s .. ..- attr(*, "names")= chr [1:8] "1|2.(Intercept)" "2|3.(Intercept)" "3|4.(Intercept)" "4|5.(Intercept)" ... 239s ..$ beta : Named logi FALSE 239s .. ..- attr(*, "names")= chr "tempwarm" 239s ..$ zeta : Named logi FALSE 239s .. ..- attr(*, "names")= chr "tempwarm" 239s $ alpha : Named num [1:8] -0.585 1.951 3.24 4.18 -6.481 ... 239s ..- attr(*, "names")= chr [1:8] "1|2.(Intercept)" "2|3.(Intercept)" "3|4.(Intercept)" "4|5.(Intercept)" ... 239s $ beta : Named num 2.12 239s ..- attr(*, "names")= chr "tempwarm" 239s $ coefficients : Named num [1:10] -0.585 1.951 3.24 4.18 -6.481 ... 239s ..- attr(*, "names")= chr [1:10] "1|2.(Intercept)" "2|3.(Intercept)" "3|4.(Intercept)" "4|5.(Intercept)" ... 239s $ cond.H : num 634 239s $ convergence :List of 3 239s ..$ code : int 0 239s ..$ messages : chr "successful convergence" 239s ..$ alg.message: chr "Absolute and relative convergence criteria were met" 239s $ df.residual : num 62 239s $ edf : int 10 239s $ fitted.values: num [1:72] 0.7899 0.1277 0.7 0.0888 0.1521 ... 239s $ gradient : Named num [1:10] 6.73e-12 8.06e-10 7.28e-10 -7.85e-10 1.15e-12 ... 239s ..- attr(*, "names")= chr [1:10] "1|2.(Intercept)" "2|3.(Intercept)" "3|4.(Intercept)" "4|5.(Intercept)" ... 239s $ Hessian : num [1:10, 1:10] 4.126 -1.006 0 0 0.079 ... 239s ..- attr(*, "dimnames")=List of 2 239s .. ..$ : chr [1:10] "1|2.(Intercept)" "2|3.(Intercept)" "3|4.(Intercept)" "4|5.(Intercept)" ... 239s .. ..$ : chr [1:10] "1|2.(Intercept)" "2|3.(Intercept)" "3|4.(Intercept)" "4|5.(Intercept)" ... 239s $ logLik : num -87.6 239s $ maxGradient : num 9.74e-10 239s $ message : chr "Absolute and relative convergence criteria were met" 239s $ n : int 72 239s $ niter :Warning message: 239s Cannot assess if all thresholds are increasing 239s Named num [1:2] 13 0 239s ..- attr(*, "names")= chr [1:2] "outer" "inner" 239s $ nobs : num 72 239s $ tJac : num [1:4, 1:4] 1 0 0 0 0 1 0 0 0 0 ... 239s ..- attr(*, "dimnames")=List of 2 239s .. ..$ : chr [1:4] "1|2" "2|3" "3|4" "4|5" 239s .. ..$ : chr [1:4] "1|2" "2|3" "3|4" "4|5" 239s $ vcov : num [1:10, 1:10] 0.2616 0.0523 0.0345 0.0236 -0.2449 ... 239s ..- attr(*, "dimnames")=List of 2 239s .. ..$ : chr [1:10] "1|2.(Intercept)" "2|3.(Intercept)" "3|4.(Intercept)" "4|5.(Intercept)" ... 239s .. ..$ : chr [1:10] "1|2.(Intercept)" "2|3.(Intercept)" "3|4.(Intercept)" "4|5.(Intercept)" ... 239s $ zeta : Named num -0.502 239s ..- attr(*, "names")= chr "tempwarm" 239s - attr(*, "class")= chr "clm.fit" 239s > 239s > fit <- clm.fit(fm1$y, fm1$X, fm1$S) 239s > str(fit) 239s List of 21 239s $ aliased :List of 3 239s ..$ alpha: Named logi [1:4] FALSE FALSE FALSE FALSE 239s .. ..- attr(*, "names")= chr [1:4] "1|2" "2|3" "3|4" "4|5" 239s ..$ beta : Named logi FALSE 239s .. ..- attr(*, "names")= chr "tempwarm" 239s ..$ zeta : Named logi FALSE 239s .. ..- attr(*, "names")= chr "tempwarm" 239s $ alpha : Named num [1:4] -1.988 0.418 2.648 4.306 239s ..- attr(*, "names")= chr [1:4] "1|2" "2|3" "3|4" "4|5" 239s $ beta : Named num 2.51 239s ..- attr(*, "names")= chr "tempwarm" 239s $ coefficients : Named num [1:6] -1.988 0.418 2.648 4.306 2.512 ... 239s ..- attr(*, "names")= chr [1:6] "1|2" "2|3" "3|4" "4|5" ... 239s $ cond.H : num 80.6 239s $ convergence :List of 3 239s ..$ code : int 0 239s ..$ messages : chr "successful convergence" 239s ..$ alg.message: chr "Absolute and relative convergence criteria were met" 239s $ df.residual : num 66 239s $ edf : int 6 239s $ fitted.values: num [1:72] 0.4826 0.3308 0.3308 0.0528 0.2897 ... 239s $ gradient : Named num [1:6] 7.03e-09 6.91e-08 5.99e-07 -7.42e-07 2.76e-08 ... 239s ..- attr(*, "names")= chr [1:6] "1|2" "2|3" "3|4" "4|5" ... 239s $ Hessian : num [1:6, 1:6] 4.8066 -2.4889 0 0 -0.0926 ... 239s ..- attr(*, "dimnames")=List of 2 239s .. ..$ : chr [1:6] "1|2" "2|3" "3|4" "4|5" ... 239s .. ..$ : chr [1:6] "1|2" "2|3" "3|4" "4|5" ... 239s $ logLik : num -91.8 239s $ maxGradient : num 8.53e-07 239s $ message : chr "Absolute and relative convergence criteria were met" 239s $ n : int 72 239s $ niter : Named num [1:2] 8 0 239s ..- attr(*, "names")= chr [1:2] "outer" "inner" 239s $ nobs : num 72 239s $ Theta : num [1, 1:4] -1.988 0.418 2.648 4.306 239s ..- attr(*, "dimnames")=List of 2 239s .. ..$ : NULL 239s .. ..$ : chr [1:4] "1|2" "2|3" "3|4" "4|5" 239s $ tJac : num [1:4, 1:4] 1 0 0 0 0 1 0 0 0 0 ... 239s ..- attr(*, "dimnames")=List of 2 239s .. ..$ : chr [1:4] "1|2" "2|3" "3|4" "4|5" 239s .. ..$ : chr [1:4] "1|2" "2|3" "3|4" "4|5" 239s $ vcov : num [1:6, 1:6] 0.2481 0.0622 0.0179 -0.0253 0.0197 ... 239s ..- attr(*, "dimnames")=List of 2 239s .. ..$ : chr [1:6] "1|2" "2|3" "3|4" "4|5" ... 239s .. ..$ : chr [1:6] "1|2" "2|3" "3|4" "4|5" ... 239s $ zeta : Named num 0.176 239s ..- attr(*, "names")= chr "tempwarm" 239s - attr(*, "class")= chr "clm.fit" 239s > 239s > fit <- clm.fit(fm1$y, fm1$X) 239s > str(fit) 239s List of 20 239s $ aliased :List of 2 239s ..$ alpha: Named logi [1:4] FALSE FALSE FALSE FALSE 239s .. ..- attr(*, "names")= chr [1:4] "1|2" "2|3" "3|4" "4|5" 239s ..$ beta : Named logi FALSE 239s .. ..- attr(*, "names")= chr "tempwarm" 239s $ alpha : Named num [1:4] -1.936 0.435 2.432 3.827 239s ..- attr(*, "names")= chr [1:4] "1|2" "2|3" "3|4" "4|5" 239s $ beta : Named num 2.29 239s ..- attr(*, "names")= chr "tempwarm" 239s $ coefficients : Named num [1:5] -1.936 0.435 2.432 3.827 2.287 239s ..- attr(*, "names")= chr [1:5] "1|2" "2|3" "3|4" "4|5" ... 239s $ cond.H : num 16.8 239s $ convergence :List of 3 239s ..$ code : int 0 239s ..$ messages : chr "successful convergence" 239s ..$ alg.message: chr "Absolute and relative convergence criteria were met" 239s $ df.residual : num 67 239s $ edf : int 5 239s $ fitted.values: num [1:72] 0.481 0.3122 0.3122 0.0594 0.2871 ... 239s $ gradient : Named num [1:5] 4.12e-14 8.11e-14 -1.06e-13 9.19e-16 -1.79e-14 239s ..- attr(*, "names")= chr [1:5] "1|2" "2|3" "3|4" "4|5" ... 239s $ Hessian : num [1:5, 1:5] 4.8983 -2.499 0 0 -0.0854 ... 239s ..- attr(*, "dimnames")=List of 2 239s .. ..$ : chr [1:5] "1|2" "2|3" "3|4" "4|5" ... 239s .. ..$ : chr [1:5] "1|2" "2|3" "3|4" "4|5" ... 239s $ logLik : num -92 239s $ maxGradient : num 1.06e-13 239s $ message : chr "Absolute and relative convergence criteria were met" 239s $ n : int 72 239s $ niter : Named num [1:2] 6 0 239s ..- attr(*, "names")= chr [1:2] "outer" "inner" 239s $ nobs : num 72 239s $ Theta : num [1, 1:4] -1.936 0.435 2.432 3.827 239s ..- attr(*, "dimnames")=List of 2 239s .. ..$ : NULL 239s .. ..$ : chr [1:4] "1|2" "2|3" "3|4" "4|5" 239s $ tJac : num [1:4, 1:4] 1 0 0 0 0 1 0 0 0 0 ... 239s ..- attr(*, "dimnames")=List of 2 239s .. ..$ : chr [1:4] "1|2" "2|3" "3|4" "4|5" 239s .. ..$ : chr [1:4] "1|2" "2|3" "3|4" "4|5" 239s $ vcov : num [1:5, 1:5] 0.2345 0.0577 0.0505 0.0512 0.0537 ... 239s ..- attr(*, "dimnames")=List of 2 239s .. ..$ : chr [1:5] "1|2" "2|3" "3|4" "4|5" ... 239s .. ..$ : chr [1:5] "1|2" "2|3" "3|4" "4|5" ... 239s - attr(*, "class")= chr "clm.fit" 239s > 239s > fit <- clm.fit(fm1$y) 239s > coef(fit) 239s 1|2 2|3 3|4 4|5 239s -2.5952547 -0.5108256 1.0258529 2.2284771 239s > str(fit) 239s List of 19 239s $ aliased :List of 2 239s ..$ alpha: Named logi [1:4] FALSE FALSE FALSE FALSE 239s .. ..- attr(*, "names")= chr [1:4] "1|2" "2|3" "3|4" "4|5" 239s ..$ beta : Named logi(0) 239s .. ..- attr(*, "names")= chr(0) 239s $ alpha : Named num [1:4] -2.595 -0.511 1.026 2.228 239s ..- attr(*, "names")= chr [1:4] "1|2" "2|3" "3|4" "4|5" 239s $ coefficients : Named num [1:4] -2.595 -0.511 1.026 2.228 239s ..- attr(*, "names")= chr [1:4] "1|2" "2|3" "3|4" "4|5" 239s $ cond.H : num 8.38 239s $ convergence :List of 3 239s ..$ code : int 0 239s ..$ messages : chr "successful convergence" 239s ..$ alg.message: chr "Absolute and relative convergence criteria were met" 239s $ df.residual : num 68 239s $ edf : int 4 239s $ fitted.values: num [1:72] 0.306 0.361 0.361 0.167 0.167 ... 239s $ gradient : Named num [1:4] 7.23e-08 -5.51e-08 -1.72e-11 -4.87e-12 239s ..- attr(*, "names")= chr [1:4] "1|2" "2|3" "3|4" "4|5" 239s $ Hessian : num [1:4, 1:4] 5.31 -3.57 0 0 -3.57 ... 239s ..- attr(*, "dimnames")=List of 2 239s .. ..$ : chr [1:4] "1|2" "2|3" "3|4" "4|5" 239s .. ..$ : chr [1:4] "1|2" "2|3" "3|4" "4|5" 239s $ logLik : num -104 239s $ maxGradient : num 7.23e-08 239s $ message : chr "Absolute and relative convergence criteria were met" 239s $ n : int 72 239s $ niter : Named num [1:2] 5 0 239s ..- attr(*, "names")= chr [1:2] "outer" "inner" 239s $ nobs : num 72 239s $ Theta : num [1, 1:4] -2.595 -0.511 1.026 2.228 239s ..- attr(*, "dimnames")=List of 2 239s .. ..$ : NULL 239s .. ..$ : chr [1:4] "1|2" "2|3" "3|4" "4|5" 239s $ tJac : num [1:4, 1:4] 1 0 0 0 0 1 0 0 0 0 ... 239s ..- attr(*, "dimnames")=List of 2 239s .. ..$ : chr [1:4] "1|2" "2|3" "3|4" "4|5" 239s .. ..$ : chr [1:4] "1|2" "2|3" "3|4" "4|5" 239s $ vcov : num [1:4, 1:4] 0.2149 0.0398 0.0203 0.0165 0.0398 ... 239s ..- attr(*, "dimnames")=List of 2 239s .. ..$ : chr [1:4] "1|2" "2|3" "3|4" "4|5" 239s .. ..$ : chr [1:4] "1|2" "2|3" "3|4" "4|5" 239s - attr(*, "class")= chr "clm.fit" 239s > 239s > ## Remember: compare with corresponding .Rout file 239s > 239s BEGIN TEST clm.formula.R 239s 239s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 239s Copyright (C) 2024 The R Foundation for Statistical Computing 239s Platform: aarch64-unknown-linux-gnu (64-bit) 239s 239s R is free software and comes with ABSOLUTELY NO WARRANTY. 239s You are welcome to redistribute it under certain conditions. 239s Type 'license()' or 'licence()' for distribution details. 239s 239s R is a collaborative project with many contributors. 239s Type 'contributors()' for more information and 239s 'citation()' on how to cite R or R packages in publications. 239s 239s Type 'demo()' for some demos, 'help()' for on-line help, or 239s 'help.start()' for an HTML browser interface to help. 239s Type 'q()' to quit R. 239s 239s > library(ordinal) 240s > ## library(devtools) 240s > ## r2path <- "/Users/rhbc/Documents/Rpackages/ordinal/pkg/ordinal" 240s > ## clean_dll(pkg = r2path) 240s > ## load_all(r2path) 240s > 240s > ################################# 240s > ## Appropriate evaluation of formulas: 240s > 240s > ## These fail and give appropriate error messages: 240s > ## fm1 <- clm(rating ~ contact, scale=temp, data=wine) 240s > ## fm1 <- clm(rating ~ contact, scale=~Temp, data=wine) 240s > ## fm1 <- clm(rating ~ contact, scale="temp", data=wine) 240s > ## sca <- "temp" 240s > ## fm1 <- clm(rating ~ contact, scale=sca, data=wine) 240s > ## sca <- as.formula(sca) 240s > ## sca <- as.formula(temp) 240s > ## sca <- with(wine, as.formula(temp)) 240s > 240s > ## These all work as intended with no warnings or errors: 240s > fm1 <- clm(rating ~ contact, scale="~temp", data=wine) 240s > fm1 <- clm(rating ~ contact, scale=~temp, data=wine) 240s > sca <- "~temp" 240s > fm1 <- clm(rating ~ contact, scale=sca, data=wine) 240s > sca <- as.formula("~temp") 240s > fm1 <- clm(rating ~ contact, scale=sca, data=wine) 240s > fm1 <- clm(rating ~ contact, scale=as.formula(~temp), data=wine) 240s > fm1 <- clm(rating ~ contact, scale=as.formula("~temp"), data=wine) 240s > 240s > ################################# 240s > ## can evaluate if 'formula' is a character: 240s > f <- "rating ~ contact + temp" 240s > clm(f, data=wine) 240s formula: rating ~ contact + temp 240s data: wine 240s 240s link threshold nobs logLik AIC niter max.grad cond.H 240s logit flexible 72 -86.49 184.98 6(0) 4.01e-12 2.7e+01 240s 240s Coefficients: 240s contactyes tempwarm 240s 1.528 2.503 240s 240s Threshold coefficients: 240s 1|2 2|3 3|4 4|5 240s -1.344 1.251 3.467 5.006 240s > clm(as.formula(f), data=wine) 240s formula: rating ~ contact + temp 240s data: wine 240s 240s link threshold nobs logLik AIC niter max.grad cond.H 240s logit flexible 72 -86.49 184.98 6(0) 4.01e-12 2.7e+01 240s 240s Coefficients: 240s contactyes tempwarm 240s 1.528 2.503 240s 240s Threshold coefficients: 240s 1|2 2|3 3|4 4|5 240s -1.344 1.251 3.467 5.006 240s > 240s > ################################# 240s > 240s > ### finding variables in the environment of the formula: 240s > makeform <- function() { 240s + f1 <- as.formula(rating ~ temp + contact) 240s + rating <- wine$rating 240s + temp <- wine$temp 240s + contact <- wine$contact 240s + f1 240s + } 240s > ## 'makeform' makes are formula object in the environment of the 240s > ## function makeform: 240s > f1 <- makeform() 240s > f1 # print 240s rating ~ temp + contact 240s 240s > class(f1) 240s [1] "formula" 240s > ## If we give the data, we can evaluate the model: 240s > fm1 <- clm(f1, data=wine) 240s > ## We can also evaluate the model because the data are available in 240s > ## the environment associated with the formula: 240s > fm1 <- clm(f1) 240s > ## For instance, the 'rating' variable is not found in the Global 240s > ## environment; we have to evaluate the 'name' of 'rating' in the 240s > ## appropriate environment: 240s > (try(rating, silent=TRUE)) 240s [1] "Error : object 'rating' not found\n" 240s attr(,"class") 240s [1] "try-error" 240s attr(,"condition") 240s 240s > eval(as.name("rating"), envir=environment(f1)) 240s [1] 2 3 3 4 4 4 5 5 1 2 1 3 2 3 5 4 2 3 3 2 5 5 4 4 3 2 3 2 3 2 5 3 2 3 4 3 3 3 240s [39] 3 3 3 2 3 2 2 4 5 4 1 1 2 2 2 3 2 3 2 2 2 3 3 3 3 4 1 2 3 2 3 2 4 4 240s Levels: 1 < 2 < 3 < 4 < 5 240s > ## If instead we generate the formula in the Global environment where 240s > ## the variables are not found, we cannot evaluate the model: 240s > f2 <- as.formula(rating ~ temp + contact) 240s > (try(fm2 <- clm(f2), silent=TRUE)) 240s [1] "Error in eval(predvars, data, env) : object 'rating' not found\n" 240s attr(,"class") 240s [1] "try-error" 240s attr(,"condition") 240s 240s > environment(f2) <- environment(f1) 240s > fm2 <- clm(f2) 240s > 240s > 240s > ################################# 240s > ## Use of formula-objects in location, scale and nominal: 240s > ## Bug-report from Lluís Marco Almagro 240s > ## 5 May 2010 17:58 240s > f <- formula(rating ~ temp) 240s > fs <- formula( ~ contact) 240s > m2 <- clm(f, scale = fs, data = wine) 240s > summary(m2) 240s formula: rating ~ temp 240s scale: ~contact 240s data: wine 240s 240s link threshold nobs logLik AIC niter max.grad cond.H 240s logit flexible 72 -91.92 195.83 8(0) 1.57e-09 5.6e+01 240s 240s Coefficients: 240s Estimate Std. Error z value Pr(>|z|) 240s tempwarm 2.1690 0.5527 3.924 8.69e-05 *** 240s --- 240s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 240s 240s log-scale coefficients: 240s Estimate Std. Error z value Pr(>|z|) 240s contactyes -0.1222 0.2775 -0.44 0.66 240s 240s Threshold coefficients: 240s Estimate Std. Error z value 240s 1|2 -1.8957 0.4756 -3.986 240s 2|3 0.3668 0.3442 1.066 240s 3|4 2.2483 0.5932 3.790 240s 4|5 3.5393 0.8336 4.246 240s > 240s > ################################# 240s > ## Other ways to construct formulas: 240s > set.seed(12345) 240s > y <- factor(sample(1:4,20,replace=TRUE)) 240s > x <- rnorm(20) 240s > data <- data.frame(y=y,x=x) 240s > rm(x, y) 240s > fit <- clm(data$y ~ data$x) 240s > fit 240s formula: data$y ~ data$x 240s 240s link threshold nobs logLik AIC niter max.grad cond.H 240s logit flexible 20 -25.37 58.74 5(0) 2.68e-09 8.4e+00 240s 240s Coefficients: 240s data$x 240s 0.2527 240s 240s Threshold coefficients: 240s 1|2 2|3 3|4 240s -2.18234 0.06059 0.92746 240s > fit <- clm(data[,1] ~ data[,2]) 240s > fit 240s formula: data[, 1] ~ data[, 2] 240s 240s link threshold nobs logLik AIC niter max.grad cond.H 240s logit flexible 20 -25.37 58.74 5(0) 2.68e-09 8.4e+00 240s 240s Coefficients: 240s data[, 2] 240s 0.2527 240s 240s Threshold coefficients: 240s 1|2 2|3 3|4 240s -2.18234 0.06059 0.92746 240s > ## This previously failed, but now works: 240s > fit <- clm(data$y ~ data$x, ~data$x) 240s > fit 240s formula: data$y ~ data$x 240s scale: ~data$x 240s 240s link threshold nobs logLik AIC niter max.grad cond.H 240s logit flexible 20 -25.32 60.64 7(0) 1.86e-09 9.7e+00 240s 240s Coefficients: 240s data$x 240s 0.2477 240s 240s log-scale coefficients: 240s data$x 240s -0.1136 240s 240s Threshold coefficients: 240s 1|2 2|3 3|4 240s -2.16950 0.07039 0.91381 240s > 240s > ################################# 240s > ## Evaluation within other functions: 240s > ## date: January 18th 2012. 240s > ## 240s > ## The problem was raised by Stefan Herzog (stefan.herzog@unibas.ch) 240s > ## January 12th 2012 in trying to make clm work with glmulti. 240s > 240s > fun.clm <- function(formula, data) 240s + ### This only works because clm via eclm.model.frame is careful to 240s + ### evaluate the 'formula' in the parent environment such it is not the 240s + ### character "formula" that is attempted evaluated. 240s + clm(formula, data = data) 240s > 240s > fun2.clm <- function(formula, data, weights, subset) { 240s + ### This should be the safe way to ensure evaluation of clm in the 240s + ### right environment. 240s + mc <- match.call() 240s + mc[[1]] <- as.name("clm") 240s + eval.parent(mc) 240s + } 240s > 240s > fun.clm(rating ~ temp + contact, data=wine) ## works 240s formula: rating ~ temp + contact 240s data: data 240s 240s link threshold nobs logLik AIC niter max.grad cond.H 240s logit flexible 72 -86.49 184.98 6(0) 4.01e-12 2.7e+01 240s 240s Coefficients: 240s tempwarm contactyes 240s 2.503 1.528 240s 240s Threshold coefficients: 240s 1|2 2|3 3|4 4|5 240s -1.344 1.251 3.467 5.006 240s > fun2.clm(rating ~ temp + contact, data=wine) ## works 240s formula: rating ~ temp + contact 240s data: wine 240s 240s link threshold nobs logLik AIC niter max.grad cond.H 240s logit flexible 72 -86.49 184.98 6(0) 4.01e-12 2.7e+01 240s 240s Coefficients: 240s tempwarm contactyes 240s 2.503 1.528 240s 240s Threshold coefficients: 240s 1|2 2|3 3|4 4|5 240s -1.344 1.251 3.467 5.006 240s > 240s > form1 <- "rating ~ temp + contact" 240s > fun.clm(form1, data=wine) ## works 240s formula: rating ~ temp + contact 240s data: data 240s 240s link threshold nobs logLik AIC niter max.grad cond.H 240s logit flexible 72 -86.49 184.98 6(0) 4.01e-12 2.7e+01 240s 240s Coefficients: 240s tempwarm contactyes 240s 2.503 1.528 240s 240s Threshold coefficients: 240s 1|2 2|3 3|4 4|5 240s -1.344 1.251 3.467 5.006 240s > fun2.clm(form1, data=wine) ## works 240s formula: rating ~ temp + contact 240s data: wine 240s 240s link threshold nobs logLik AIC niter max.grad cond.H 240s logit flexible 72 -86.49 184.98 6(0) 4.01e-12 2.7e+01 240s 240s Coefficients: 240s tempwarm contactyes 240s 2.503 1.528 240s 240s Threshold coefficients: 240s 1|2 2|3 3|4 4|5 240s -1.344 1.251 3.467 5.006 240s > 240s > form2 <- formula(rating ~ temp + contact) 240s > fun.clm(form2, data=wine) ## works 240s formula: rating ~ temp + contact 240s data: data 240s 240s link threshold nobs logLik AIC niter max.grad cond.H 240s logit flexible 72 -86.49 184.98 6(0) 4.01e-12 2.7e+01 240s 240s Coefficients: 240s tempwarm contactyes 240s 2.503 1.528 240s 240s Threshold coefficients: 240s 1|2 2|3 3|4 4|5 240s -1.344 1.251 3.467 5.006 240s > fun2.clm(form2, data=wine) ## works 240s formula: rating ~ temp + contact 240s data: wine 240s 240s link threshold nobs logLik AIC niter max.grad cond.H 240s logit flexible 72 -86.49 184.98 6(0) 4.01e-12 2.7e+01 240s 240s Coefficients: 240s tempwarm contactyes 240s 2.503 1.528 240s 240s Threshold coefficients: 240s 1|2 2|3 3|4 4|5 240s -1.344 1.251 3.467 5.006 240s > ## Notice that clm is not able to get the name of the data (wine) 240s > ## correct when using fun.clm. 240s > 240s > ################################# 240s > ## Evaluation of long formulas: no line breaking in getFullForm: 240s > data(soup, package="ordinal") 240s > 240s > rhs <- paste(names(soup)[c(3, 5:12)], collapse=" + ") 240s > Location <- as.formula(paste("SURENESS ~ ", rhs, sep=" ")) 240s > Scale <- as.formula("~ PROD") 240s > 240s > fm5 <- clm(Location, scale=Scale, data=soup) 240s > summary(fm5) 240s formula: 240s SURENESS ~ PRODID + DAY + SOUPTYPE + SOUPFREQ + COLD + EASY + GENDER + AGEGROUP + LOCATION 240s scale: ~PROD 240s data: soup 240s 240s link threshold nobs logLik AIC niter max.grad cond.H 240s logit flexible 1847 -2651.65 5367.30 8(1) 4.65e-07 1.1e+04 240s 240s Coefficients: 240s Estimate Std. Error z value Pr(>|z|) 240s PRODID2 1.09324 0.14790 7.392 1.45e-13 *** 240s PRODID3 1.54233 0.21252 7.257 3.95e-13 *** 240s PRODID4 0.95602 0.18180 5.258 1.45e-07 *** 240s PRODID5 1.52404 0.20311 7.504 6.21e-14 *** 240s PRODID6 1.83964 0.21750 8.458 < 2e-16 *** 240s DAY2 -0.26999 0.10280 -2.626 0.00863 ** 240s SOUPTYPECanned -0.31340 0.11745 -2.668 0.00762 ** 240s SOUPTYPEDry-mix 0.22429 0.14295 1.569 0.11665 240s SOUPFREQ1-4/month -0.06459 0.10551 -0.612 0.54046 240s SOUPFREQ<1/month 0.03664 0.21310 0.172 0.86350 240s COLDYes 0.31373 0.14894 2.106 0.03517 * 240s EASY2 0.16689 0.55063 0.303 0.76182 240s EASY3 0.34765 0.50432 0.689 0.49061 240s EASY4 0.30008 0.48283 0.621 0.53428 240s EASY5 0.23492 0.47686 0.493 0.62226 240s EASY6 -0.03205 0.46993 -0.068 0.94562 240s EASY7 0.02823 0.46963 0.060 0.95208 240s EASY8 -0.04600 0.47066 -0.098 0.92215 240s EASY9 -0.04084 0.49595 -0.082 0.93437 240s EASY10 1.03641 0.60080 1.725 0.08452 . 240s GENDERFemale -0.05092 0.10738 -0.474 0.63534 240s AGEGROUP31-40 0.02098 0.14822 0.142 0.88745 240s AGEGROUP41-50 0.23712 0.15824 1.498 0.13401 240s AGEGROUP51-65 -0.13791 0.14393 -0.958 0.33798 240s LOCATIONRegion 2 -0.09641 0.13225 -0.729 0.46599 240s LOCATIONRegion 3 0.06062 0.11981 0.506 0.61290 240s --- 240s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 240s 240s log-scale coefficients: 240s Estimate Std. Error z value Pr(>|z|) 240s PRODTest 0.14545 0.06621 2.197 0.028 * 240s --- 240s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 240s 240s Threshold coefficients: 240s Estimate Std. Error z value 240s 1|2 -1.64700 0.49982 -3.295 240s 2|3 -0.58840 0.49681 -1.184 240s 3|4 -0.23496 0.49669 -0.473 240s 4|5 0.04394 0.49679 0.088 240s 5|6 0.78551 0.49869 1.575 240s > 240s > ################################# 240s > ## Check that "."-notation works in formula: 240s > ## December 25th 2014, RHBC 240s > data(wine) 240s > wine2 <- wine[c("rating", "contact", "temp")] 240s > str(wine2) 240s 'data.frame': 72 obs. of 3 variables: 240s $ rating : Ord.factor w/ 5 levels "1"<"2"<"3"<"4"<..: 2 3 3 4 4 4 5 5 1 2 ... 240s $ contact: Factor w/ 2 levels "no","yes": 1 1 2 2 1 1 2 2 1 1 ... 240s $ temp : Factor w/ 2 levels "cold","warm": 1 1 1 1 2 2 2 2 1 1 ... 240s > fm0 <- clm(rating ~ ., data=wine2) 241s > fm1 <- clm(rating ~ contact + temp, data=wine2) 241s > keep <- c("coefficients", "logLik", "info") 241s > fun <- function(x, y) stopifnot(isTRUE(all.equal(x, y))) 241s > mapply(fun, fm0[keep], fm1[keep]) 241s $coefficients 241s NULL 241s 241s $logLik 241s NULL 241s 241s $info 241s NULL 241s 241s > ################################# 241s > 241s BEGIN TEST clmm.R 241s 241s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 241s Copyright (C) 2024 The R Foundation for Statistical Computing 241s Platform: aarch64-unknown-linux-gnu (64-bit) 241s 241s R is free software and comes with ABSOLUTELY NO WARRANTY. 241s You are welcome to redistribute it under certain conditions. 241s Type 'license()' or 'licence()' for distribution details. 241s 241s R is a collaborative project with many contributors. 241s Type 'contributors()' for more information and 241s 'citation()' on how to cite R or R packages in publications. 241s 241s Type 'demo()' for some demos, 'help()' for on-line help, or 241s 'help.start()' for an HTML browser interface to help. 241s Type 'q()' to quit R. 241s 241s > library(ordinal) 242s > data(wine) 242s > 242s > ################################# 242s > ## Estimation with a single simple RE term: 242s > ## Laplace: 242s > fmm1 <- clmm(rating ~ contact + temp + (1|judge), data=wine) 242s > summary(fmm1) 242s Cumulative Link Mixed Model fitted with the Laplace approximation 242s 242s formula: rating ~ contact + temp + (1 | judge) 242s data: wine 242s 242s link threshold nobs logLik AIC niter max.grad cond.H 242s logit flexible 72 -81.57 177.13 332(999) 1.03e-05 2.8e+01 242s 242s Random effects: 242s Groups Name Variance Std.Dev. 242s judge (Intercept) 1.279 1.131 242s Number of groups: judge 9 242s 242s Coefficients: 242s Estimate Std. Error z value Pr(>|z|) 242s contactyes 1.8349 0.5125 3.580 0.000344 *** 242s tempwarm 3.0630 0.5954 5.145 2.68e-07 *** 242s --- 242s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 242s 242s Threshold coefficients: 242s Estimate Std. Error z value 242s 1|2 -1.6237 0.6824 -2.379 242s 2|3 1.5134 0.6038 2.507 242s 3|4 4.2285 0.8090 5.227 242s 4|5 6.0888 0.9725 6.261 242s > ## GHQ: 242s > fmm.ghq <- clmm(rating ~ contact + temp + (1|judge), data=wine, 242s + nAGQ=-10) 242s > summary(fmm.ghq) 242s Cumulative Link Mixed Model fitted with the Gauss-Hermite 242s quadrature approximation with 10 quadrature points 242s 242s formula: rating ~ contact + temp + (1 | judge) 242s data: wine 242s 242s link threshold nobs logLik AIC niter max.grad cond.H 242s logit flexible 72 -81.53 177.06 304(3) 1.67e-05 2.8e+01 242s 242s Random effects: 242s Groups Name Variance Std.Dev. 242s judge (Intercept) 1.288 1.135 242s Number of groups: judge 9 242s 242s Coefficients: 242s Estimate Std. Error z value Pr(>|z|) 242s contactyes 1.8335 0.5122 3.580 0.000344 *** 242s tempwarm 3.0620 0.5951 5.145 2.67e-07 *** 242s --- 242s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 242s 242s Threshold coefficients: 242s Estimate Std. Error z value 242s 1|2 -1.6231 0.6829 -2.377 242s 2|3 1.5133 0.6045 2.503 242s 3|4 4.2277 0.8094 5.223 242s 4|5 6.0869 0.9726 6.258 242s > ## AGQ: 242s > fmm.agq <- clmm(rating ~ contact + temp + (1|judge), data=wine, 242s + nAGQ=10) 242s > summary(fmm.agq) 242s Cumulative Link Mixed Model fitted with the adaptive Gauss-Hermite 242s quadrature approximation with 10 quadrature points 242s 242s formula: rating ~ contact + temp + (1 | judge) 242s data: wine 242s 242s link threshold nobs logLik AIC niter max.grad cond.H 242s logit flexible 72 -81.53 177.06 304(915) 2.26e-05 2.8e+01 242s 242s Random effects: 242s Groups Name Variance Std.Dev. 242s judge (Intercept) 1.288 1.135 242s Number of groups: judge 9 242s 242s Coefficients: 242s Estimate Std. Error z value Pr(>|z|) 242s contactyes 1.8334 0.5122 3.580 0.000344 *** 242s tempwarm 3.0619 0.5951 5.145 2.67e-07 *** 242s --- 242s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 242s 242s Threshold coefficients: 242s Estimate Std. Error z value 242s 1|2 -1.6235 0.6834 -2.376 242s 2|3 1.5128 0.6044 2.503 242s 3|4 4.2271 0.8090 5.225 242s 4|5 6.0862 0.9719 6.262 242s > ## tests: 242s > ## Notice warning about Laplace with multiple REs when nAGQ != 1: 242s > fmm1 <- try(clmm(rating ~ contact + temp + (1|judge) + (1|bottle), 242s + data=wine, nAGQ=10)) 242s > stopifnot(inherits(fmm1, "try-error")) 242s > 242s > Error : Quadrature methods are not available with more than one random effects term 242s ################################# 242s > ## Estimation with several RE terms: 242s > data(soup, package="ordinal") 242s > fmm <- clmm(SURENESS ~ PROD + (1|RESP) + (1|PROD:RESP), data=soup, 242s + threshold="equidistant") 244s > summary(fmm) 244s Cumulative Link Mixed Model fitted with the Laplace approximation 244s 244s formula: SURENESS ~ PROD + (1 | RESP) + (1 | PROD:RESP) 244s data: soup 244s 244s link threshold nobs logLik AIC niter max.grad cond.H 244s logit equidistant 1847 -2766.32 5542.63 225(711) 1.01e-03 1.3e+02 244s 244s Random effects: 244s Groups Name Variance Std.Dev. 244s PROD:RESP (Intercept) 0.4070 0.6379 244s RESP (Intercept) 0.1308 0.3616 244s Number of groups: PROD:RESP 370, RESP 185 244s 244s Coefficients: 244s Estimate Std. Error z value Pr(>|z|) 244s PRODTest 1.2865 0.1156 11.12 <2e-16 *** 244s --- 244s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 244s 244s Threshold coefficients: 244s Estimate Std. Error z value 244s threshold.1 -1.35104 0.09526 -14.18 244s spacing 0.56472 0.01905 29.65 244s > 244s > ################################# 244s > 244s > ## Estimation with implicit intercept: 244s > fm1 <- clmm(rating ~ 1 + (1|judge), data = wine) 244s > fm2 <- clmm(rating ~ (1|judge), data = wine) 244s > fm3 <- clmm(rating ~ 0 + (1|judge), data = wine) 244s Warning message: 244s In getX(fullmf, fixedmf, contrasts) : an intercept is needed and assumed 244s > stopifnot(isTRUE(all.equal(coef(fm1), coef(fm2), tolerance=1e-5)), 244s + isTRUE(all.equal(coef(fm1), coef(fm3), tolerance=1e-5))) 244s > 244s BEGIN TEST clmm.control.R 245s 245s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 245s Copyright (C) 2024 The R Foundation for Statistical Computing 245s Platform: aarch64-unknown-linux-gnu (64-bit) 245s 245s R is free software and comes with ABSOLUTELY NO WARRANTY. 245s You are welcome to redistribute it under certain conditions. 245s Type 'license()' or 'licence()' for distribution details. 245s 245s R is a collaborative project with many contributors. 245s Type 'contributors()' for more information and 245s 'citation()' on how to cite R or R packages in publications. 245s 245s Type 'demo()' for some demos, 'help()' for on-line help, or 245s 'help.start()' for an HTML browser interface to help. 245s Type 'q()' to quit R. 245s 245s > library(ordinal) 246s > data(wine) 246s > 246s > 246s > ### 3 options for specifying control arguments: 246s > ## 1) control is a simple list, e.g. list(trace=-1) 246s > ## 2) control is a call to clmm.control 246s > ## 3) control is an empty list; list() 246s > ## all in combination with extra control arguments. 246s > 246s > ordinal:::getCtrlArgs(clmm.control(), list(maxIter=200)) 246s $method 246s [1] "nlminb" 246s 246s $useMatrix 246s [1] FALSE 246s 246s $ctrl 246s $ctrl$trace 246s [1] 0 246s 246s $ctrl$maxIter 246s [1] 200 246s 246s $ctrl$gradTol 246s [1] 1e-04 246s 246s $ctrl$maxLineIter 246s [1] 50 246s 246s $ctrl$innerCtrl 246s [1] "warnOnly" 246s 246s 246s $optCtrl 246s $optCtrl$trace 246s [1] 0 246s 246s 246s $checkRanef 246s [1] "warn" 246s 246s > ordinal:::getCtrlArgs(list(), list(maxIter=200)) 246s $method 246s [1] "nlminb" 246s 246s $useMatrix 246s [1] FALSE 246s 246s $ctrl 246s $ctrl$trace 246s [1] 0 246s 246s $ctrl$maxIter 246s [1] 200 246s 246s $ctrl$gradTol 246s [1] 1e-04 246s 246s $ctrl$maxLineIter 246s [1] 50 246s 246s $ctrl$innerCtrl 246s [1] "warnOnly" 246s 246s 246s $optCtrl 246s $optCtrl$trace 246s [1] 0 246s 246s 246s $checkRanef 246s [1] "warn" 246s 246s > ordinal:::getCtrlArgs(list(), list(trace=-1)) 246s $method 246s [1] "nlminb" 246s 246s $useMatrix 246s [1] FALSE 246s 246s $ctrl 246s $ctrl$trace 246s [1] 1 246s 246s $ctrl$maxIter 246s [1] 50 246s 246s $ctrl$gradTol 246s [1] 1e-04 246s 246s $ctrl$maxLineIter 246s [1] 50 246s 246s $ctrl$innerCtrl 246s [1] "warnOnly" 246s 246s 246s $optCtrl 246s $optCtrl$trace 246s [1] 1 246s 246s 246s $checkRanef 246s [1] "warn" 246s 246s > ordinal:::getCtrlArgs(list(), list(trace=1)) 246s $method 246s [1] "nlminb" 246s 246s $useMatrix 246s [1] FALSE 246s 246s $ctrl 246s $ctrl$trace 246s [1] 0 246s 246s $ctrl$maxIter 246s [1] 50 246s 246s $ctrl$gradTol 246s [1] 1e-04 246s 246s $ctrl$maxLineIter 246s [1] 50 246s 246s $ctrl$innerCtrl 246s [1] "warnOnly" 246s 246s 246s $optCtrl 246s $optCtrl$trace 246s [1] 1 246s 246s 246s $checkRanef 246s [1] "warn" 246s 246s > ordinal:::getCtrlArgs(list(), list()) 246s $method 246s [1] "nlminb" 246s 246s $useMatrix 246s [1] FALSE 246s 246s $ctrl 246s $ctrl$trace 246s [1] 0 246s 246s $ctrl$maxIter 246s [1] 50 246s 246s $ctrl$gradTol 246s [1] 1e-04 246s 246s $ctrl$maxLineIter 246s [1] 50 246s 246s $ctrl$innerCtrl 246s [1] "warnOnly" 246s 246s 246s $optCtrl 246s $optCtrl$trace 246s [1] 0 246s 246s 246s $checkRanef 246s [1] "warn" 246s 246s > ordinal:::getCtrlArgs(list(maxIter=2), list()) 246s $method 246s [1] "nlminb" 246s 246s $useMatrix 246s [1] FALSE 246s 246s $ctrl 246s $ctrl$trace 246s [1] 0 246s 246s $ctrl$maxIter 246s [1] 2 246s 246s $ctrl$gradTol 246s [1] 1e-04 246s 246s $ctrl$maxLineIter 246s [1] 50 246s 246s $ctrl$innerCtrl 246s [1] "warnOnly" 246s 246s 246s $optCtrl 246s $optCtrl$trace 246s [1] 0 246s 246s 246s $checkRanef 246s [1] "warn" 246s 246s > 246s > ordinal:::getCtrlArgs(clmm.control(), list()) 246s $method 246s [1] "nlminb" 246s 246s $useMatrix 246s [1] FALSE 246s 246s $ctrl 246s $ctrl$trace 246s [1] 0 246s 246s $ctrl$maxIter 246s [1] 50 246s 246s $ctrl$gradTol 246s [1] 1e-04 246s 246s $ctrl$maxLineIter 246s [1] 50 246s 246s $ctrl$innerCtrl 246s [1] "warnOnly" 246s 246s 246s $optCtrl 246s $optCtrl$trace 246s [1] 0 246s 246s 246s $checkRanef 246s [1] "warn" 246s 246s > ordinal:::getCtrlArgs(clmm.control(maxIter=100), list(maxIter=200)) 246s $method 246s [1] "nlminb" 246s 246s $useMatrix 246s [1] FALSE 246s 246s $ctrl 246s $ctrl$trace 246s [1] 0 246s 246s $ctrl$maxIter 246s [1] 200 246s 246s $ctrl$gradTol 246s [1] 1e-04 246s 246s $ctrl$maxLineIter 246s [1] 50 246s 246s $ctrl$innerCtrl 246s [1] "warnOnly" 246s 246s 246s $optCtrl 246s $optCtrl$trace 246s [1] 0 246s 246s 246s $checkRanef 246s [1] "warn" 246s 246s > ordinal:::getCtrlArgs(clmm.control(maxIter=100), list(maxIter=200)) 246s $method 246s [1] "nlminb" 246s 246s $useMatrix 246s [1] FALSE 246s 246s $ctrl 246s $ctrl$trace 246s [1] 0 246s 246s $ctrl$maxIter 246s [1] 200 246s 246s $ctrl$gradTol 246s [1] 1e-04 246s 246s $ctrl$maxLineIter 246s [1] 50 246s 246s $ctrl$innerCtrl 246s [1] "warnOnly" 246s 246s 246s $optCtrl 246s $optCtrl$trace 246s [1] 0 246s 246s 246s $checkRanef 246s [1] "warn" 246s 246s > ordinal:::getCtrlArgs(clmm.control(), list(trace=1)) 246s $method 246s [1] "nlminb" 246s 246s $useMatrix 246s [1] FALSE 246s 246s $ctrl 246s $ctrl$trace 246s [1] 0 246s 246s $ctrl$maxIter 246s [1] 50 246s 246s $ctrl$gradTol 246s [1] 1e-04 246s 246s $ctrl$maxLineIter 246s [1] 50 246s 246s $ctrl$innerCtrl 246s [1] "warnOnly" 246s 246s 246s $optCtrl 246s $optCtrl$trace 246s [1] 1 246s 246s 246s $checkRanef 246s [1] "warn" 246s 246s > ordinal:::getCtrlArgs(clmm.control(), list(trace=-1)) 246s $method 246s [1] "nlminb" 246s 246s $useMatrix 246s [1] FALSE 246s 246s $ctrl 246s $ctrl$trace 246s [1] 1 246s 246s $ctrl$maxIter 246s [1] 50 246s 246s $ctrl$gradTol 246s [1] 1e-04 246s 246s $ctrl$maxLineIter 246s [1] 50 246s 246s $ctrl$innerCtrl 246s [1] "warnOnly" 246s 246s 246s $optCtrl 246s $optCtrl$trace 246s [1] 1 246s 246s 246s $checkRanef 246s [1] "warn" 246s 246s > ordinal:::getCtrlArgs(clmm.control(trace=1), list()) 246s $method 246s [1] "nlminb" 246s 246s $useMatrix 246s [1] FALSE 246s 246s $ctrl 246s $ctrl$trace 246s [1] 0 246s 246s $ctrl$maxIter 246s [1] 50 246s 246s $ctrl$gradTol 246s [1] 1e-04 246s 246s $ctrl$maxLineIter 246s [1] 50 246s 246s $ctrl$innerCtrl 246s [1] "warnOnly" 246s 246s 246s $optCtrl 246s $optCtrl$trace 246s [1] 1 246s 246s 246s $checkRanef 246s [1] "warn" 246s 246s > ordinal:::getCtrlArgs(clmm.control(trace=-1), list()) 246s $method 246s [1] "nlminb" 246s 246s $useMatrix 246s [1] FALSE 246s 246s $ctrl 246s $ctrl$trace 246s [1] 1 246s 246s $ctrl$maxIter 246s [1] 50 246s 246s $ctrl$gradTol 246s [1] 1e-04 246s 246s $ctrl$maxLineIter 246s [1] 50 246s 246s $ctrl$innerCtrl 246s [1] "warnOnly" 246s 246s 246s $optCtrl 246s $optCtrl$trace 246s [1] 1 246s 246s 246s $checkRanef 246s [1] "warn" 246s 246s > ordinal:::getCtrlArgs(clmm.control(trace=0), list()) 246s $method 246s [1] "nlminb" 246s 246s $useMatrix 246s [1] FALSE 246s 246s $ctrl 246s $ctrl$trace 246s [1] 0 246s 246s $ctrl$maxIter 246s [1] 50 246s 246s $ctrl$gradTol 246s [1] 1e-04 246s 246s $ctrl$maxLineIter 246s [1] 50 246s 246s $ctrl$innerCtrl 246s [1] "warnOnly" 246s 246s 246s $optCtrl 246s $optCtrl$trace 246s [1] 0 246s 246s 246s $checkRanef 246s [1] "warn" 246s 246s > ## Don't specify trace twice - surprising behavior might occur: 246s > ordinal:::getCtrlArgs(clmm.control(trace=1), list(trace=-1)) 246s $method 246s [1] "nlminb" 246s 246s $useMatrix 246s [1] FALSE 246s 246s $ctrl 246s $ctrl$trace 246s [1] 1 246s 246s $ctrl$maxIter 246s [1] 50 246s 246s $ctrl$gradTol 246s [1] 1e-04 246s 246s $ctrl$maxLineIter 246s [1] 50 246s 246s $ctrl$innerCtrl 246s [1] "warnOnly" 246s 246s 246s $optCtrl 246s $optCtrl$trace 246s [1] 1 246s 246s 246s $checkRanef 246s [1] "warn" 246s 246s > ordinal:::getCtrlArgs(clmm.control(trace=-1), list(trace=1)) 246s $method 246s [1] "nlminb" 246s 246s $useMatrix 246s [1] FALSE 246s 246s $ctrl 246s $ctrl$trace 246s [1] 1 246s 246s $ctrl$maxIter 246s [1] 50 246s 246s $ctrl$gradTol 246s [1] 1e-04 246s 246s $ctrl$maxLineIter 246s [1] 50 246s 246s $ctrl$innerCtrl 246s [1] "warnOnly" 246s 246s 246s $optCtrl 246s $optCtrl$trace 246s [1] 1 246s 246s 246s $checkRanef 246s [1] "warn" 246s 246s > 246s BEGIN TEST clmm.formula.R 246s 246s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 246s Copyright (C) 2024 The R Foundation for Statistical Computing 246s Platform: aarch64-unknown-linux-gnu (64-bit) 246s 246s R is free software and comes with ABSOLUTELY NO WARRANTY. 246s You are welcome to redistribute it under certain conditions. 246s Type 'license()' or 'licence()' for distribution details. 246s 246s R is a collaborative project with many contributors. 246s Type 'contributors()' for more information and 246s 'citation()' on how to cite R or R packages in publications. 246s 246s Type 'demo()' for some demos, 'help()' for on-line help, or 246s 'help.start()' for an HTML browser interface to help. 246s Type 'q()' to quit R. 246s 246s > library(ordinal) 247s > data(wine) 247s > 247s > ################################# 247s > ## Appropriate evaluation of formulas: 247s > 247s > ## These all work as intended with no warnings or errors: 247s > fm1 <- clmm(rating ~ contact + (1|judge), data=wine) 247s > fm1 247s Cumulative Link Mixed Model fitted with the Laplace approximation 247s 247s formula: rating ~ contact + (1 | judge) 247s data: wine 247s 247s link threshold nobs logLik AIC niter max.grad 247s logit flexible 72 -98.80 209.59 228(686) 3.67e-06 247s 247s Random effects: 247s Groups Name Variance Std.Dev. 247s judge (Intercept) 0.4428 0.6654 247s Number of groups: judge 9 247s 247s Coefficients: 247s contactyes 247s 1.3 247s 247s Thresholds: 247s 1|2 2|3 3|4 4|5 247s -2.28331 0.04325 1.86062 3.20298 247s > fm1 <- clmm("rating ~ contact + (1|judge)", data=wine) 247s > fm1 247s Cumulative Link Mixed Model fitted with the Laplace approximation 247s 247s formula: rating ~ contact + (1 | judge) 247s data: wine 247s 247s link threshold nobs logLik AIC niter max.grad 247s logit flexible 72 -98.80 209.59 228(686) 3.67e-06 247s 247s Random effects: 247s Groups Name Variance Std.Dev. 247s judge (Intercept) 0.4428 0.6654 247s Number of groups: judge 9 247s 247s Coefficients: 247s contactyes 247s 1.3 247s 247s Thresholds: 247s 1|2 2|3 3|4 4|5 247s -2.28331 0.04325 1.86062 3.20298 247s > fm1 <- clmm(as.formula("rating ~ contact + (1|judge)"), data=wine) 247s > fm1 247s Cumulative Link Mixed Model fitted with the Laplace approximation 247s 247s formula: rating ~ contact + (1 | judge) 247s data: wine 247s 247s link threshold nobs logLik AIC niter max.grad 247s logit flexible 72 -98.80 209.59 228(686) 3.67e-06 247s 247s Random effects: 247s Groups Name Variance Std.Dev. 247s judge (Intercept) 0.4428 0.6654 247s Number of groups: judge 9 247s 247s Coefficients: 247s contactyes 247s 1.3 247s 247s Thresholds: 247s 1|2 2|3 3|4 4|5 247s -2.28331 0.04325 1.86062 3.20298 247s > fm1 <- clmm(as.formula(rating ~ contact + (1|judge)), data=wine) 247s > fm1 247s Cumulative Link Mixed Model fitted with the Laplace approximation 247s 247s formula: rating ~ contact + (1 | judge) 247s data: wine 247s 247s link threshold nobs logLik AIC niter max.grad 247s logit flexible 72 -98.80 209.59 228(686) 3.67e-06 247s 247s Random effects: 247s Groups Name Variance Std.Dev. 247s judge (Intercept) 0.4428 0.6654 247s Number of groups: judge 9 247s 247s Coefficients: 247s contactyes 247s 1.3 247s 247s Thresholds: 247s 1|2 2|3 3|4 4|5 247s -2.28331 0.04325 1.86062 3.20298 247s > 247s > ################################# 247s > 247s > ### finding variables in the environment of the formula: 247s > makeform <- function() { 247s + f1 <- as.formula(rating ~ temp + contact + (1|judge)) 247s + rating <- wine$rating 247s + temp <- wine$temp 247s + contact <- wine$contact 247s + judge <- wine$judge 247s + f1 247s + } 247s > ## 'makeform' makes are formula object in the environment of the 247s > ## function makeform: 247s > f1 <- makeform() 247s > f1 # print 247s rating ~ temp + contact + (1 | judge) 247s 247s > class(f1) 247s [1] "formula" 247s > ## If we give the data, we can evaluate the model: 247s > fm1 <- clmm(f1, data=wine) 247s > ## We can also evaluate the model because the data are available in 247s > ## the environment associated with the formula: 247s > fm1 <- clmm(f1) 247s > ## For instance, the 'rating' variable is not found in the Global 247s > ## environment; we have to evaluate the 'name' of 'rating' in the 247s > ## appropriate environment: 247s > (try(rating, silent=TRUE)) 247s [1] "Error : object 'rating' not found\n" 247s attr(,"class") 247s [1] "try-error" 247s attr(,"condition") 247s 247s > eval(as.name("rating"), envir=environment(f1)) 247s [1] 2 3 3 4 4 4 5 5 1 2 1 3 2 3 5 4 2 3 3 2 5 5 4 4 3 2 3 2 3 2 5 3 2 3 4 3 3 3 247s [39] 3 3 3 2 3 2 2 4 5 4 1 1 2 2 2 3 2 3 2 2 2 3 3 3 3 4 1 2 3 2 3 2 4 4 247s Levels: 1 < 2 < 3 < 4 < 5 247s > ## If instead we generate the formula in the Global environment where 247s > ## the variables are not found, we cannot evaluate the model: 247s > f2 <- as.formula(rating ~ temp + contact + (1|judge)) 247s > (try(fm2 <- clmm(f2), silent=TRUE)) 247s [1] "Error in eval(predvars, data, env) : object 'rating' not found\n" 247s attr(,"class") 247s [1] "try-error" 247s attr(,"condition") 247s 247s > environment(f2) <- environment(f1) 247s > fm2 <- clmm(f2) 247s > 247s > ################################# 247s > ## Use of formula-objects 247s > f <- formula(rating ~ temp + contact + (1|judge)) 247s > m2 <- clmm(f, data = wine) 247s > summary(m2) 247s Cumulative Link Mixed Model fitted with the Laplace approximation 247s 247s formula: rating ~ temp + contact + (1 | judge) 247s data: wine 247s 247s link threshold nobs logLik AIC niter max.grad cond.H 247s logit flexible 72 -81.57 177.13 332(999) 1.05e-05 2.8e+01 247s 247s Random effects: 247s Groups Name Variance Std.Dev. 247s judge (Intercept) 1.279 1.131 247s Number of groups: judge 9 247s 247s Coefficients: 247s Estimate Std. Error z value Pr(>|z|) 247s tempwarm 3.0630 0.5954 5.145 2.68e-07 *** 247s contactyes 1.8349 0.5125 3.580 0.000344 *** 247s --- 247s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 247s 247s Threshold coefficients: 247s Estimate Std. Error z value 247s 1|2 -1.6237 0.6824 -2.379 247s 2|3 1.5134 0.6038 2.507 247s 3|4 4.2285 0.8090 5.227 247s 4|5 6.0888 0.9725 6.261 247s > 247s > ################################# 247s > ## Other ways to construct formulas: 247s > set.seed(12345) 247s > y <- factor(sample(1:4,20,replace=TRUE)) 247s > x <- rnorm(20) 247s > b <- gl(5, 4, labels=letters[1:5]) 247s > data <- data.frame(y=y, x=x, b=b) 247s > rm(x, y, b) 247s > clmm(y ~ x + (1|b), data=data) 247s Cumulative Link Mixed Model fitted with the Laplace approximation 247s 247s formula: y ~ x + (1 | b) 247s data: data 247s 247s link threshold nobs logLik AIC niter max.grad 247s logit flexible 20 -25.37 60.74 334(288) 1.25e-07 247s 247s Random effects: 247s Groups Name Variance Std.Dev. 247s b (Intercept) 2.676e-09 5.173e-05 247s Number of groups: b 5 247s 247s Coefficients: 247s x 247s 0.2527 247s 247s Thresholds: 247s 1|2 2|3 3|4 247s -2.18234 0.06059 0.92746 247s > fit <- clmm(data$y ~ data$x + (1|data$b)) 247s > fit 247s Cumulative Link Mixed Model fitted with the Laplace approximation 247s 247s formula: data$y ~ data$x + (1 | data$b) 247s 247s link threshold nobs logLik AIC niter max.grad 247s logit flexible 20 -25.37 60.74 334(288) 1.25e-07 247s 247s Random effects: 247s Groups Name Variance Std.Dev. 247s data$b (Intercept) 2.676e-09 5.173e-05 247s Number of groups: data$b 5 247s 247s Coefficients: 247s data$x 247s 0.2527 247s 247s Thresholds: 247s 1|2 2|3 3|4 247s -2.18234 0.06059 0.92746 247s > fit <- clmm(data[, 1] ~ data[, 2] + (1|data[, 3])) 247s > fit 247s Cumulative Link Mixed Model fitted with the Laplace approximation 247s 247s formula: data[, 1] ~ data[, 2] + (1 | data[, 3]) 247s 247s link threshold nobs logLik AIC niter max.grad 247s logit flexible 20 -25.37 60.74 334(288) 1.25e-07 247s 247s Random effects: 247s Groups Name Variance Std.Dev. 247s data[, 3] (Intercept) 2.676e-09 5.173e-05 247s Number of groups: data[, 3] 5 247s 247s Coefficients: 247s data[, 2] 247s 0.2527 247s 247s Thresholds: 247s 1|2 2|3 3|4 247s -2.18234 0.06059 0.92746 247s > 247s > ################################# 247s > ## Evaluation within other functions: 247s > ## date: January 18th 2012. 247s > ## 247s > ## The problem was raised by Stefan Herzog (stefan.herzog@unibas.ch) 247s > ## January 12th 2012 in trying to make clmm work with glmulti. 247s > 247s > fun.clmm <- function(formula, data) 247s + ### This only works because clmm via eclmm.model.frame is careful to 247s + ### evaluate the 'formula' in the parent environment such it is not the 247s + ### character "formula" that is attempted evaluated. 247s + clmm(formula, data = data) 247s > 247s > fun2.clmm <- function(formula, data, weights, subset) { 247s + ### This should be the safe way to ensure evaluation of clmm in the 247s + ### right environment. 247s + mc <- match.call() 247s + mc[[1]] <- as.name("clmm") 247s + eval.parent(mc) 247s + } 247s > 247s > fun.clmm(rating ~ temp + contact + (1|judge), data=wine) ## works 247s Cumulative Link Mixed Model fitted with the Laplace approximation 247s 247s formula: rating ~ temp + contact + (1 | judge) 247s data: data 247s 247s link threshold nobs logLik AIC niter max.grad 247s logit flexible 72 -81.57 177.13 332(999) 1.05e-05 247s 247s Random effects: 247s Groups Name Variance Std.Dev. 247s judge (Intercept) 1.279 1.131 247s Number of groups: judge 9 247s 247s Coefficients: 247s tempwarm contactyes 247s 3.063 1.835 247s 247s Thresholds: 247s 1|2 2|3 3|4 4|5 247s -1.624 1.513 4.229 6.089 247s > fun2.clmm(rating ~ temp + contact + (1|judge), data=wine) ## works 247s Cumulative Link Mixed Model fitted with the Laplace approximation 247s 247s formula: rating ~ temp + contact + (1 | judge) 247s data: wine 247s 247s link threshold nobs logLik AIC niter max.grad 247s logit flexible 72 -81.57 177.13 332(999) 1.05e-05 247s 247s Random effects: 247s Groups Name Variance Std.Dev. 247s judge (Intercept) 1.279 1.131 247s Number of groups: judge 9 247s 247s Coefficients: 247s tempwarm contactyes 247s 3.063 1.835 247s 247s Thresholds: 247s 1|2 2|3 3|4 4|5 247s -1.624 1.513 4.229 6.089 247s > 247s > form1 <- "rating ~ temp + contact + (1|judge)" 247s > fun.clmm(form1, data=wine) ## works 247s Cumulative Link Mixed Model fitted with the Laplace approximation 247s 247s formula: rating ~ temp + contact + (1 | judge) 247s data: data 247s 247s link threshold nobs logLik AIC niter max.grad 247s logit flexible 72 -81.57 177.13 332(999) 1.05e-05 247s 247s Random effects: 247s Groups Name Variance Std.Dev. 247s judge (Intercept) 1.279 1.131 247s Number of groups: judge 9 247s 247s Coefficients: 247s tempwarm contactyes 247s 3.063 1.835 247s 247s Thresholds: 247s 1|2 2|3 3|4 4|5 247s -1.624 1.513 4.229 6.089 247s > fun2.clmm(form1, data=wine) ## works 247s Cumulative Link Mixed Model fitted with the Laplace approximation 247s 247s formula: rating ~ temp + contact + (1 | judge) 247s data: wine 247s 247s link threshold nobs logLik AIC niter max.grad 247s logit flexible 72 -81.57 177.13 332(999) 1.05e-05 247s 247s Random effects: 247s Groups Name Variance Std.Dev. 247s judge (Intercept) 1.279 1.131 247s Number of groups: judge 9 247s 247s Coefficients: 247s tempwarm contactyes 247s 3.063 1.835 247s 247s Thresholds: 247s 1|2 2|3 3|4 4|5 247s -1.624 1.513 4.229 6.089 247s > 247s > form2 <- formula(rating ~ temp + contact + (1|judge)) 247s > fun.clmm(form2, data=wine) ## works 247s Cumulative Link Mixed Model fitted with the Laplace approximation 247s 247s formula: rating ~ temp + contact + (1 | judge) 247s data: data 247s 247s link threshold nobs logLik AIC niter max.grad 247s logit flexible 72 -81.57 177.13 332(999) 1.05e-05 247s 247s Random effects: 247s Groups Name Variance Std.Dev. 247s judge (Intercept) 1.279 1.131 247s Number of groups: judge 9 247s 247s Coefficients: 247s tempwarm contactyes 247s 3.063 1.835 247s 247s Thresholds: 247s 1|2 2|3 3|4 4|5 247s -1.624 1.513 4.229 6.089 247s > fun2.clmm(form2, data=wine) ## works 247s Cumulative Link Mixed Model fitted with the Laplace approximation 247s 247s formula: rating ~ temp + contact + (1 | judge) 247s data: wine 247s 247s link threshold nobs logLik AIC niter max.grad 247s logit flexible 72 -81.57 177.13 332(999) 1.05e-05 247s 247s Random effects: 247s Groups Name Variance Std.Dev. 247s judge (Intercept) 1.279 1.131 247s Number of groups: judge 9 247s 247s Coefficients: 247s tempwarm contactyes 247s 3.063 1.835 247s 247s Thresholds: 247s 1|2 2|3 3|4 4|5 247s -1.624 1.513 4.229 6.089 247s > ## Notice that clmm is not able to get the name of the data (wine) 247s > ## correct when using fun.clmm. 247s > 247s > ################################# 247s > 247s > ## ## Example 2: using clmm function 247s > ## # 247s > ## ## Now I want to consider judge as a random effect to account for 247s > ## ## grouping structure of data 247s > ## mod2 <- clmm(rating ~ temp + contact + (1|judge), data=wine) 247s > ## 247s > ## ##Again, I started by using my own code to run all potential models: 247s > ## ## put names of all your variables in this vector: 247s > ## vl2 <- c("temp", "contact") 247s > ## ## generate list of possible combinations of variables: 247s > ## combos2 <- NULL 247s > ## for(i in 1:length(vl2)) { 247s > ## combos2 <- c(combos2, combn(vl2, i, simplify = F)) 247s > ## } 247s > ## ## create formulae and run models one by one, saving them as model1, 247s > ## ## model2 etc... 247s > ## for (i in 1:length(combos2)) { 247s > ## vs2 <- paste(combos2[[i]], collapse=" + ") 247s > ## f2 <- formula(paste("rating ~ ", vs2, "+(1|judge)", sep="")) 247s > ## print(f2) 247s > ## assign(paste("model", i, sep=""), clmm(f2, data=wine)) 247s > ## } 247s > ## summary(model1) # etc 247s > ## summary(model2) # etc 247s > ## summary(model3) # etc 247s > ## 247s > ## models <- vector("list", length(combos2)) 247s > ## for(i in 1:length(combos2)) { 247s > ## vs2 <- paste(combos2[[i]], collapse=" + ") 247s > ## f2 <- formula(paste("rating ~ ", vs2, "+(1|judge)", sep="")) 247s > ## print(f2) 247s > ## models[[i]] <- clmm(f2, data=wine) 247s > ## ## assign(paste("model", i, sep=""), clmm(f2, data=wine)) 247s > ## } 247s > ## 247s > ## ## Coefficients, AIC and BIC: 247s > ## lapply(models, function(m) coef(summary(m))) 247s > ## lapply(models, AIC) 247s > ## lapply(models, BIC) 247s > ## 247s > ## ## library(MuMIn) 247s > ## ## dd2 <- dredge(mod2) ## does not work 247s > ## ## ?dredge 247s > ## ## traceback() 247s > ## ## mod2$formula 247s > ## ## terms(as.formula(formula(mod2))) 247s > ## ## 247s > ## ## library(lme4) 247s > ## ## fmm1 <- lmer(response ~ temp + contact + (1|judge), data=wine) 247s > ## ## fmm1 247s > ## ## terms(as.formula(lme4:::formula(fmm1))) 247s > ## ## terms(as.formula(formula(fmm1))) 247s > 247s BEGIN TEST clmm.methods.R 247s 247s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 247s Copyright (C) 2024 The R Foundation for Statistical Computing 247s Platform: aarch64-unknown-linux-gnu (64-bit) 247s 247s R is free software and comes with ABSOLUTELY NO WARRANTY. 247s You are welcome to redistribute it under certain conditions. 247s Type 'license()' or 'licence()' for distribution details. 247s 247s R is a collaborative project with many contributors. 247s Type 'contributors()' for more information and 247s 'citation()' on how to cite R or R packages in publications. 247s 247s Type 'demo()' for some demos, 'help()' for on-line help, or 247s 'help.start()' for an HTML browser interface to help. 247s Type 'q()' to quit R. 247s 248s > library(ordinal) 248s > data(wine) 248s > 248s > ################################# 248s > ## model.matrix method for clmm-objects: 248s > fmm1 <- clmm(rating ~ contact + temp + (1|judge), data=wine) 249s > mm <- model.matrix(fmm1) 249s > stopifnot(inherits(mm, "matrix"), 249s + dim(mm) == c(72, 3)) 249s > 249s > ################################# 249s > ## anova.clmm works even if formula does not have an environment: 249s > fmm1 <- clmm(rating ~ temp * contact + (1|judge), data = wine) 249s > fmm2 <- clmm(rating ~ temp + contact + (1|judge), data = wine) 249s > environment(fmm1$formula) <- NULL 249s > environment(fmm2$formula) <- NULL 249s > anova(fmm1, fmm2) 249s Likelihood ratio tests of cumulative link models: 249s 249s formula: link: threshold: 249s fmm2 rating ~ temp + contact + (1 | judge) logit flexible 249s fmm1 rating ~ temp * contact + (1 | judge) logit flexible 249s 249s no.par AIC logLik LR.stat df Pr(>Chisq) 249s fmm2 7 177.13 -81.565 249s fmm1 8 179.07 -81.536 0.0589 1 0.8082 249s > 249s > 249s > ################################# 249s > ## Test that ranef, condVar and VarCorr work as they are supposed to whether or 249s > ## not nlme and lme4 are loaded: 249s > 249s > fm <- clmm(rating ~ temp + contact + (1|judge), data = wine) 249s > fm 249s Cumulative Link Mixed Model fitted with the Laplace approximation 249s 249s formula: rating ~ temp + contact + (1 | judge) 249s data: wine 249s 249s link threshold nobs logLik AIC niter max.grad 249s logit flexible 72 -81.57 177.13 332(999) 1.05e-05 249s 249s Random effects: 249s Groups Name Variance Std.Dev. 249s judge (Intercept) 1.279 1.131 249s Number of groups: judge 9 249s 249s Coefficients: 249s tempwarm contactyes 249s 3.063 1.835 249s 249s Thresholds: 249s 1|2 2|3 3|4 4|5 249s -1.624 1.513 4.229 6.089 249s > ranef(fm) 249s $judge 249s (Intercept) 249s 1 1.6961783 249s 2 -0.5657831 249s 3 0.9688083 249s 4 -0.0595499 249s 5 0.2305101 249s 6 0.4770387 249s 7 -1.9109736 249s 8 -0.2729439 249s 9 -0.5546758 249s 249s > VarCorr(fm) 249s $judge 249s (Intercept) 249s (Intercept) 1.279461 249s attr(,"stddev") 249s (Intercept) 249s 1.131133 249s 249s > condVar(fm) 249s $judge 249s (Intercept) 249s 1 0.3067453 249s 2 0.3779358 249s 3 0.3545529 249s 4 0.3651870 249s 5 0.3566067 249s 6 0.3485475 249s 7 0.3435693 249s 8 0.3050453 249s 9 0.3183194 249s 249s > summary(fm) 249s Cumulative Link Mixed Model fitted with the Laplace approximation 249s 249s formula: rating ~ temp + contact + (1 | judge) 249s data: wine 249s 249s link threshold nobs logLik AIC niter max.grad cond.H 249s logit flexible 72 -81.57 177.13 332(999) 1.05e-05 2.8e+01 249s 249s Random effects: 249s Groups Name Variance Std.Dev. 249s judge (Intercept) 1.279 1.131 249s Number of groups: judge 9 249s 249s Coefficients: 249s Loading required package: Matrix 249s Estimate Std. Error z value Pr(>|z|) 249s tempwarm 3.0630 0.5954 5.145 2.68e-07 *** 249s contactyes 1.8349 0.5125 3.580 0.000344 *** 249s --- 249s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 249s 249s Threshold coefficients: 249s Estimate Std. Error z value 249s 1|2 -1.6237 0.6824 -2.379 249s 2|3 1.5134 0.6038 2.507 249s 3|4 4.2285 0.8090 5.227 249s 4|5 6.0888 0.9725 6.261 249s > 249s > library(nlme) 249s > ranef(fm) 249s $judge 249s (Intercept) 249s 1 1.6961783 249s 2 -0.5657831 249s 3 0.9688083 249s 4 -0.0595499 249s 5 0.2305101 249s 6 0.4770387 249s 7 -1.9109736 249s 8 -0.2729439 249s 9 -0.5546758 249s 249s > VarCorr(fm) 249s $judge 249s (Intercept) 249s (Intercept) 1.279461 249s attr(,"stddev") 249s (Intercept) 249s 1.131133 249s 249s > condVar(fm) 249s $judge 249s (Intercept) 249s 1 0.3067453 249s 2 0.3779358 249s 3 0.3545529 249s 4 0.3651870 249s 5 0.3566067 249s 6 0.3485475 249s 7 0.3435693 249s 8 0.3050453 249s 9 0.3183194 249s 249s > library(lme4) 249s 249s Attaching package: ‘lme4’ 249s 249s > ranef(fm) 249s The following object is masked from ‘package:nlme’: 249s 249s lmList 249s 249s $judge 249s (Intercept) 249s 1 1.6961783 249s 2 -0.5657831 249s 3 0.9688083 249s 4 -0.0595499 249s 5 0.2305101 249s 6 0.4770387 249s 7 -1.9109736 249s 8 -0.2729439 249s 9 -0.5546758 249s 249s > VarCorr(fm) 249s $judge 249s (Intercept) 249s (Intercept) 1.279461 249s attr(,"stddev") 249s (Intercept) 249s 1.131133 249s 249s > condVar(fm) 249s $judge 249s (Intercept) 249s 1 0.3067453 249s 2 0.3779358 249s 3 0.3545529 249s 4 0.3651870 249s 5 0.3566067 249s 6 0.3485475 249s 7 0.3435693 249s 8 0.3050453 249s 9 0.3183194 249s 249s > fm1 <- lmer(Reaction ~ Days + (Days | Subject), data=sleepstudy) 249s > ranef(fm1) 249s $Subject 249s (Intercept) Days 249s 308 2.2585510 9.1989758 249s 309 -40.3987381 -8.6196806 249s 310 -38.9604090 -5.4488565 249s 330 23.6906196 -4.8143503 249s 331 22.2603126 -3.0699116 249s 332 9.0395679 -0.2721770 249s 333 16.8405086 -0.2236361 249s 334 -7.2326151 1.0745816 249s 335 -0.3336684 -10.7521652 249s 337 34.8904868 8.6282652 249s 349 -25.2102286 1.1734322 249s 350 -13.0700342 6.6142178 249s 351 4.5778642 -3.0152621 249s 352 20.8636782 3.5360011 249s 369 3.2754656 0.8722149 249s 370 -25.6129993 4.8224850 249s 371 0.8070461 -0.9881562 249s 372 12.3145921 1.2840221 249s 249s with conditional variances for “Subject†249s > VarCorr(fm1) 249s Groups Name Std.Dev. Corr 249s Subject (Intercept) 24.7407 249s Days 5.9221 0.066 249s Residual 25.5918 249s > 249s > ranef(fm) 249s $judge 249s (Intercept) 249s 1 1.6961783 249s 2 -0.5657831 249s 3 0.9688083 249s 4 -0.0595499 249s 5 0.2305101 249s 6 0.4770387 249s 7 -1.9109736 249s 8 -0.2729439 249s 9 -0.5546758 249s 249s > VarCorr(fm) 249s $judge 249s (Intercept) 249s (Intercept) 1.279461 249s attr(,"stddev") 249s (Intercept) 249s 1.131133 249s 249s > condVar(fm) 249s $judge 249s (Intercept) 249s 1 0.3067453 249s 2 0.3779358 249s 3 0.3545529 249s 4 0.3651870 249s 5 0.3566067 249s 6 0.3485475 249s 7 0.3435693 249s 8 0.3050453 249s 9 0.3183194 249s 249s > summary(fm) 249s Cumulative Link Mixed Model fitted with the Laplace approximation 249s 249s formula: rating ~ temp + contact + (1 | judge) 249s data: wine 249s 249s link threshold nobs logLik AIC niter max.grad cond.H 249s logit flexible 72 -81.57 177.13 332(999) 1.05e-05 2.8e+01 249s 249s Random effects: 249s Groups Name Variance Std.Dev. 249s judge (Intercept) 1.279 1.131 249s Number of groups: judge 9 249s 249s Coefficients: 249s Estimate Std. Error z value Pr(>|z|) 249s tempwarm 3.0630 0.5954 5.145 2.68e-07 *** 249s contactyes 1.8349 0.5125 3.580 0.000344 *** 249s --- 249s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 249s 249s Threshold coefficients: 249s Estimate Std. Error z value 249s 1|2 -1.6237 0.6824 -2.379 249s 2|3 1.5134 0.6038 2.507 249s 3|4 4.2285 0.8090 5.227 249s 4|5 6.0888 0.9725 6.261 249s > 249s BEGIN TEST confint.R 249s 249s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 249s Copyright (C) 2024 The R Foundation for Statistical Computing 249s Platform: aarch64-unknown-linux-gnu (64-bit) 249s 249s R is free software and comes with ABSOLUTELY NO WARRANTY. 249s You are welcome to redistribute it under certain conditions. 249s Type 'license()' or 'licence()' for distribution details. 249s 249s R is a collaborative project with many contributors. 249s Type 'contributors()' for more information and 249s 'citation()' on how to cite R or R packages in publications. 249s 249s Type 'demo()' for some demos, 'help()' for on-line help, or 249s 'help.start()' for an HTML browser interface to help. 249s Type 'q()' to quit R. 249s 249s > ################################# 249s > ## test profile and confint methods: 249s > library(ordinal) 250s > data(wine) 250s > fm1 <- clm(rating ~ contact + temp, data = wine) 250s > summary(fm1) 250s formula: rating ~ contact + temp 250s data: wine 250s 250s link threshold nobs logLik AIC niter max.grad cond.H 250s logit flexible 72 -86.49 184.98 6(0) 4.01e-12 2.7e+01 250s 250s Coefficients: 250s Estimate Std. Error z value Pr(>|z|) 250s contactyes 1.5278 0.4766 3.205 0.00135 ** 250s tempwarm 2.5031 0.5287 4.735 2.19e-06 *** 250s --- 250s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 250s 250s Threshold coefficients: 250s Estimate Std. Error z value 250s 1|2 -1.3444 0.5171 -2.600 250s 2|3 1.2508 0.4379 2.857 250s 3|4 3.4669 0.5978 5.800 250s 4|5 5.0064 0.7309 6.850 250s > 250s > ## profile.clm and confint.clm: 250s > pr1 <- profile(fm1) 250s > confint(pr1) 250s 2.5 % 97.5 % 250s contactyes 0.6158045 2.492424 250s tempwarm 1.5097839 3.595251 250s > pr1 <- profile(fm1, which.beta = 1:2) 250s > confint(pr1) 250s 2.5 % 97.5 % 250s contactyes 0.6158045 2.492424 250s tempwarm 1.5097839 3.595251 250s > pr1 <- profile(fm1, which.beta = 2:1) 250s > confint(pr1) 250s 2.5 % 97.5 % 250s tempwarm 1.5097839 3.595251 250s contactyes 0.6158045 2.492424 250s > pr1 <- profile(fm1, which.beta = 1) 250s > confint(pr1) 250s 2.5 % 97.5 % 250s contactyes 0.6158045 2.492424 250s > pr1 <- profile(fm1, which.beta = 2) 250s > confint(pr1) 250s 2.5 % 97.5 % 250s tempwarm 1.509784 3.595251 250s > pr1 <- try(profile(fm1, which.beta = 0), silent = TRUE) ## error 250s > pr1 <- try(profile(fm1, which.beta = "no.par"), silent = TRUE) ## error 250s > pr1 <- try(profile(fm1, which.beta = -1), silent = TRUE) ## error 250s > pr1 <- profile(fm1, which.beta = "tempwarm") 251s > confint(pr1) 251s 2.5 % 97.5 % 251s tempwarm 1.509784 3.595251 251s > pr1 <- profile(fm1, alpha = 0.1) 251s > confint(pr1) ## should give NA in this case? 251s 2.5 % 97.5 % 251s contactyes NA NA 251s tempwarm NA NA 251s > pr1 <- profile(fm1, max.steps = 9) 251s > pr1 <- profile(fm1, step.warn = 7) 251s > pr1 <- profile(fm1, nsteps = 6) 251s > pr1 <- profile(fm1, trace = 1) 251s 251s Parameter: contactyes down 251s 251s Parameter: contactyes up 251s 251s Parameter: tempwarm down 251s 251s Parameter: tempwarm up 251s > pr1 <- profile(fm1, control = list(gradTol = .1)) 251s > confint(pr1) ## not at all unreliable... 251s 2.5 % 97.5 % 251s contactyes 0.6158045 2.492424 251s tempwarm 1.5097839 3.595251 251s > 251s > ## single regression coef setting: 251s > fm2 <- clm(rating ~ contact, data = wine) 251s > summary(fm2) 251s formula: rating ~ contact 251s data: wine 251s 251s link threshold nobs logLik AIC niter max.grad cond.H 251s logit flexible 72 -99.96 209.91 5(0) 1.67e-07 1.7e+01 251s 251s Coefficients: 251s Estimate Std. Error z value Pr(>|z|) 251s contactyes 1.2070 0.4499 2.683 0.0073 ** 251s --- 251s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 251s 251s Threshold coefficients: 251s Estimate Std. Error z value 251s 1|2 -2.13933 0.48981 -4.368 251s 2|3 0.04257 0.32063 0.133 251s 3|4 1.71449 0.38637 4.437 251s 4|5 2.97875 0.50207 5.933 251s > pr2 <- profile(fm2) 251s > confint(pr2) 251s 2.5 % 97.5 % 251s contactyes 0.3403978 2.110952 251s > 251s > ## confint.clm: 251s > confint(fm1) 251s argument 'parm' ignored 251s 2.5 % 97.5 % 251s contactyes 0.6157925 2.492404 251s tempwarm 1.5097627 3.595225 251s > confint(fm1, 2) 251s 2.5 % 97.5 % 251s contactyes 0.6157925 2.492404 251s tempwarm 1.5097627 3.595225 251s > confint(fm1, 1) 251s argument 'parm' ignored 251s 2.5 % 97.5 % 251s contactyes 0.6157925 2.492404 251s tempwarm 1.5097627 3.595225 251s > confint(fm1, "tempwarm") 251s argument 'parm' ignored 251s 2.5 % 97.5 % 251s contactyes 0.6157925 2.492404 251s tempwarm 1.5097627 3.595225 251s > confint(fm1, type = "profile") 251s 2.5 % 97.5 % 251s contactyes 0.6157925 2.492404 251s tempwarm 1.5097627 3.595225 251s > confint(fm1, type = "Wald") 251s 2.5 % 97.5 % 251s 1|2 -2.3578848 -0.330882 251s 2|3 0.3925794 2.109038 251s 3|4 2.2952980 4.638476 251s 4|5 3.5738541 6.438954 251s contactyes 0.5936345 2.461961 251s tempwarm 1.4669081 3.539296 251s > confint(fm1, 2, type = "Wald") 251s argument 'parm' ignored 251s 2.5 % 97.5 % 251s 1|2 -2.3578848 -0.330882 251s 2|3 0.3925794 2.109038 251s 3|4 2.2952980 4.638476 251s 4|5 3.5738541 6.438954 251s contactyes 0.5936345 2.461961 251s tempwarm 1.4669081 3.539296 251s > confint(fm1, level = 0.5) 251s 25 % 75 % 251s contactyes 1.209254 1.852544 251s tempwarm 2.152051 2.865757 251s > confint(fm1, level = 1 - 1e-6) 251s 0 % 100 % 251s contactyes -0.7003630 4.091731 251s tempwarm 0.1351282 5.520007 251s > confint(fm1, level = 1 - 1e-10) ## extreme, but it works 251s Wait for profiling to be done... 251s 0 % 100 % 251s contactyes -1.4045009 5.059182 251s tempwarm -0.5753928 6.774556 251s > confint(fm1, trace = 1) 251s 251s Parameter: contactyes down 251s 251s Parameter: contactyes up 251s 251s Parameter: tempwarm down 251s 251s Parameter: tempwarm up 251s 2.5 % 97.5 % 251s contactyes 0.6157925 2.492404 251s tempwarm 1.5097627 3.595225 251s > 251s > ## plot.profile: 251s > pr1 <- profile(fm1, which.beta=1:2, alpha = 1e-3) 251s > par(mfrow = c(1,2)) 251s > plot(pr1) 251s > plot(pr1, 1) 251s > plot(pr1, "contactyes") 251s > plot(pr1, level = .97) 251s > plot(pr1, Log = TRUE) 251s > plot(pr1, relative = FALSE) 251s > plot(pr1, root = TRUE) 251s > plot(pr1, approx = TRUE) 251s > plot(pr1, n=10) 251s > plot(pr1, ylim = c(0,2)) 251s > plot(pr1, las = 1) 251s > plot(pr2) 251s > 251s > 251s BEGIN TEST nominal.test.R 251s 251s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 251s Copyright (C) 2024 The R Foundation for Statistical Computing 251s Platform: aarch64-unknown-linux-gnu (64-bit) 251s 251s R is free software and comes with ABSOLUTELY NO WARRANTY. 251s You are welcome to redistribute it under certain conditions. 251s Type 'license()' or 'licence()' for distribution details. 251s 251s R is a collaborative project with many contributors. 251s Type 'contributors()' for more information and 251s 'citation()' on how to cite R or R packages in publications. 251s 251s Type 'demo()' for some demos, 'help()' for on-line help, or 251s 'help.start()' for an HTML browser interface to help. 251s Type 'q()' to quit R. 251s 251s > library(ordinal) 252s Loading required package: MASS 252s > 252s > if(require(MASS)) { 252s + fm1 <- clm(Sat ~ Infl + Type + Cont, data=housing, weights=Freq) 252s + scale_test(fm1) 252s + nominal_test(fm1) 252s + 252s + fm2 <- update(fm1, scale=~Cont) 252s + scale_test(fm2) 252s + nominal_test(fm2) 252s + fm3 <- update(fm1, nominal=~ Cont) 252s + fm3$Theta 252s + anova(fm2, fm3) 252s + fm3$alpha.mat 252s + summary(fm3) 252s + } 253s formula: Sat ~ Infl + Type + Cont 253s nominal: ~Cont 253s data: housing 253s 253s link threshold nobs logLik AIC niter max.grad cond.H 253s logit flexible 1681 -1738.35 3494.70 4(0) 1.31e-07 6.3e+01 253s 253s Coefficients: (1 not defined because of singularities) 253s Estimate Std. Error z value Pr(>|z|) 253s InflMedium 0.5695 0.1048 5.436 5.45e-08 *** 253s InflHigh 1.2884 0.1271 10.137 < 2e-16 *** 253s TypeApartment -0.5706 0.1192 -4.788 1.68e-06 *** 253s TypeAtrium -0.3643 0.1552 -2.348 0.0189 * 253s TypeTerrace -1.0980 0.1516 -7.242 4.43e-13 *** 253s ContHigh NA NA NA NA 253s --- 253s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 253s 253s Threshold coefficients: 253s Estimate Std. Error z value 253s Low|Medium.(Intercept) -0.4494 0.1279 -3.515 253s Medium|High.(Intercept) 0.6480 0.1279 5.066 253s Low|Medium.ContHigh -0.4440 0.1095 -4.056 253s Medium|High.ContHigh -0.2861 0.1063 -2.691 253s > 253s > ################################# 253s > ### Testing nominal_test and scale_test: 253s > fm1 <- clm(rating ~ temp * contact, data=wine) 253s > ## names(fm1) 253s > fm2 <- clm(rating ~ temp * contact, data=wine, nominal=~contact) 253s > (an <- anova(fm1, fm2)) 253s Likelihood ratio tests of cumulative link models: 253s 253s formula: nominal: link: threshold: 253s fm1 rating ~ temp * contact ~1 logit flexible 253s fm2 rating ~ temp * contact ~contact logit flexible 253s 253s no.par AIC logLik LR.stat df Pr(>Chisq) 253s fm1 7 186.83 -86.416 253s fm2 10 192.17 -86.083 0.6669 3 0.881 253s > (nm <- nominal_test(fm1)) 253s Tests of nominal effects 253s 253s formula: rating ~ temp * contact 253s Df logLik AIC LRT Pr(>Chi) 253s -86.416 186.83 253s temp 3 -84.874 189.75 3.08352 0.3789 253s contact 3 -86.083 192.16 0.66691 0.8810 253s temp:contact 253s > stopifnot(isTRUE(all.equal(an[2, 6], nm["contact", 5]))) 253s > 253s > fm2 <- clm(rating ~ temp * contact, data=wine, scale=~contact) 253s > (an <- anova(fm1, fm2)) 253s Likelihood ratio tests of cumulative link models: 253s 253s formula: scale: link: threshold: 253s fm1 rating ~ temp * contact ~1 logit flexible 253s fm2 rating ~ temp * contact ~contact logit flexible 253s 253s no.par AIC logLik LR.stat df Pr(>Chisq) 253s fm1 7 186.83 -86.416 253s fm2 8 188.60 -86.300 0.2325 1 0.6297 253s > (sc <- scale_test(fm1)) 253s Tests of scale effects 253s 253s formula: rating ~ temp * contact 253s Df logLik AIC LRT Pr(>Chi) 253s -86.416 186.83 253s temp 1 -86.326 188.65 0.18061 0.6709 253s contact 1 -86.300 188.60 0.23252 0.6297 253s temp:contact 3 -86.259 192.52 0.31391 0.9574 253s > stopifnot(isTRUE(all.equal(an[2, 6], sc["contact", "Pr(>Chi)"]))) 253s > 253s > fm1 <- clm(rating ~ temp + contact, 253s + nominal=~temp + contact, data=wine) 253s Warning message: 253s (1) Hessian is numerically singular: parameters are not uniquely determined 253s In addition: Absolute convergence criterion was met, but relative criterion was not met 253s 253s no additional terms to add to nominal 253s 253s > fm1 253s formula: rating ~ temp + contact 253s nominal: ~temp + contact 253s data: wine 253s 253s link threshold nobs logLik AIC niter max.grad cond.H 253s logit flexible 72 -84.61 193.22 20(0) 4.36e-09 5.0e+10 253s 253s Coefficients: (2 not defined because of singularities) 253s tempwarm contactyes 253s NA NA 253s 253s Threshold coefficients: 253s 1|2 2|3 3|4 4|5 253s (Intercept) -1.226 1.033 3.946 24.553 253s tempwarm -21.118 -2.111 -2.940 -22.432 253s contactyes -1.659 -1.343 -1.693 -1.162 253s > try(nominal_test(fm1), silent=TRUE)[1] ## gives error OK 253s Df 253s 253s > scale_test(fm1) 253s Tests of scale effects 253s 253s formula: rating ~ temp + contactWarning messages: 253s 1: (1) Hessian is numerically singular: parameters are not uniquely determined 253s In addition: Absolute convergence criterion was met, but relative criterion was not met 253s 2: (1) Hessian is numerically singular: parameters are not uniquely determined 253s In addition: Absolute convergence criterion was met, but relative criterion was not met 253s 253s nominal: ~temp + contact 253s Df logLik AIC LRT Pr(>Chi) 253s -84.611 193.22 253s temp 1 -84.604 195.21 0.0129568 0.9094 253s contact 1 -84.610 195.22 0.0012219 0.9721 253s > fm1 <- clm(rating ~ temp + contact, 253s + scale=~temp + contact, data=wine) 253s > fm1 253s formula: rating ~ temp + contact 253s scale: ~temp + contact 253s data: wine 253s 253s link threshold nobs logLik AIC niter max.grad cond.H 253s logit flexible 72 -86.34 188.68 8(0) 7.40e-09 2.0e+02 253s 253s Coefficients: 253s tempwarm contactyes 253s 2.446 1.482 253s 253s log-scale coefficients: 253s tempwarm contactyes 253s 0.05008 -0.11418 253s 253s Threshold coefficients: 253s 1|2 2|3 3|4 4|5 253s -1.303 1.219 3.377 4.872 253s > try(scale_test(fm1), silent=TRUE)[1] ## gives error OK 253s 253s no relevant terms to add to scale 253s 253s Df 253s 253s > nominal_test(fm1) 253s Tests of nominal effects 253s 253s formula: rating ~ temp + contact 253s scale: ~temp + contact 253s Df logLik AIC LRT Pr(>Chi) 253s -86.342 188.69 253s temp 3 -84.851 191.70 2.98202 0.3944 253s contact 3 -86.008 194.02 0.66808 0.8807 253s > 253s > 253s > ## Using weights: 253s > set.seed(123454321) 253s > wt <- runif(nrow(wine)) 253s > fm1 <- clm(rating ~ temp * contact, data=wine, weigths=wt) 253s > nominal_test(fm1) 253s Tests of nominal effects 253s 253s formula: rating ~ temp * contact 253s Df logLik AIC LRT Pr(>Chi) 253s -86.416 186.83 253s temp 3 -84.874 189.75 3.08352 0.3789 253s contact 3 -86.083 192.16 0.66691 0.8810 253s temp:contact 253s > scale_test(fm1) 253s Tests of scale effects 253s 253s formula: rating ~ temp * contact 253s Df logLik AIC LRT Pr(>Chi) 253s -86.416 186.83 253s temp 1 -86.326 188.65 0.18061 0.6709 253s contact 1 -86.300 188.60 0.23252 0.6297 253s temp:contact 3 -86.259 192.52 0.31391 0.9574 253s > 253s > ## No nominal test for judge since that model is not identifiable: 253s > fm1 <- clm(rating ~ judge + temp + contact, data=wine) 253s > nominal_test(fm1) 253s Tests of nominal effects 253s 253s formula: rating ~ judge + temp + contact 253s Df logLik AIC LRT Pr(>Chi) 253s -70.921 169.84 253s judge 253s temp 3 -69.900 173.80 2.04253 0.5636 253s contact 3 -70.708 175.42 0.42612 0.9348 253s > scale_test(fm1) 253s Tests of scale effects 253s 253s formula: rating ~ judge + temp + contact 253s Df logLik AIC LRT Pr(>Chi) 253s -70.921 169.84 253s judge 8 -64.731 173.46 12.3790 0.1351 253s temp 1 -70.897 171.79 0.0474 0.8276 253s contact 1 -70.870 171.74 0.1018 0.7497 253s > fm1 <- clm(rating ~ judge + temp, nominal=~contact, data=wine) 253s > nominal_test(fm1) 254s Tests of nominal effects 254s 254s formula: rating ~ judge + temp 254s nominal: ~contact 254s Df logLik AIC LRT Pr(>Chi) 254s -70.708 175.42 254s judge 254s temp 3 -69.707 179.41 2.0015 0.5721 254s > summary(fm1) 254s formula: rating ~ judge + temp 254s nominal: ~contact 254s data: wine 254s 254s link threshold nobs logLik AIC niter max.grad cond.H 254s logit flexible 72 -70.71 175.42 6(0) 8.07e-08 9.9e+01 254s 254s Coefficients: 254s Estimate Std. Error z value Pr(>|z|) 254s judge2 -3.2395 1.0683 -3.032 0.00243 ** 254s judge3 -0.9556 0.9699 -0.985 0.32452 254s judge4 -2.4613 1.0321 -2.385 0.01709 * 254s judge5 -2.0248 1.0093 -2.006 0.04484 * 254s judge6 -1.6379 0.9770 -1.677 0.09364 . 254s judge7 -5.2222 1.1381 -4.589 4.46e-06 *** 254s judge8 -2.7648 0.9776 -2.828 0.00468 ** 254s judge9 -3.1751 1.0028 -3.166 0.00154 ** 254s tempwarm 3.3309 0.6174 5.395 6.87e-08 *** 254s --- 254s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 254s 254s Threshold coefficients: 254s Estimate Std. Error z value 254s 1|2.(Intercept) -4.1549 0.9897 -4.198 254s 2|3.(Intercept) -0.7354 0.7920 -0.928 254s 3|4.(Intercept) 2.3388 0.8909 2.625 254s 4|5.(Intercept) 3.8873 1.0352 3.755 254s 1|2.contactyes -2.0216 1.3072 -1.547 254s 2|3.contactyes -1.9865 0.6904 -2.877 254s 3|4.contactyes -2.1825 0.7774 -2.807 254s 4|5.contactyes -1.5077 1.0044 -1.501 254s > 254s > ## A continuous variable: 254s > set.seed(123454321) 254s > x <- rnorm(nrow(wine), sd=1) 254s > fm <- clm(rating ~ temp, nominal=~contact * x, data=wine) 254s Warning message: 254s (1) Hessian is numerically singular: parameters are not uniquely determined 254s In addition: Absolute convergence criterion was met, but relative criterion was not met 254s > nominal_test(fm) 254s Tests of nominal effects 254s 254s formula: rating ~ temp 254s nominal: ~contact * x 254s Df logLik AIC LRT Pr(>Chi) 254s -77.858 189.72 254s temp 3 -76.738 193.48 2.24 0.5241 254s > scale_test(fm) 254s Tests of scale effects 254s 254s formula: rating ~ temp 254s nominal: ~contact * x 254s Df logLik AIC LRT Pr(>Chi) 254s -77.858 189.72 Warning message: 254s (1) Hessian is numerically singular: parameters are not uniquely determined 254s In addition: Absolute convergence criterion was met, but relative criterion was not met 254s 254s temp 1 -77.684 191.37 0.34804 0.5552 254s > fm <- clm(rating ~ temp + x, nominal=~contact, data=wine) 254s > nominal_test(fm) 254s Tests of nominal effects 254s 254s formula: rating ~ temp + x 254s nominal: ~contact 254s Df logLik AIC LRT Pr(>Chi) 254s -84.949 189.90 254s temp 3 -83.421 192.84 3.0560 0.3831 254s x 3 -84.333 194.67 1.2322 0.7453 254s > scale_test(fm) 254s Tests of scale effects 254s 254s formula: rating ~ temp + x 254s nominal: ~contact 254s Df logLik AIC LRT Pr(>Chi) 254s -84.949 189.90 254s temp 1 -84.737 191.47 0.42504 0.5144 254s x 1 -84.896 191.79 0.10781 0.7426 254s > ## poly: 254s > fm <- clm(rating ~ temp + poly(x, 2), nominal=~contact, data=wine) 254s > nominal_test(fm) 254s Tests of nominal effects 254s 254s formula: rating ~ temp + poly(x, 2) 254s nominal: ~contact 254s Df logLik AIC LRT Pr(>Chi) 254s -84.079 190.16 254s temp 3 -82.694 193.39 2.7693 0.4286 254s poly(x, 2) 6 -80.941 195.88 6.2762 0.3930 254s > scale_test(fm) 254s Tests of scale effects 254s 254s formula: rating ~ temp + poly(x, 2) 254s nominal: ~contact 254s Df logLik AIC LRT Pr(>Chi) 254s -84.079 190.16 254s temp 1 -84.020 192.04 0.11784 0.7314 254s poly(x, 2) 2 -83.314 192.63 1.53017 0.4653 254s > ## another combination: 254s > fm1 <- clm(SURENESS ~ PRODID + DAY + SOUPTYPE + SOUPFREQ, 254s + scale=~PROD, 254s + nominal=~ DAY*GENDER, data=soup) 254s > fm1 254s formula: SURENESS ~ PRODID + DAY + SOUPTYPE + SOUPFREQ 254s scale: ~PROD 254s nominal: ~DAY * GENDER 254s data: soup 254s 254s link threshold nobs logLik AIC niter max.grad cond.H 254s logit flexible 1847 -2657.84 5375.68 8(2) 3.50e-07 4.0e+03 254s 254s Coefficients: (1 not defined because of singularities) 254s PRODID2 PRODID3 PRODID4 PRODID5 254s 1.0780 1.5090 0.9482 1.4910 254s PRODID6 DAY2 SOUPTYPECanned SOUPTYPEDry-mix 254s 1.8174 NA -0.2337 0.1832 254s SOUPFREQ1-4/month SOUPFREQ<1/month 254s -0.0954 -0.1137 254s 254s log-scale coefficients: 254s PRODTest 254s 0.1427 254s 254s Threshold coefficients: 254s 1|2 2|3 3|4 4|5 5|6 254s (Intercept) -1.65979 -0.75912 -0.36903 0.02374 0.66929 254s DAY2 -0.22291 0.13711 0.16406 0.10279 0.23721 254s GENDERFemale 0.06531 0.06089 -0.01938 -0.13670 -0.01594 254s DAY2:GENDERFemale 0.36194 0.25429 0.25482 0.23375 0.05243 254s > nominal_test(fm1) 254s Tests of nominal effects 254s 254s formula: SURENESS ~ PRODID + DAY + SOUPTYPE + SOUPFREQ 254s scale: ~PROD 254s nominal: ~DAY * GENDER 254s Df logLik AIC LRT Pr(>Chi) 254s -2657.8 5375.7 254s PRODID 20 -2644.7 5389.4 26.2387 0.1580707 254s SOUPTYPE 8 -2654.0 5384.1 7.5969 0.4738067 254s SOUPFREQ 8 -2644.6 5365.1 26.5587 0.0008423 *** 254s PROD 4 -2654.7 5377.5 6.2011 0.1846258 254s --- 254s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 254s > scale_test(fm1) 255s Tests of scale effects 255s 255s formula: SURENESS ~ PRODID + DAY + SOUPTYPE + SOUPFREQ 255s scale: ~PROD 255s nominal: ~DAY * GENDER 255s Df logLik AIC LRT Pr(>Chi) 255s -2657.8 5375.7 255s PRODID 4 -2657.3 5382.5 1.1526 0.885842 255s DAY 1 -2655.9 5373.8 3.8544 0.049616 * 255s SOUPTYPE 2 -2657.6 5379.1 0.5416 0.762771 255s SOUPFREQ 2 -2652.7 5369.3 10.3447 0.005671 ** 255s --- 255s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 255s > 255s > ################################# 255s > 255s > 255s BEGIN TEST ranef.loading.R 255s 255s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 255s Copyright (C) 2024 The R Foundation for Statistical Computing 255s Platform: aarch64-unknown-linux-gnu (64-bit) 255s 255s R is free software and comes with ABSOLUTELY NO WARRANTY. 255s You are welcome to redistribute it under certain conditions. 255s Type 'license()' or 'licence()' for distribution details. 255s 255s R is a collaborative project with many contributors. 255s Type 'contributors()' for more information and 255s 'citation()' on how to cite R or R packages in publications. 255s 255s Type 'demo()' for some demos, 'help()' for on-line help, or 255s 'help.start()' for an HTML browser interface to help. 255s Type 'q()' to quit R. 255s 255s > # check that ranef and VarCorr work even after loading ordinal: 255s > library(lme4) 255s Loading required package: Matrix 256s > fm1 <- lmer(Reaction ~ Days + (Days | Subject), data=sleepstudy) 256s > ranef(fm1) 256s $Subject 256s (Intercept) Days 256s 308 2.2585510 9.1989758 256s 309 -40.3987381 -8.6196806 256s 310 -38.9604090 -5.4488565 256s 330 23.6906196 -4.8143503 256s 331 22.2603126 -3.0699116 256s 332 9.0395679 -0.2721770 257s 333 16.8405086 -0.2236361 257s 334 -7.2326151 1.0745816 257s 335 -0.3336684 -10.7521652 257s 337 34.8904868 8.6282652 257s 349 -25.2102286 1.1734322 257s 350 -13.0700342 6.6142178 257s 351 4.5778642 -3.0152621 257s 352 20.8636782 3.5360011 257s 369 3.2754656 0.8722149 257s 370 -25.6129993 4.8224850 257s 371 0.8070461 -0.9881562 257s 372 12.3145921 1.2840221 257s 257s with conditional variances for “Subject†257s > VarCorr(fm1) 257s Groups Name Std.Dev. Corr 257s Subject (Intercept) 24.7407 257s Days 5.9221 0.066 257s Residual 25.5918 257s > library(ordinal) 257s > ranef(fm1) 257s $Subject 257s (Intercept) Days 257s 308 2.2585510 9.1989758 257s 309 -40.3987381 -8.6196806 257s 310 -38.9604090 -5.4488565 257s 330 23.6906196 -4.8143503 257s 331 22.2603126 -3.0699116 257s 332 9.0395679 -0.2721770 257s 333 16.8405086 -0.2236361 257s 334 -7.2326151 1.0745816 257s 335 -0.3336684 -10.7521652 257s 337 34.8904868 8.6282652 257s 349 -25.2102286 1.1734322 257s 350 -13.0700342 6.6142178 257s 351 4.5778642 -3.0152621 257s 352 20.8636782 3.5360011 257s 369 3.2754656 0.8722149 257s 370 -25.6129993 4.8224850 257s 371 0.8070461 -0.9881562 257s 372 12.3145921 1.2840221 257s 257s with conditional variances for “Subject†257s > VarCorr(fm1) 257s Groups Name Std.Dev. Corr 257s Subject (Intercept) 24.7407 257s Days 5.9221 0.066 257s Residual 25.5918 257s > 257s BEGIN TEST test-all.R 257s 257s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 257s Copyright (C) 2024 The R Foundation for Statistical Computing 257s Platform: aarch64-unknown-linux-gnu (64-bit) 257s 257s R is free software and comes with ABSOLUTELY NO WARRANTY. 257s You are welcome to redistribute it under certain conditions. 257s Type 'license()' or 'licence()' for distribution details. 257s 257s R is a collaborative project with many contributors. 257s Type 'contributors()' for more information and 257s 'citation()' on how to cite R or R packages in publications. 257s 257s Type 'demo()' for some demos, 'help()' for on-line help, or 257s 'help.start()' for an HTML browser interface to help. 257s Type 'q()' to quit R. 257s 257s > 257s > if(require(testthat) && require(ordinal)) { 257s + test_check("ordinal") 257s + } 257s Loading required package: testthat 257s Loading required package: ordinal 265s [ FAIL 0 | WARN 0 | SKIP 0 | PASS 81 ] 265s > 265s BEGIN TEST test.clm.Theta.R 265s 265s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 265s Copyright (C) 2024 The R Foundation for Statistical Computing 265s Platform: aarch64-unknown-linux-gnu (64-bit) 265s 265s R is free software and comes with ABSOLUTELY NO WARRANTY. 265s You are welcome to redistribute it under certain conditions. 265s Type 'license()' or 'licence()' for distribution details. 265s 265s R is a collaborative project with many contributors. 265s Type 'contributors()' for more information and 265s 'citation()' on how to cite R or R packages in publications. 265s 265s Type 'demo()' for some demos, 'help()' for on-line help, or 265s 'help.start()' for an HTML browser interface to help. 265s Type 'q()' to quit R. 265s 265s > library(ordinal) 266s > 266s > ################################# 266s > ## 1 categorical variable in nominal: 266s > fm <- clm(rating ~ temp, nominal=~contact, data=wine) 266s > fm$Theta 266s contact 1|2 2|3 3|4 4|5 266s 1 no -1.323043 1.2464435 3.550044 4.660247 266s 2 yes -2.938103 -0.2651238 1.875288 3.609624 266s > fm$alpha.mat 266s 1|2 2|3 3|4 4|5 266s (Intercept) -1.323043 1.246444 3.550044 4.660247 266s contactyes -1.615059 -1.511567 -1.674756 -1.050623 266s > ## Threshold effects: 266s > fm <- clm(rating ~ temp, nominal=~contact, data=wine, 266s + threshold="symmetric") 266s > fm$Theta 266s contact 1|2 2|3 3|4 4|5 266s 1 no -1.054279 1.083892 3.383980 5.522152 266s 2 yes -2.360683 -0.356889 1.753317 3.757111 266s > fm$alpha.mat 266s central.1 central.2 spacing.1 266s (Intercept) 1.083892 3.383980 2.1381713 266s contactyes -1.440781 -1.630663 -0.1343777 266s > fm <- clm(rating ~ temp, nominal=~contact, data=wine, 266s + threshold="equidistant") 266s > fm$Theta 266s contact 1|2 2|3 3|4 4|5 266s 1 no -1.089140 1.1176064 3.324353 5.531099 266s 2 yes -2.386361 -0.3365063 1.713348 3.763202 266s > fm$alpha.mat 266s threshold.1 spacing 266s (Intercept) -1.08914Warning message: 266s (1) Hessian is numerically singular: parameters are not uniquely determined 266s In addition: Absolute convergence criterion was met, but relative criterion was not met 266s 2.2067465 266s contactyes -1.29722 -0.1568922 266s > ## Singular fit is still ok (with a warning, though) 266s > fm <- clm(rating ~ contact, nominal=~temp, data=wine) 266s > fm$alpha.mat 266s 1|2 2|3 3|4 4|5 266s (Intercept) -1.265638 1.104045 3.765661 24.89643 266s tempwarm -21.095417 -2.153024 -2.873317 -22.55000 266s > fm$Theta 266s temp 1|2 2|3 3|4 4|5 266s 1 cold -1.265638 1.104045 3.7656606 24.896432 266s 2 warm -22.361055 -1.048979 0.8923431 2.346436 266s > 266s > ################################# 266s > ## 1 continuous variable: 266s > set.seed(123) 266s > x <- rnorm(nrow(wine), sd=1) 266s > fm <- clm(rating ~ temp, nominal=~ x, data=wine) 266s > fm$alpha.mat 266s 1|2 2|3 3|4 4|5 266s (Intercept) -1.93392115 0.4251062 2.4798775 3.9190335 266s x 0.09463825 0.3805713 0.4261607 0.3809099 266s > fm$Theta 266s 1|2 2|3 3|4 4|5 266s 1 -1.933921 0.4251062 2.479878 3.919034 266s > fm <- clm(rating ~ temp, nominal=~ poly(x, 2), data=wine) 266s > fm$alpha.mat 266s 1|2 2|3 3|4 4|5 266s (Intercept) -1.9310988 0.4469436 2.517523 4.094448 266s poly(x, 2)1 0.8763914 3.2908002 3.471603 4.422045 266s poly(x, 2)2 -0.3826811 0.2518184 -2.064209 5.810095 266s > fm$Theta 266s 1|2 2|3 3|4 4|5 266s 1 -1.931099 0.4469436 2.517523 4.094448 266s > 266s > ################################# 266s > ## 1 categorical + 1 continuous variable: 266s > set.seed(123) 266s > x <- rnorm(nrow(wine), sd=1) 266s > fm <- clm(rating ~ temp, nominal=~contact + x, data=wine) 266s > fm$alpha.mat 266s 1|2 2|3 3|4 4|5 266s (Intercept) -1.279484 1.2782515 3.612766 4.7496630 266s contactyes -1.770377 -1.6715296 -1.647335 -0.9575417 266s x 0.300792 0.5330593 0.351517 0.3320371 266s > fm$Theta 266s contact 1|2 2|3 3|4 4|5 266s 1 no -1.279484 1.2782515 3.612766 4.749663 266s 2 yes -3.049860 -0.3932781 1.965431 3.792121 266s > fm <- clm(rating ~ temp, nominal=~contact + x, data=wine, 266s + threshold="symmetric") 266s > fm$alpha.mat 266s central.1 central.2 spacing.1 266s (Intercept) 1.1195535 3.4384752 2.134429723 266s contactyes -1.5864032 -1.5904314 -0.007568099 266s x 0.5069573 0.3485632 0.137951085 266s > fm$Theta 266s contact 1|2 2|3 3|4 4|5 266s 1 no -1.014876 1.1195535 3.438475 5.572905 266s 2 yes -2.593711 -0.4668497 1.848044 3.974905 266s > ################################# 266s > ### NOTE: To get the by-threshold nominal effects of continuous terms 266s > ## use: 266s > with(fm, t(apply(alpha.mat, 1, function(th) tJac %*% th))) 266s [,1] [,2] [,3] [,4] 266s (Intercept) -1.0148763 1.1195535 3.4384752 5.5729049 266s contactyes -1.5788351 -1.5864032 -1.5904314 -1.5979995 266s x 0.3690062 0.5069573 0.3485632 0.4865143 266s > ################################# 266s > ## Interactions: 266s > fm <- clm(rating ~ temp, nominal=~contact:x, data=wine) 266s > fm$alpha.mat 266s 1|2 2|3 3|4 4|5 266s (Intercept) -1.9577944 0.5997213 2.6863244 4.1510613 266s contactno:x 0.1127629 0.7818026 0.4423216 0.9364319 266s contactyes:x 0.2129232 -0.2720801 0.3848893 0.1730418 266s > fm$Theta 266s 1|2 2|3 3|4 4|5 266s 1 -1.957794 0.5997213 2.686324 4.151061 266s > fm <- clm(rating ~ temp, nominal=~contact+x+contact:x, data=wine) 266s > fm$alpha.mat 266s 1|2 2|3 3|4 4|5 266s (Intercept) -1.3000385 1.4056290 3.8340494 5.195521 266s contactyes -2.2801110 -1.5685386 -1.7308097 -1.318630 266s x 0.1790630 0.8754972 0.5140440 1.061857 266s contactyes:x 0.7541913 -0.8829449 -0.2203363 -1.055090 266s > fm$Theta 266s contact 1|2 2|3 3|4 4|5 266s 1 no -1.300039 1.4056290 3.834049 5.195521 266s 2 yes -3.580150 -0.1629096 2.103240 3.876891 266s > fm <- clm(rating ~ temp, nominal=~contact*x, data=wine) 266s > fm$alpha.mat 266s 1|2 2|3 3|4 4|5 266s (Intercept) -1.3000385 1.4056290 3.8340494 5.195521 266s contactyes -2.2801110 -1.5685386 -1.7308097 -1.318630 266s x 0.1790630 0.8754972 0.5140440 1.061857 266s contactyes:x 0.7541913 -0.8829449 -0.2203363 -1.055090 266s > fm$Theta 266s contact 1|2 2|3 3|4 4|5 266s 1 no -1.300039 1.4056290 3.834049 5.195521 266s 2 yes -3.580150 -0.1629096 2.103240 3.876891 266s > ## polynomial terms: 266s > fm <- clm(rating ~ temp, nominal=~contact + poly(x, 2), data=wine) 266s > fm$alpha.mat 266s 1|2 2|3 3|4 4|5 266s (Intercept) -1.2704762 1.3058436 3.635351 4.984803 266s contactyes -1.7725959 -1.6863567 -1.668402 -1.045016 266s poly(x, 2)1 2.4660191 4.4257770 3.395876 4.572499 266s poly(x, 2)2 -0.5079931 -0.4326472 -2.815490 5.853814 266s > fm$Theta 266s contact 1|2 2|3 3|4 4|5 266s 1 no -1.270476 1.3058436 3.635351 4.984803 266s 2 yes -3.043072 -0.3805131 1.966949 3.939787 266s > ## logical variables: (treated like numeric variables) 266s > wine$Con <- as.character(wine$contact) == "yes" 266s > fm <- clm(rating ~ temp, nominal=~Con, data=wine) 266s > fm$Theta 266s 1|2 2|3 3|4 4|5 266s 1 -1.323043 1.246444 3.550044 4.660247 266s > fm$alpha.mat 266s 1|2 2|3 3|4 4|5 266s (Intercept) -1.323043 1.246444 3.550044 4.660247 266s ConTRUE -1.615059 -1.511567 -1.674756 -1.050623 266s > wine$Con.num <- 1 * wine$Con 266s > fm <- clm(rating ~ temp, nominal=~Con.num, data=wine) 266s > fm$Theta 266s 1|2 2|3 3|4 4|5 266s 1 -1.323043 1.246444 3.550044 4.660247 266s > fm$alpha.mat 266s 1|2 2|3 3|4 4|5 266s (Intercept) -1.323043 1.246444 3.550044 4.660247 266s Con.num -1.615059 -1.511567 -1.674756 -1.050623 266s > ################################# 266s > ## Two continuous variables: 266s > set.seed(321) 266s > y <- rnorm(nrow(wine), sd=1) 266s > fm1 <- clm(rating ~ temp, nominal=~y + x, data=wine) 266s > fm1$alpha.mat 266s 1|2 2|3 3|4 4|5 266s (Intercept) -2.0361734 0.4221202 2.4970718 3.92796873 266s y 0.4687950 0.1396038 0.3125431 0.08012751 266s x 0.1283933 0.3903469 0.4322374 0.37584062 266s > fm1$Theta 266s 1|2 2|3 3|4 4|5 266s 1 -2.036173 0.4221202 2.497072 3.927969 266s > ## summary(fm1) 266s > 266s > ################################# 267s > ## 1 categorical + 2 continuous variables: 267s > fm1 <- clm(rating ~ temp, nominal=~y + contact + x, data=wine) 267s > fm1$alpha.mat 267s 1|2 2|3 3|4 4|5 267s (Intercept) -1.3789903 1.2645381 3.5778844 4.76356985 267s y 0.4385042 0.1049073 0.2439721 -0.01655843 267s contactyes -1.7688345 -1.6608152 -1.5801690 -0.98076349 267s x 0.3414184 0.5436276 0.3683201 0.33263316 267s > fm1$Theta 267s contact 1|2 2|3 3|4 4|5 267s 1 no -1.378990 1.2645381 3.577884 4.763570 267s 2 yes -3.147825 -0.3962771 1.997715 3.782806 267s > 267s > fm1 <- clm(rating ~ temp, nominal=~contact + x + contact:x + y, 267s + data=wine) 267s > summary(fm1) 267s formula: rating ~ temp 267s nominal: ~contact + x + contact:x + y 267s data: wine 267s 267s link threshold nobs logLik AIC niter max.grad cond.H 267s logit flexible 72 -81.86 205.72 7(0) 6.30e-12 9.3e+01 267s 267s Coefficients: 267s Estimate Std. Error z value Pr(>|z|) 267s tempwarm 2.8541 0.6159 4.634 3.58e-06 *** 267s --- 267s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 267s 267s Threshold coefficients: 267s Estimate Std. Error z value 267s 1|2.(Intercept) -1.40166 0.63306 -2.214 267s 2|3.(Intercept) 1.38723 0.49672 2.793 267s 3|4.(Intercept) 3.78725 0.71352 5.308 267s 4|5.(Intercept) 5.19478 1.07162 4.848 267s 1|2.contactyes -2.25974 1.68593 -1.340 267s 2|3.contactyes -1.54343 0.62658 -2.463 267s 3|4.contactyes -1.65472 0.68161 -2.428 267s 4|5.contactyes -1.34417 1.10192 -1.220 267s 1|2.x 0.21217 0.60781 0.349 267s 2|3.x 0.88433 0.41592 2.126 267s 3|4.x 0.47072 0.57857 0.814 267s 4|5.x 0.98582 0.94345 1.045 267s 1|2.y 0.41959 0.59889 0.701 267s 2|3.y 0.08377 0.27912 0.300 267s 3|4.y 0.27724 0.33118 0.837 267s 4|5.y -0.03370 0.59652 -0.056 267s 1|2.contactyes:x 0.71850 1.19479 0.601 267s 2|3.contactyes:x -0.89167 0.68974 -1.293 267s 3|4.contactyes:x -0.10843 0.74237 -0.146 267s 4|5.contactyes:x -0.98243 1.06343 -0.924 267s > fm1$Theta 267s contact 1|2 2|3 3|4 4|5 267s 1 no -1.401661 1.3872281 3.787248 5.194782 267s 2 yes -3.661402 -0.1562067 2.132530 3.850615 267s > fm1$alpha.mat 267s 1|2 2|3 3|4 4|5 267s (Intercept) -1.4016606 1.38722808 3.7872478 5.19478152 267s contactyes -2.2597419 -1.54343480 -1.6547177 -1.34416691 267s x 0.2121750 0.88432858 0.4707237 0.98581604 267s y 0.4195947 0.08377343 0.2772447 -0.03369796 267s contactyes:x 0.7184952 -0.89166532 -0.1084271 -0.98242663 267s > fm1 <- clm(rating ~ temp, nominal=~contact*x + y, data=wine) 267s > fm1$Theta 267s contact 1|2 2|3 3|4 4|5 267s 1 no -1.401661 1.3872281 3.787248 5.194782 267s 2 yes -3.661402 -0.1562067 2.132530 3.850615 267s > fm1$alpha.mat 267s 1|2 2|3 3|4 4|5 267s (Intercept) -1.4016606 1.38722808 3.7872478 5.19478152 267s contactyes -2.2597419 -1.54343480 -1.6547177 -1.34416691 267s x 0.2121750 0.88432858 0.4707237 0.98581604 267s y 0.4195947 0.08377343 0.2772447 -0.03369796 267s contactyes:x 0.7184952 -0.89166532 -0.1084271 -0.98242663 267s > t(fm1$alpha.mat) 267s (Intercept) contactyes x y contactyes:x 267s 1|2 -1.401661 -2.259742 0.2121750 0.41959467 0.7184952 267s 2|3 1.387228 -1.543435 0.8843286 0.08377343 -0.8916653 267s 3|4 3.787248 -1.654718 0.4707237 0.27724473 -0.1084271 267s 4|5 5.194782 -1.344167 0.9858160 -0.03369796 -0.9824266 267s > fm1 267s formula: rating ~ temp 267s nominal: ~contact * x + y 267s data: wine 267s 267s link threshold nobs logLik AIC niter max.grad cond.H 267s logit flexible 72 -81.86 205.72 7(0) 6.30e-12 9.3e+01 267s 267s Coefficients: 267s tempwarm 267s 2.854 267s 267s Threshold coefficients: 267s 1|2 2|3 3|4 4|5 267s (Intercept) -1.40166 1.38723 3.78725 5.19478 267s contactyes -2.25974 -1.54343 -1.65472 -1.34417 267s x 0.21217 0.88433 0.47072 0.98582 267s y 0.41959 0.08377 0.27724 -0.03370 267s contactyes:x 0.71850 -0.89167 -0.10843 -0.98243 267s > 267s > ################################# 267s > ## ordered factors (behaves like numerical variables): 267s > data(soup, package="ordinal") 267s > fm2 <- clm(SURENESS ~ 1, nominal=~PRODID + DAY, data=soup) 267s > fm2$Theta 267s PRODID DAY 1|2 2|3 3|4 4|5 5|6 267s 1 1 1 -1.541481 -0.5738506 -0.21399538 0.04222703 0.75684062 267s 2 2 1 -2.260759 -1.5442697 -1.21890789 -0.91689299 -0.24659733 267s 3 3 1 -2.662588 -1.8500284 -1.67612929 -1.15745279 -0.65265582 267s 4 4 1 -2.230317 -1.3875834 -1.10527201 -0.70760465 -0.16454916 267s 5 5 1 -2.291960 -1.8870049 -1.51852627 -1.32708454 -0.64222204 267s 6 6 1 -2.765844 -2.1222058 -1.93080891 -1.76177831 -0.87239437 267s 7 1 2 -1.497366 -0.2765643 0.08617449 0.27652240 0.97863135 267s 8 2 2 -2.216645 -1.2469835 -0.91873802 -0.68259762 -0.02480661 267s 9 3 2 -2.618473 -1.5527421 -1.37595942 -0.92315742 -0.43086509 267s 10 4 2 -2.186203 -1.0902972 -0.80510215 -0.47330927 0.05724157 267s 11 5 2 -2.247845 -1.5897187 -1.21835640 -1.09278917 -0.42043131 267s 12 6 2 -2.721729 -1.8249196 -1.63063905 -1.52748294 -0.65060365 267s > fm2$alpha.mat 267s 1|2 2|3 3|4 4|5 5|6 267s (Intercept) -1.54148084 -0.5738506 -0.2139954 0.04222703 0.7568406 267s PRODID2 -0.71927809 -0.9704192 -1.0049125 -0.95912001 -1.0034380 267s PRODID3 -1.12110698 -1.2761778 -1.4621339 -1.19967981 -1.4094964 267s PRODID4 -0.68883656 -0.8137329 -0.8912766 -0.74983167 -0.9213898 267s PRODID5 -0.75047874 -1.3131544 -1.3045309 -1.36931157 -1.3990627 267s PRODID6 -1.22436292 -1.5483553 -1.7168135 -1.80400534 -1.6292350 267s DAY2 0.04411439 0.2972862 0.3001699 0.23429537 0.2217907 267s > prodid <- factor(soup$PRODID, ordered=TRUE) 267s > fm2 <- clm(SURENESS ~ 1, nominal=~prodid + DAY, data=soup) 267s > fm2$alpha.mat 267s 1|2 2|3 3|4 4|5 5|6 267s (Intercept) -2.29215806 -1.5608238 -1.2772733 -0.9714310 -0.3035963 267s prodid.L -0.69121817 -0.9929406 -1.0651956 -1.1714141 -1.0571728 267s prodid.Q 0.28234300 0.3165731 0.3424949 0.1207237 0.3905959 267s prodid.C -0.56889235 -0.5360906 -0.6536897 -0.5924148 -0.5462885 267s prodid^4 -0.08220340 0.2121409 0.0953785 0.2423256 0.1732012 267s prodid^5 0.20500444 0.3017272 0.3458281 0.2989342 0.3294562 267s DAY2 0.04411439 0.2972862 0.3001699 0.2342954 0.2217907 267s > fm2$Theta 267s DAY 1|2 2|3 3|4 4|5 5|6 267s 1 1 -2.292158 -1.560824 -1.2772733 -0.9714310 -0.30359635 267s 2 2 -2.248044 -1.263538 -0.9771034 -0.7371357 -0.08180562 267s > fm2 <- clm(SURENESS ~ 1, nominal=~prodid, data=soup) 267s > fm2$alpha.mat 267s 1|2 2|3 3|4 4|5 5|6 267s (Intercept) -2.2615449 -1.4231189 -1.13844940 -0.8610163 -0.20025662 267s prodid.L -0.6802192 -1.0171675 -1.08713192 -1.1713363 -1.05578526 267s prodid.Q 0.2551357 0.3521163 0.37511177 0.1651463 0.43182970 267s prodid.C -0.6064464 -0.5635065 -0.68182671 -0.6050149 -0.55490977 267s prodid^4 -0.1115795 0.1036958 -0.01443457 0.1577696 0.09355651 267s prodid^5 0.2349647 0.4222560 0.46856405 0.3867234 0.41280490 267s > fm2$Theta 267s 1|2 2|3 3|4 4|5 5|6 267s 1 -2.261545 -1.423119 -1.138449 -0.8610163 -0.2002566 267s > ################################# 267s > ## Aliased Coefficients: 267s > ## 267s > ## Example where the interaction in the nominal effects is aliased (by 267s > ## design). Here the two Theta matrices coincide. The alpha.mat 267s > ## matrices are similar except one has an extra row with NAs: 267s > soup2 <- soup 267s > levels(soup2$DAY) 267s [1] "1" "2" 267s > levels(soup2$GENDER) 267s [1] "Male" "Female" 267s > xx <- with(soup2, DAY == "2" & GENDER == "Female") 267s > ## Model with additive nominal effects: 267s > fm8 <- clm(SURENESS ~ PRODID, nominal= ~ DAY + GENDER, data=soup2, subset=!xx) 267s > fm8$alpha.mat 267s 1|2 2|3 3|4 4|5 5|6 267s (Intercept) -1.5296912 -0.68765358 -0.3255117394 0.03773041 0.629325973 267s DAY2 -0.2553049 0.08584421 0.1101987830 0.05149732 0.168514829 267s GENDERFemale 0.0790841 0.07464904 -0.0001589362 -0.11045608 -0.005418789 267s > fm8$Theta 267s DAY GENDER 1|2 2|3 3|4 4|5 5|6 267s 1 1 Male -1.529691 -0.6876536 -0.3255117 0.03773041 0.6293260 267s 2 2 Male -1.784996 -0.6018094 -0.2153130 0.08922773 0.7978408 267s 3 1 Female -1.450607 -0.6130045 -0.3256707 -0.07272568 0.6239072 267s 4 2 Female -1.705912 -0.5271603 -0.2154719 -0.02122835 0.7924220 267s > ## Model with non-additive, but aliased nominal effects: 267s > fm9 <- clm(SURENESS ~ PRODID, nominal= ~ DAY * GENDER, data=soup2, subset=!xx) 267s > fm9$alpha.mat 267s 1|2 2|3 3|4 4|5 5|6 267s (Intercept) -1.5296912 -0.68765358 -0.3255117394 0.03773041 0.629325973 267s DAY2 -0.2553049 0.08584421 0.1101987830 0.05149732 0.168514829 267s GENDERFemale 0.0790841 0.07464904 -0.0001589362 -0.11045608 -0.005418789 267s DAY2:GENDERFemale NA NA NA NA NA 267s > fm9$Theta 267s DAY GENDER 1|2 2|3 3|4 4|5 5|6 267s 1 1 Male -1.529691 -0.6876536 -0.3255117 0.03773041 0.6293260 267s 2 2 Male -1.784996 -0.6018094 -0.2153130 0.08922773 0.7978408 267s 3 1 Female -1.450607 -0.6130045 -0.3256707 -0.07272568 0.6239072 267s 4 2 Female -1.705912 -0.5271603 -0.2154719 -0.02122835 0.7924220 267s > 267s > stopEqual <- function(x, y, ca=FALSE) 267s + stopifnot(isTRUE(all.equal(x, y, check.attributes=ca))) 267s > 267s > stopEqual(fm8$alpha.mat, fm9$alpha.mat[1:3, ]) 267s > stopEqual(fm8$Theta, fm9$Theta) 267s > stopEqual(logLik(fm8), logLik(fm9)) 267s > 267s > ################################# 267s > ## Weights: 267s > set.seed(12345) 267s > wts <- runif(nrow(soup)) 267s > fm2 <- clm(SURENESS ~ 1, nominal=~SOUPTYPE + DAY, data=soup, weights=wts) 267s > fm2$Theta 267s SOUPTYPE DAY 1|2 2|3 3|4 4|5 5|6 267s 1 Self-made 1 -1.957136 -1.2051740 -0.8829317 -0.6651699 -0.03270025 267s 2 Canned 1 -1.665918 -0.9408556 -0.6818962 -0.4277315 0.14356406 267s 3 Dry-mix 1 -2.180024 -1.2221288 -1.1502087 -0.8113657 -0.24840514 267s 4 Self-made 2 -1.988269 -0.9456030 -0.5614139 -0.3852570 0.23978932 267s 5 Canned 2 -1.697051 -0.6812846 -0.3603783 -0.1478186 0.41605363 267s 6 Dry-mix 2 -2.211157 -0.9625577 -0.8286909 -0.5314528 0.02408443 267s > 267s > ## Offset (correctly gives and error) 267s > fm2 <- try(clm(SURENESS ~ 1, nominal=~SOUPTYPE + DAY + offset(wts), 267s + data=soup), silent=TRUE) 267s > stopifnot(inherits(fm2, "try-error")) 267s > 267s > ################################# 267s > ### Other (misc) examples: 267s > fm2 <- clm(SURENESS ~ 1, nominal=~SOUPTYPE + DAY, data=soup) 267s > fm2$Theta 267s SOUPTYPE DAY 1|2 2|3 3|4 4|5 5|6 267s 1 Self-made 1 -2.040111 -1.2615146 -0.9302684 -0.6740629 -0.05003069 267s 2 Canned 1 -1.816274 -1.0347697 -0.7305192 -0.4563265 0.15972072 267s 3 Dry-mix 1 -2.313198 -1.3029029 -1.1328903 -0.8076982 -0.23529457 267s 4 Self-made 2 -1.956698 -0.9371883 -0.5968669 -0.4131354 0.21403949 267s 5 Canned 2 -1.732861 -0.7104435 -0.3971177 -0.1953990 0.42379090 267s 6 Dry-mix 2 -2.229785 -0.9785767 -0.7994888 -0.5467707 0.02877561 267s > fm2 267s formula: SURENESS ~ 1 267s nominal: ~SOUPTYPE + DAY 267s data: soup 267s 267s link threshold nobs logLik AIC niter max.grad cond.H 267s logit flexible 1847 -2758.02 5556.03 6(2) 1.74e-11 8.7e+02 267s 267s Threshold coefficients: 267s 1|2 2|3 3|4 4|5 5|6 267s (Intercept) -2.04011 -1.26151 -0.93027 -0.67406 -0.05003 267s SOUPTYPECanned 0.22384 0.22674 0.19975 0.21774 0.20975 267s SOUPTYPEDry-mix -0.27309 -0.04139 -0.20262 -0.13364 -0.18526 267s DAY2 0.08341 0.32433 0.33340 0.26093 0.26407 267s > fm2 <- clm(SURENESS ~ 1, nominal=~SOUPTYPE * DAY, data=soup) 267s > fm2$Theta 267s SOUPTYPE DAY 1|2 2|3 3|4 4|5 5|6 267s 1 Self-made 1 -2.062794 -1.3083328 -0.9935434 -0.7187896 -0.05107493 267s 2 Canned 1 -1.757074 -0.9398212 -0.6286087 -0.3721287 0.15415068 267s 3 Dry-mix 1 -2.369525 -1.3618033 -1.1700713 -0.8661663 -0.23795864 267s 4 Self-made 2 -1.945910 -0.9005649 -0.5459555 -0.3731219 0.21392690 267s 5 Canned 2 -1.775759 -0.7985077 -0.4924765 -0.2776317 0.43428555 267s 6 Dry-mix 2 -2.182299 -0.9257695 -0.7649729 -0.4964369 0.02702867 267s > fm2 267s formula: SURENESS ~ 1 267s nominal: ~SOUPTYPE * DAY 267s data: soup 267s 267s link threshold nobs logLik AIC niter max.grad cond.H 267s logit flexible 1847 -2755.60 5571.21 6(2) 1.75e-11 4.9e+03 267s 267s Threshold coefficients: 267s 1|2 2|3 3|4 4|5 5|6 267s (Intercept) -2.063e+00 -1.308e+00 -9.935e-01 -7.188e-01 -5.107e-02 267s SOUPTYPECanned 3.057e-01 3.685e-01 3.649e-01 3.467e-01 2.052e-01 267s SOUPTYPEDry-mix -3.067e-01 -5.347e-02 -1.765e-01 -1.474e-01 -1.869e-01 267s DAY2 1.169e-01 4.078e-01 4.476e-01 3.457e-01 2.650e-01 267s SOUPTYPECanned:DAY2 -1.356e-01 -2.665e-01 -3.115e-01 -2.512e-01 1.513e-02 267s SOUPTYPEDry-mix:DAY2 7.034e-02 2.827e-02 -4.249e-02 2.406e-02 -1.452e-05 267s > fm2$alpha.mat 267s 1|2 2|3 3|4 4|5 267s (Intercept) -2.06279431 -1.30833282 -0.99354336 -0.71878961 267s SOUPTYPECanned 0.30572040 0.36851159 0.36493470 0.34666092 267s SOUPTYPEDry-mix -0.30673027 -0.05347052 -0.17652789 -0.14737673 267s DAY2 0.11688416 0.40776793 0.44758789 0.34566775 267s SOUPTYPECanned:DAY2 -0.13556938 -0.26645440 -0.31145572 -0.25117080 267s SOUPTYPEDry-mix:DAY2 0.07034149 0.02826594 -0.04248955 0.02406171 267s 5|6 267s (Intercept) -5.107493e-02 267s SOUPTYPECanned 2.052256e-01 267s SOUPTYPEDry-mix -1.868837e-01 267s DAY2 2.650018e-01 267s SOUPTYPECanned:DAY2 1.513304e-02 267s SOUPTYPEDry-mix:DAY2 -1.451666e-05 267s > fm2 <- clm(SURENESS ~ 1, nominal=~SOUPTYPE * DAY, data=soup, 267s + threshold="symmetric") 267s > fm2$Theta 267s SOUPTYPE DAY 1|2 2|3 3|4 4|5 5|6 267s 1 Self-made 1 -2.023473 -1.3261580 -1.0328445 -0.7395310 -0.04221610 267s 2 Canned 1 -1.650803 -1.0121961 -0.7301243 -0.4480525 0.19055466 267s 3 Dry-mix 1 -2.214507 -1.4643357 -1.2132431 -0.9621504 -0.21197912 267s 4 Self-made 2 -1.757994 -1.0009894 -0.7422397 -0.4834900 0.27351461 267s 5 Canned 2 -1.673970 -0.8581393 -0.5997040 -0.3412687 0.47456211 267s 6 Dry-mix 2 -1.899340 -1.1167968 -0.9013722 -0.6859476 0.09659551 267s > fm2$alpha.mat 267s central spacing.1 spacing.2 267s (Intercept) -1.03284450 0.293313471 0.99062841 267s SOUPTYPECanned 0.30272022 -0.011241697 -0.06994946 267s SOUPTYPEDry-mix -0.18039855 -0.042220836 0.01063552 267s DAY2 0.29060480 -0.034563797 0.02512591 267s SOUPTYPECanned:DAY2 -0.16018453 0.010927306 0.12846128 267s SOUPTYPEDry-mix:DAY2 0.02126607 -0.001104241 -0.02842214 267s > 267s > ################################# 267s > ### Check correctness of Theta matrix when intercept is removed in 267s > ### nominal formula: 267s > ### December 25th 2014, RHBC 267s > fm1 <- clm(rating ~ temp, nominal=~contact-1, data=wine) 267s > fm2 <- clm(rating ~ temp, nominal=~contact, data=wine) 267s > stopifnot(isTRUE(all.equal(fm1$Theta, fm2$Theta))) 267s > stopifnot(isTRUE(all.equal(fm1$logLik, fm2$logLik))) 267s > wine2 <- wine 267s > wine2$contact <- relevel(wine2$contact, "yes") 267s > fm3 <- clm(rating ~ temp, nominal=~contact, data=wine2) 267s Warning message: 267s an intercept is needed and assumed in 'nominal' 267s > stopifnot(isTRUE(all.equal(coef(fm1, na.rm=TRUE), coef(fm3)))) 267s > ################################# 267s > 267s > 267s BEGIN TEST test.clm.convergence.R 267s 267s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 267s Copyright (C) 2024 The R Foundation for Statistical Computing 267s Platform: aarch64-unknown-linux-gnu (64-bit) 267s 267s R is free software and comes with ABSOLUTELY NO WARRANTY. 267s You are welcome to redistribute it under certain conditions. 267s Type 'license()' or 'licence()' for distribution details. 267s 267s R is a collaborative project with many contributors. 267s Type 'contributors()' for more information and 267s 'citation()' on how to cite R or R packages in publications. 267s 267s Type 'demo()' for some demos, 'help()' for on-line help, or 267s 'help.start()' for an HTML browser interface to help. 267s Type 'q()' to quit R. 267s 267s > library(ordinal) 268s > 268s > 268s > ## Testing that errors in chol() are caught soon enough: 268s > cy <- with(wine, which(temp == "cold" & contact == "yes")) 268s > wine2 <- subset(wine, subset=(!1:nrow(wine) %in% cy)) 268s > wine2[c(9, 15, 46), "rating"] <- NA 268s > fm1 <- clm(rating ~ temp, scale=~contact, nominal=~contact, 268s + data=wine2) 268s > fm1 <- try(clm(rating ~ temp, scale=~contact, nominal=~contact, 268s + data=wine2, control=list(gradTol=1e-12)), silent=TRUE) 268s Warning message: 268s (1) Hessian is numerically singular: parameters are not uniquely determined 268s In addition: Absolute convergence criterion was met, but relative criterion was not met 268s > fm2 <- try(clm(rating ~ temp, scale=~contact, nominal=~contact, 268s + data=wine2, control=list(gradTol=1e-15)), silent=TRUE) 268s Warning message: 268s (1) Hessian is numerically singular: parameters are not uniquely determined 268s In addition: Absolute convergence criterion was met, but relative criterion was not met 268s > ## These gave errors in version 2014.11-12. 268s > stopifnot(!inherits(fm1, "try-error")) 268s > stopifnot(!inherits(fm2, "try-error")) 268s > summary(fm1) 268s Warning message: 268s (-1) Model failed to converge with max|grad| = 3.74003e-09 (tol = 1e-15) 268s In addition: step factor reduced below minimum 268s formula: rating ~ temp 268s scale: ~contact 268s nominal: ~contact 268s data: wine2 268s 268s link threshold nobs logLik AIC niter max.grad cond.H 268s logit flexible 51 -60.44 140.87 62(38) 7.12e-14 1.5e+17 268s 268s Coefficients: 268s Estimate Std. Error z value Pr(>|z|) 268s tempwarm 2.306 NA NA NA 268s 268s log-scale coefficients: 268s Estimate Std. Error z value Pr(>|z|) 268s contactyes -0.07128 NA NA NA 268s 268s Threshold coefficients: 268s Estimate Std. Error z value 268s 1|2.(Intercept) -1.354 NA NA 268s 2|3.(Intercept) 1.092 NA NA 268s 3|4.(Intercept) 3.469 NA NA 268s 4|5.(Intercept) 5.066 NA NA 268s 1|2.contactyes -30.565 NA NA 268s 2|3.contactyes -1.425 NA NA 268s 3|4.contactyes -1.808 NA NA 268s 4|5.contactyes -1.870 NA NA 268s (3 observations deleted due to missingness) 268s > summary(fm2) 268s formula: rating ~ temp 268s scale: ~contact 268s nominal: ~contact 268s data: wine2 268s 268s link threshold nobs logLik AIC niter max.grad cond.H 268s logit flexible 51 -60.44 140.87 92(76) 3.74e-09 1.2e+16 268s 268s Coefficients: 268s Estimate Std. Error z value Pr(>|z|) 268s tempwarm 2.3060 0.7713 2.99 0.00279 ** 268s --- 268s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 268s 268s log-scale coefficients: 268s Estimate Std. Error z value Pr(>|z|) 268s contactyes -7.137e-02 1.635e+04 0 1 268s 268s Threshold coefficients: 268s Estimate Std. Error z value 268s 1|2.(Intercept) -1.354e+00 5.707e-01 -2.373 268s 2|3.(Intercept) 1.092e+00 5.251e-01 2.080 268s 3|4.(Intercept) 3.469e+00 7.982e-01 4.346 268s 4|5.(Intercept) 5.066e+00 1.193e+00 4.246 268s 1|2.contactyes -3.917e+01 2.138e+09 0.000 268s 2|3.contactyes -1.425e+00 4.314e+04 0.000 268s 3|4.contactyes -1.808e+00 1.055e+04 0.000 268s 4|5.contactyes -1.870e+00 1.455e+04 0.000 268s (3 observations deleted due to missingness) 268s > 268s > ## Error in convergence.clm() due to bad evaluation of model 268s > ## environment with update(object, doFit=FALSE): 268s > wine3 <- wine 268s > set.seed(1234) 268s > wts <- runif(nrow(wine3), 0, 2) 268s > fm3 <- clm(rating ~ temp + contact, data=wine3, 268s + weights=wts) 268s > c0 <- convergence(fm3) 268s > set.seed(1234) 268s > fm3 <- clm(rating ~ temp + contact, data=wine3, 268s + weights=runif(nrow(wine3), 0, 2)) 268s > c1 <- convergence(fm3) 268s > c0$info$logLik.Error 268s [1] "<1e-10" 268s > c1$info$logLik.Error 268s [1] "<1e-10" 268s > all.equal(c0$info$logLik.Error, c1$info$logLik.Error) 268s [1] TRUE 268s > ## In version 2014.11-14: 268s > ## > wine3 <- wine 268s > ## > set.seed(1234) 268s > ## > wts <- runif(nrow(wine3), 0, 2) 268s > ## > fm3 <- clm(rating ~ temp + contact, data=wine3, 268s > ## + weights=wts) 268s > ## > c0 <- convergence(fm3) 268s > ## > set.seed(1234) 268s > ## > fm3 <- clm(rating ~ temp + contact, data=wine3, 268s > ## + weights=runif(nrow(wine3), 0, 2)) 268s > ## > c1 <- convergence(fm3) 268s > ## > c0$info$logLik.Error 268s > ## [1] "<1e-10" 268s > ## > c1$info$logLik.Error 268s > ## [1] "4.80e+00" 268s > ## > all.equal(c0$info$logLik.Error, c1$info$logLik.Error) 268s > ## [1] "1 string mismatch" 268s > stopifnot(c0$info$logLik.Error == 268s + c1$info$logLik.Error) 268s > 268s BEGIN TEST test.clm.flex.link.R 268s 268s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 268s Copyright (C) 2024 The R Foundation for Statistical Computing 268s Platform: aarch64-unknown-linux-gnu (64-bit) 268s 268s R is free software and comes with ABSOLUTELY NO WARRANTY. 268s You are welcome to redistribute it under certain conditions. 268s Type 'license()' or 'licence()' for distribution details. 268s 268s R is a collaborative project with many contributors. 268s Type 'contributors()' for more information and 268s 'citation()' on how to cite R or R packages in publications. 268s 268s Type 'demo()' for some demos, 'help()' for on-line help, or 268s 'help.start()' for an HTML browser interface to help. 268s Type 'q()' to quit R. 268s 269s > # test.clm.flex.link.R 269s > 269s > library(ordinal) 270s > 270s > fm <- clm(rating ~ contact + temp, data=wine, link="log-gamma") 270s Changing to 'nlminb' optimizer for flexible link function 270s > fm 270s Warning message: 270s (-1) Model failed to converge with max|grad| = 9.9099e-05 (tol = 1e-06) 270s formula: rating ~ contact + temp 270s data: wine 270s 270s link threshold nobs logLik AIC niter max.grad cond.H 270s log-gamma flexible 72 -85.72 185.44 27(179) 9.91e-05 5.9e+01 270s 270s Coefficients: 270s contactyes tempwarm 270s 0.8614 1.5072 270s 270s Link coefficient: 270s lambda 270s 0.1615 270s 270s Threshold coefficients: 270s 1|2 2|3 3|4 4|5 270s -0.8798 0.6678 1.9807 2.8593 270s > summary(fm) 270s formula: rating ~ contact + temp 270s data: wine 270s 270s link threshold nobs logLik AIC niter max.grad cond.H 270s log-gamma flexible 72 -85.72 185.44 27(179) 9.91e-05 5.9e+01 270s 270s Coefficients: 270s Estimate Std. Error z value Pr(>|z|) 270s contactyes 0.8614 0.2675 3.220 0.00128 ** 270s tempwarm 1.5072 0.2947 5.114 3.16e-07 *** 270s --- 270s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 270s 270s Link coefficients: 270s Estimate Std. Error z value Pr(>|z|) 270s lambda 0.1615 0.5752 0.281 0.779 270s 270s Threshold coefficients: 270s Estimate Std. Error z value 270s 1|2 -0.8798 0.5003 -1.759 270s 2|3 0.6678 0.3450 1.936 270s 3|4 1.9807 0.3826 5.177 270s 4|5 2.8593 0.4656 6.141 270s > vcov(fm) 270s 1|2 2|3 3|4 4|5 contactyes 270s 1|2 0.25029667 0.12858124 0.11888120 0.14341730 0.03339111 270s 2|3 0.12858124 0.11899385 0.10688715 0.12363922 0.04117758 270s 3|4 0.11888120 0.10688715 0.14635447 0.15493865 0.05320442 270s 4|5 0.14341730 0.12363922 0.15493865 0.21676904 0.06051103 270s contactyes 0.03339111 0.04117758 0.05320442 0.06051103 0.07156735 270s tempwarm 0.00707258 0.03006561 0.05390802 0.06549176 0.01159715 270s lambda -0.23173315 -0.13979171 -0.12509774 -0.15581154 -0.01157951 270s tempwarm lambda 270s 1|2 0.00707258 -0.23173315 270s 2|3 0.03006561 -0.13979171 270s 3|4 0.05390802 -0.12509774 270s 4|5 0.06549176 -0.15581154 270s contactyes 0.01159715 -0.01157951 270s tempwarm 0.08687099 0.01970691 270s lambda 0.01970691 0.33082448 270s > logLik(fm) 270s 'log Lik.' -85.72141 (df=7) 270s > extractAIC(fm) 270s [1] 7.0000 185.4428 270s > fm2 <- update(fm, link="probit") 270s > anova(fm, fm2) 270s Likelihood ratio tests of cumulative link models: 270s 270s formula: link: threshold: 270s fm2 rating ~ contact + temp probit flexible 270s fm rating ~ contact + temp log-gamma flexible 270s 270s no.par AIC logLik LR.stat df Pr(>Chisq) 270s fm2 6 183.52 -85.761 270s fm 7 185.44 -85.721 0.0795 1 0.778 270s > head(model.matrix(fm)$X) 270s (Intercept) contactyes tempwarm 270s 1 1 0 0 270s 2 1 0 0 270s 3 1 1 0 270s 4 1 1 0 270s 5 1 0 1 270s 6 1 0 1 270s > head(model.frame(fm)) 270s rating contact temp 270s 1 2 no cold 270s 2 3 no cold 270s 3 3 yes cold 270s 4 4 yes cold 270s 5 4 no warm 270s 6 4 no warm 270s > coef(fm) 270s 1|2 2|3 3|4 4|5 contactyes tempwarm lambda 270s -0.8797774 0.6678307 1.9806826 2.8593125 0.8614400 1.5071959 0.1614741 270s > coef(summary(fm)) 270s Estimate Std. Error z value Pr(>|z|) 270s 1|2 -0.8797774 0.5002966 -1.7585116 7.866049e-02 270s 2|3 0.6678307 0.3449548 1.9359945 5.286838e-02 270s 3|4 1.9806826 0.3825630 5.1774020 2.249971e-07 270s 4|5 2.8593125 0.4655846 6.1413379 8.182930e-10 270s contactyes 0.8614400 0.2675208 3.2200868 1.281518e-03 270s tempwarm 1.5071959 0.2947388 5.1136658 3.159661e-07 270s lambda 0.1614741 0.5751734 0.2807398 7.789100e-01 270s > nobs(fm) 270s [1] 72 270s > terms(fm) 270s rating ~ contact + temp 270s attr(,"variables") 270s list(rating, contact, temp) 270s attr(,"factors") 270s contact temp 270s rating 0 0 270s contact 1 0 270s temp 0 1 270s attr(,"term.labels") 270s [1] "contact" "temp" 270s attr(,"order") 270s [1] 1 1 270s attr(,"intercept") 270s [1] 1 270s attr(,"response") 270s [1] 1 270s attr(,".Environment") 270s 270s attr(,"predvars") 270s list(rating, contact, temp) 270s attr(,"dataClasses") 270s rating contact temp 270s "ordered" "factor" "factor" 270s > # profile(fm) # not implemented 270s > confint(fm) 270s Profile intervals not available for models with flexible link function: 270s reporting Wald intervals instead 270s 2.5 % 97.5 % 270s 1|2 -1.860340646 0.1007859 270s 2|3 -0.008268391 1.3439298 270s 3|4 1.230872844 2.7304924 270s 4|5 1.946783402 3.7718416 270s contactyes 0.337108995 1.3857711 270s tempwarm 0.929518433 2.0848735 270s lambda -0.965845151 1.2887933 270s > 270s > predict(fm, se=TRUE, interval = TRUE) 270s $fit 270s [1] 0.55792544 0.21565445 0.44140778 0.09846706 0.22428321 0.22428321 270s [7] 0.29090567 0.29090567 0.21042288 0.55792544 0.05388914 0.44140778 270s [13] 0.20737472 0.48129483 0.29090567 0.33832254 0.55792544 0.21565445 270s [19] 0.44140778 0.39099052 0.07269587 0.07269587 0.33832254 0.33832254 270s [25] 0.21565445 0.55792544 0.44140778 0.39099052 0.48129483 0.20737472 270s [31] 0.29090567 0.31272339 0.55792544 0.21565445 0.09846706 0.44140778 270s [37] 0.48129483 0.48129483 0.31272339 0.31272339 0.21565445 0.55792544 270s [43] 0.44140778 0.39099052 0.20737472 0.22428321 0.29090567 0.33832254 270s [49] 0.21042288 0.21042288 0.39099052 0.39099052 0.20737472 0.48129483 270s [55] 0.05636253 0.31272339 0.55792544 0.55792544 0.39099052 0.44140778 270s [61] 0.48129483 0.48129483 0.31272339 0.33832254 0.21042288 0.55792544 270s [67] 0.44140778 0.39099052 0.48129483 0.20737472 0.33832254 0.33832254 270s 270s $se.fit 270s [1] 0.09164058 0.09494135 0.08777656 0.05464347 0.08112461 0.08112461 270s [7] 0.13494788 0.13494788 0.13693811 0.09164058 0.04809909 0.08777656 270s [13] 0.09512593 0.07373113 0.13494788 0.08236628 0.09164058 0.09494135 270s [19] 0.08777656 0.09756681 0.06362571 0.06362571 0.08236628 0.08236628 270s [25] 0.09494135 0.09164058 0.08777656 0.09756681 0.07373113 0.09512593 270s [31] 0.13494788 0.09451059 0.09164058 0.09494135 0.05464347 0.08777656 270s [37] 0.07373113 0.07373113 0.09451059 0.09451059 0.09494135 0.09164058 270s [43] 0.08777656 0.09756681 0.09512593 0.08112461 0.13494788 0.08236628 270s [49] 0.13693811 0.13693811 0.09756681 0.09756681 0.09512593 0.07373113 270s [55] 0.03866211 0.09451059 0.09164058 0.09164058 0.09756681 0.08777656 270s [61] 0.07373113 0.07373113 0.09451059 0.08236628 0.13693811 0.09164058 270s [67] 0.08777656 0.09756681 0.07373113 0.09512593 0.08236628 0.08236628 270s 270s $lwr 270s [1] 0.378604421 0.083839589 0.282278454 0.031650565 0.103885179 0.103885179 270s [7] 0.102183449 0.102183449 0.050316476 0.378604421 0.008885132 0.282278454 270s [13] 0.077621510 0.342154616 0.102183449 0.199101468 0.378604421 0.083839589 270s [19] 0.282278454 0.223352983 0.012177666 0.012177666 0.199101468 0.199101468 270s [25] 0.083839589 0.378604421 0.282278454 0.223352983 0.342154616 0.077621510 270s [31] 0.102183449 0.161206608 0.378604421 0.083839589 0.031650565 0.282278454 270s [37] 0.342154616 0.342154616 0.161206608 0.161206608 0.083839589 0.378604421 270s [43] 0.282278454 0.223352983 0.077621510 0.103885179 0.102183449 0.199101468 270s [49] 0.050316476 0.050316476 0.223352983 0.223352983 0.077621510 0.342154616 270s [55] 0.014165414 0.161206608 0.378604421 0.378604421 0.223352983 0.282278454 270s [61] 0.342154616 0.342154616 0.161206608 0.199101468 0.050316476 0.378604421 270s [67] 0.282278454 0.223352983 0.342154616 0.077621510 0.199101468 0.199101468 270s 270s $upr 270s [1] 0.7233159 0.4523801 0.6135565 0.2673887 0.4189772 0.4189772 0.5965756 270s [8] 0.5965756 0.5727401 0.7233159 0.2657272 0.6135565 0.4485489 0.6233979 270s [15] 0.5965756 0.5125880 0.7233159 0.4523801 0.6135565 0.5890239 0.3326787 270s [22] 0.3326787 0.5125880 0.5125880 0.4523801 0.7233159 0.6135565 0.5890239 270s [29] 0.6233979 0.4485489 0.5965756 0.5186019 0.7233159 0.4523801 0.2673887 270s [36] 0.6135565 0.6233979 0.6233979 0.5186019 0.5186019 0.4523801 0.7233159 270s [43] 0.6135565 0.5890239 0.4485489 0.4189772 0.5965756 0.5125880 0.5727401 270s [50] 0.5727401 0.5890239 0.5890239 0.4485489 0.6233979 0.1988990 0.5186019 270s [57] 0.7233159 0.7233159 0.5890239 0.6135565 0.6233979 0.6233979 0.5186019 270s [64] 0.5125880 0.5727401 0.7233159 0.6135565 0.5890239 0.6233979 0.4485489 270s [71] 0.5125880 0.5125880 270s 270s > predict(fm, type="class") 270s $fit 270s [1] 2 2 3 3 3 3 4 4 2 2 3 3 3 3 4 4 2 2 3 3 3 3 4 4 2 2 3 3 3 3 4 4 2 2 3 3 3 3 270s [39] 4 4 2 2 3 3 3 3 4 4 2 2 3 3 3 3 4 4 2 2 3 3 3 3 4 4 2 2 3 3 3 3 4 4 270s Levels: 1 2 3 4 5 270s 270s > newData <- expand.grid(temp = c("cold", "warm"), 270s + contact = c("no", "yes")) 270s > 270s > ## Predicted probabilities in all five response categories for each of 270s > ## the four cases in newData: 270s > predict(fm, newdata=newData, type="prob") 270s $fit 270s 1 2 3 4 5 270s 1 0.210422883 0.55792544 0.2156544 0.01517801 0.0008192111 270s 2 0.014351371 0.20737472 0.4812948 0.22428321 0.0726958744 270s 3 0.053889141 0.39099052 0.4414078 0.09846706 0.0152454933 270s 4 0.001685878 0.05636253 0.3127234 0.33832254 0.2909056650 270s 270s > predict(fm, newdata=newData, type="class") 270s $fit 270s [1] 2 3 3 4 270s Levels: 1 2 3 4 5 270s 270s > 270s > predict(fm, newdata=newData, type="prob", se.fit = TRUE, interval = TRUE) 270s $fit 270s 1 2 3 4 5 270s 1 0.210422883 0.55792544 0.2156544 0.01517801 0.0008192111 270s 2 0.014351371 0.20737472 0.4812948 0.22428321 0.0726958744 270s 3 0.053889141 0.39099052 0.4414078 0.09846706 0.0152454933 270s 4 0.001685878 0.05636253 0.3127234 0.33832254 0.2909056650 270s 270s $se.fit 270s 1 2 3 4 5 270s 1 0.136938110 0.09164058 0.09494135 0.01696529 0.002047363 270s 2 0.016247015 0.09512593 0.07373113 0.08112461 0.063625711 270s 3 0.048099092 0.09756681 0.08777656 0.05464347 0.019268560 270s 4 0.002046575 0.03866211 0.09451059 0.08236628 0.134947885 270s 270s $lwr 270s 1 2 3 4 5 270s 1 0.050316476 0.37860442 0.08383959 0.001663553 6.091052e-06 270s 2 0.001530524 0.07762151 0.34215462 0.103885179 1.217767e-02 270s 3 0.008885132 0.22335298 0.28227845 0.031650565 1.249665e-03 270s 4 0.000155750 0.01416541 0.16120661 0.199101468 1.021834e-01 270s 270s $upr 270s 1 2 3 4 5 270s 1 0.57274013 0.7233159 0.4523801 0.1247616 0.09939055 270s 2Changing to 'nlminb' optimizer for flexible link function 270s 0.12150065 0.4485489 0.6233979 0.4189772 0.33267865 270s 3 0.26572719 0.5890239 0.6135565 0.2673887 0.16075952 270s 4 0.01797808 0.1988990 0.5186019 0.5125880 0.59657563 270s 270s > 270s > 270s > ## Aranda-Ordaz link: 270s > fm <- clm(rating ~ contact + temp, data=wine, link="Aranda-Ordaz") 270s Warning message: 270s (-1) Model failed to converge with max|grad| = 1.63026e-05 (tol = 1e-06) 270s > fm 270s formula: rating ~ contact + temp 270s data: wine 270s 270s link threshold nobs logLik AIC niter max.grad cond.H 270s Aranda-Ordaz flexible 72 -86.34 186.68 31(219) 1.63e-05 3.9e+02 270s 270s Coefficients: 270s contactyes tempwarm 270s 1.193 2.076 270s 270s Link coefficient: 270s lambda 270s 0.4994 270s 270s Threshold coefficients: 270s 1|2 2|3 3|4 4|5 270s -1.5284 0.7669 2.6021 3.7962 270s > summary(fm) 270s formula: rating ~ contact + temp 270s data: wine 270s 270s link threshold nobs logLik AIC niter max.grad cond.H 270s Aranda-Ordaz flexible 72 -86.34 186.68 31(219) 1.63e-05 3.9e+02 270s 270s Coefficients: 270s Estimate Std. Error z value Pr(>|z|) 270s contactyes 1.1927 0.6526 1.828 0.0676 . 270s tempwarm 2.0758 0.8196 2.533 0.0113 * 270s --- 270s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 270s 270s Link coefficients: 270s Estimate Std. Error z value Pr(>|z|) 270s lambda 0.4994 0.7840 0.637 0.524 270s 270s Threshold coefficients: 270s Estimate Std. Error z value 270s 1|2 -1.5284 0.5775 -2.647 270s 2|3 0.7669 0.8234 0.931 270s 3|4 2.6021 1.4335 1.815 270s 4|5 3.7962 1.9674 1.930 270s > vcov(fm) 270s 1|2 2|3 3|4 4|5 contactyes tempwarm 270s 1|2 0.3335060 0.2983830 0.4851477 0.6557866 0.2132243 0.2586679 270s 2|3 0.2983830 0.6780278 1.1261329 1.5330564 0.4699069 0.5953101 270s 3|4 0.4851477 1.1261329 2.0550132 2.7755716 0.8214403 1.0831428 270s 4|5 0.6557866 1.5330564 2.7755716 3.8705158 1.1194941 1.4831343 270s contactyes 0.2132243 0.4699069 0.8214403 1.1194941 0.4259333 0.3965112 270s tempwarm 0.2586679 0.5953101 1.0831428 1.4831343 0.3965112 0.6717720 270s lambda 0.2424389 0.5895693 1.0675177 1.4810302 0.4153797 0.5471765 270s lambda 270s 1|2 0.2424389 270s 2|3 0.5895693 270s 3|4 1.0675177 270s 4|5 1.4810302 270s contactyes 0.4153797 270s tempwarm 0.5471765 270s lambda 0.6146953 270s > logLik(fm) 270s 'log Lik.' -86.34171 (df=7) 270s > extractAIC(fm) 270s [1] 7.0000 186.6834 270s > fm2 <- update(fm, link="logit") 270s > anova(fm, fm2) 270s Likelihood ratio tests of cumulative link models: 270s 270s formula: link: threshold: 270s fm2 rating ~ contact + temp logit flexible 270s fm rating ~ contact + temp Aranda-Ordaz flexible 270s 270s no.par AIC logLik LR.stat df Pr(>Chisq) 270s fm2 6 184.98 -86.492 270s fm 7 186.68 -86.342 0.3004 1 0.5836 270s > head(model.matrix(fm)$X) 270s (Intercept) contactyes tempwarm 270s 1 1 0 0 270s 2 1 0 0 270s 3 1 1 0 270s 4 1 1 0 270s 5 1 0 1 270s 6 1 0 1 270s > head(model.frame(fm)) 270s rating contact temp 270s 1 2 no cold 270s 2 3 no cold 270s 3 3 yes cold 270s 4 4 yes cold 270s 5 4 no warm 270s 6 4 no warm 270s > coef(fm) 270s 1|2 2|3 Profile intervals not available for models with flexible link function: 270s reporting Wald intervals instead 270s 3|4 4|5 contactyes tempwarm lambda 270s -1.5283885 0.7668892 2.6021281 3.7962200 1.1927244 2.0757936 0.4994415 270s > coef(summary(fm)) 270s Estimate Std. Error z value Pr(>|z|) 270s 1|2 -1.5283885 0.5774998 -2.6465611 0.008131482 270s 2|3 0.7668892 0.8234244 0.9313413 0.351677025 270s 3|4 2.6021281 1.4335317 1.8151869 0.069495186 270s 4|5 3.7962200 1.9673627 1.9295985 0.053656609 270s contactyes 1.1927244 0.6526357 1.8275501 0.067617099 270s tempwarm 2.0757936 0.8196170 2.5326386 0.011320761 270s lambda 0.4994415 0.7840251 0.6370223 0.524110286 270s > nobs(fm) 270s [1] 72 270s > terms(fm) 270s rating ~ contact + temp 270s attr(,"variables") 270s list(rating, contact, temp) 270s attr(,"factors") 270s contact temp 270s rating 0 0 270s contact 1 0 270s temp 0 1 270s attr(,"term.labels") 270s [1] "contact" "temp" 270s attr(,"order") 270s [1] 1 1 270s attr(,"intercept") 270s [1] 1 270s attr(,"response") 270s [1] 1 270s attr(,".Environment") 270s 270s attr(,"predvars") 270s list(rating, contact, temp) 270s attr(,"dataClasses") 270s rating contact temp 270s "ordered" "factor" "factor" 270s > # profile(fm) # not implemented 270s > confint(fm) 270s 2.5 % 97.5 % 270s 1|2 -2.66026726 -0.3965097 270s 2|3 -0.84699302 2.3807714 270s 3|4 -0.20754249 5.4117986 270s 4|5 -0.05973999 7.6521799 270s contactyes -0.08641802 2.4718668 270s tempwarm 0.46937382 3.6822133 270s lambda -1.03721941 2.0361024 270s > 270s > predict(fm, se=TRUE, interval = TRUE) 270s $fit 270s [1] 0.58209325 0.21518056 0.46054754 0.09103825 0.22383779 0.22383779 270s [7] 0.29286866 0.29286866 0.18610435 0.58209325 0.06269201 0.46054754 270s [13] 0.19716614 0.48293297 0.29286866 0.34021081 0.58209325 0.21518056 270s [19] 0.46054754 0.36913993 0.06939859 0.06939859 0.34021081 0.34021081 270s [25] 0.21518056 0.58209325 0.46054754 0.36913993 0.48293297 0.19716614 270s [31] 0.29286866 0.28974275 0.58209325 0.21518056 0.09103825 0.46054754 270s [37] 0.48293297 0.48293297 0.28974275 0.28974275 0.21518056 0.58209325 270s [43] 0.46054754 0.36913993 0.19716614 0.22383779 0.29286866 0.34021081 270s [49] 0.18610435 0.18610435 0.36913993 0.36913993 0.19716614 0.48293297 270s [55] 0.06897335 0.28974275 0.58209325 0.58209325 0.36913993 0.46054754 270s [61] 0.48293297 0.48293297 0.28974275 0.34021081 0.18610435 0.58209325 270s [67] 0.46054754 0.36913993 0.48293297 0.19716614 0.34021081 0.34021081 270s 270s $se.fit 270s [1] 0.14151187 0.09458704 0.10284384 0.06173010 0.06089158 0.06089158 270s [7] 0.17401323 0.17401323 0.08458282 0.14151187 0.03342713 0.10284384 270s [13] 0.06151480 0.16022480 0.17401323 0.14317221 0.14151187 0.09458704 270s [19] 0.10284384 0.09671235 0.16165494 0.16165494 0.14317221 0.14317221 270s [25] 0.09458704 0.14151187 0.10284384 0.09671235 0.16022480 0.06151480 270s [31] 0.17401323 0.08680263 0.14151187 0.09458704 0.06173010 0.10284384 270s [37] 0.16022480 0.16022480 0.08680263 0.08680263 0.09458704 0.14151187 270s [43] 0.10284384 0.09671235 0.06151480 0.06089158 0.17401323 0.14317221 270s [49] 0.08458282 0.08458282 0.09671235 0.09671235 0.06151480 0.16022480 270s [55] 0.03861752 0.08680263 0.14151187 0.14151187 0.09671235 0.10284384 270s [61] 0.16022480 0.16022480 0.08680263 0.14317221 0.08458282 0.14151187 270s [67] 0.10284384 0.09671235 0.16022480 0.06151480 0.14317221 0.14317221 270s 270s $lwr 270s [1] 0.3081470903 0.0838051147 0.2749859871 0.0226847128 0.1267084215 270s [6] 0.1267084215 0.0738941549 0.0738941549 0.0710944694 0.3081470903 270s [11] 0.0214631497 0.2749859871 0.1028661816 0.2098384782 0.0738941549 270s [16] 0.1287024770 0.3081470903 0.0838051147 0.2749859871 0.2058910205 270s [21] 0.0005517244 0.0005517244 0.1287024770 0.1287024770 0.0838051147 270s [26] 0.3081470903 0.2749859871 0.2058910205 0.2098384782 0.1028661816 270s [31] 0.0738941549 0.1514410899 0.3081470903 0.0838051147 0.0226847128 270s [36] 0.2749859871 0.2098384782 0.2098384782 0.1514410899 0.1514410899 270s [41] 0.0838051147 0.3081470903 0.2749859871 0.2058910205 0.1028661816 270s [46] 0.1267084215 0.0738941549 0.1287024770 0.0710944694 0.0710944694 270s [51] 0.2058910205 0.2058910205 0.1028661816 0.2098384782 0.0222866429 270s [56] 0.1514410899 0.3081470903 0.3081470903 0.2058910205 0.2749859871 270s [61] 0.2098384782 0.2098384782 0.1514410899 0.1287024770 0.0710944694 270s [66] 0.3081470903 0.2749859871 0.2058910205 0.2098384782 0.1028661816 270s [71] 0.1287024770 0.1287024770 270s 270s $upr 270s [1] 0.8132915 0.4511024 0.6577298 0.3017605 0.3643579 0.3643579 0.6825186 270s [8] 0.6825186 0.4058732 0.8132915 0.1694071 0.6577298 0.3446983 0.7666176 270s [15] 0.6825186 0.6428534 0.8132915 0.4511024 0.6577298 0.5690698 0.9097003 270s [22] 0.9097003 0.6428534 0.6428534 0.4511024 0.8132915 0.6577298 0.5690698 270s [29] 0.7666176 0.3446983 0.6825186 0.4825259 0.8132915 0.4511024 0.3017605 270s [36] 0.6577298 0.7666176 0.7666176 0.4825259 0.4825259 0.4511024 0.8132915 270s [43] 0.6577298 0.5690698 0.3446983 0.3643579 0.6825186 0.6428534 0.4058732 270s [50] 0.4058732 0.5690698 0.5690698 0.3446983 0.7666176 0.1940499 0.4825259 270s [57] 0.8132915 0.8132915 0.5690698 0.6577298 0.7666176 0.7666176 0.4825259 270s [64] 0.6428534 0.4058732 0.8132915 0.6577298 0.5690698 0.7666176 0.3446983 270s [71] 0.6428534 0.6428534 270s 270s > predict(fm, type="class") 270s $fit 270s [1] 2 2 3 3 3 3 4 4 2 2 3 3 3 3 4 4 2 2 3 3 3 3 4 4 2 2 3 3 3 3 4 4 2 2 3 3 3 3 270s [39] 4 4 2 2 3 3 3 3 4 4 2 2 3 3 3 3 4 4 2 2 3 3 3 3 4 4 2 2 3 3 3 3 4 4 270s Levels: 1 2 3 4 5 270s 270s > newData <- expand.grid(temp = c("cold", "warm"), 270s + contact = c("no", "yes")) 270s > 270s > ## Predicted probabilities in all five response categories for each of 270s > ## the four cases in newData: 270s > predict(fm, newdata=newData, type="prob") 270s $fit 270s 1 2 3 4 5 270s 1 0.186104347 0.58209325 0.2151806 0.01478353 0.001838315 270s 2 0.026664518 0.19716614 0.4829330 0.22383779 0.069398588 270s 3 0.062692012 0.36913993 0.4605475 0.09103825 0.016582262 270s 4 0.008204432 0.06897335 0.2897428 0.34021081 0.292868655 270s 270s > predict(fm, newdata=newData, type="class") 270s $fit 270s [1] 2 3 3 4 270s Levels: 1 2 3 4 5 270s 270s > 270s > predict(fm, newdata=newData, type="prob", se.fit = TRUE, interval = TRUE) 270s $fit 270s 1 2 3 4 5 270s 1 0.186104347 0.58209325 0.2151806 0.01478353 0.001838315 270s 2 0.026664518 0.19716614 0.4829330 0.22383779 0.069398588 270s 3 0.062692012 0.36913993 0.4605475 0.09103825 0.016582262 270s 4 0.008204432 0.06897335 0.2897428 0.34021081 0.292868655 270s 270s $se.fit 270s 1 2 3 4 5 270s 1 0.084582817Changing to 'nlminb' optimizer for flexible link function 270s 0.14151187 0.09458704 0.05105462 0.04225890 270s 2 0.018013146 0.06151480 0.16022480 0.06089158 0.16165494 270s 3 0.033427133 0.09671235 0.10284384 0.06173010 0.09203687 270s 4 0.009189041 0.03861752 0.08680263 0.14317221 0.17401323 270s 270s $lwr 270s 1 2 3 4 5 270s 1 0.0710944694 0.30814709 0.08380511 1.557841e-05 4.590853e-23 270s 2 0.0069799027 0.10286618 0.20983848 1.267084e-01 5.517244e-04 270s 3 0.0214631497 0.20589102 0.27498599 2.268471e-02 2.647288e-07 270s 4 0.0009036362 0.02228664 0.15144109 1.287025e-01 7.389415e-02 270s 270s $upr 270s 1 2 3 4 5 270s 1 0.40587324 0.8132915 0.4511024 0.9352884 1.0000000 270s 2 0.09647027 0.3446983 0.7666176 0.3643579 0.9097003 270s 3 0.16940714 0.5690698 0.6577298 0.3017605 0.9990698 270s 4 0.07033824 0.1940499 0.4825259 0.6428534 0.6825186 270s 270s > 270s > ######################################################################## 270s > ### Models with scale + flex link (or cauchit link) 270s > ######################################################################## 270s > 270s > fm <- clm(SURENESS ~ PRODID, scale=~PROD, data = soup, link="Aranda-Ordaz") 271s > summary(fm) 271s Warning message: 271s (-1) Model failed to converge with max|grad| = 0.000374096 (tol = 1e-06) 271s formula: SURENESS ~ PRODID 271s scale: ~PROD 271s data: soup 271s 271s link threshold nobs logLik AIC niter max.grad cond.H 271s Aranda-Ordaz flexible 1847 -2674.65 5373.30 57(719) 3.74e-04 9.0e+03 271s 271s Coefficients: 271s Estimate Std. Error z value Pr(>|z|) 271s PRODID2 1.3604 0.4137 3.289 0.001007 ** 271s PRODID3 2.2066 0.6659 3.314 0.000921 *** 271s PRODID4 1.2553 0.4086 3.072 0.002124 ** 271s PRODID5 1.9820 0.5886 3.367 0.000759 *** 271s PRODID6 2.4715 0.7713 3.204 0.001355 ** 271s --- 271s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 271s 271s log-scale coefficients: 271s Estimate Std. Error z value Pr(>|z|) 271s PRODTest 0.2807 0.1553 1.808 0.0706 . 271s --- 271s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 271s 271s Link coefficients: 271s Estimate Std. Error z value Pr(>|z|) 271s lambda 2.063 1.136 1.816 0.0693 . 271s --- 271s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 271s 271s Threshold coefficients: 271s Estimate Std. Error z value 271s 1|2 -1.3927 0.1491 -9.344 271s 2|3 -0.1449 0.3533 -0.410 271s 3|4 0.3051 0.4699 0.649 271s 4|5 0.6733 0.5802 1.160 271s 5|6 1.7210 0.9594 1.794 271s > 271s > fm <- clm(SURENESS ~ PRODID, scale=~PROD, data = soup, link="log-gamma") 271s Changing to 'nlminb' optimizer for flexible link function 273s > summary(fm) 273s formula: SURENESS ~ PRODID 273s scale: ~PROD 273s data: soup 273s 273s link threshold nobs logLik AIC niter max.grad cond.H 273s log-gamma flexible 1847 -2676.84 5377.68 90(1050) 3.34e-03 8.9e+03 273s 273s Coefficients: 273s Estimate Std. Error z value Pr(>|z|) 273s PRODID2 0.62877 0.09223 6.818 9.26e-12 *** 273s PRODID3 1.02758 0.13449 7.640 2.16e-14 *** 273s PRODID4 0.59157 0.11435 5.173 2.30e-07 *** 273s PRODID5 0.91937 0.12977 7.085 1.39e-12 *** 273s PRODID6 1.13202 0.13927 8.128 4.35e-16 *** 273s --- 273s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 273s 273s log-scale coefficients: 273s Estimate Std. Error z value Pr(>|z|) 273s PRODTest 0.09065 0.18402 0.493 0.622 273s 273s Link coefficients: 273s Estimate Std. Error z value Pr(>|z|) 273s lambda 0.475 0.703 0.676 0.499 273s 273s Threshold coefficients: 273s Estimate Std. Error z value 273s 1|2 -1.15651 0.45764 -2.527 273s 2|3 -0.47330 0.29569 -1.601 273s 3|4 -0.24746 0.26538 -0.932 273s 4|5 -0.07225 0.24982 -0.289 273s 5|6 0.37912 0.24130 1.571 273s > 273s > fm <- clm(SURENESS ~ PRODID, scale=~PROD, data = soup, link="cauchit") 273s Warning message: 273s (-1) Model failed to converge with max|grad| = 0.00333727 (tol = 1e-06) 273s > summary(fm) 273s formula: SURENESS ~ PRODID 273s scale: ~PROD 273s data: soup 273s 273s link threshold nobs logLik AIC niter max.grad cond.H 273s cauchit flexible 1847 -2679.34 5380.67 11(1) 3.10e-07 3.0e+02 273s 273s Coefficients: 273s Estimate Std. Error z value Pr(>|z|) 273s PRODID2 0.70550 0.09611 7.341 2.12e-13 *** 273s PRODID3 1.06186 0.13882 7.649 2.02e-14 *** 273s PRODID4 0.66876 0.11911 5.614 1.97e-08 *** 273s PRODID5 1.01135 0.13277 7.617 2.59e-14 *** 273s PRODID6 1.12784 0.14159 7.966 1.64e-15 *** 273s --- 273s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 273s 273s log-scale coefficients: 273s Estimate Std. Error z value Pr(>|z|)Changing to 'nlminb' optimizer for flexible link function 273s 273s PRODTest -0.20801 0.09524 -2.184 0.029 * 273s --- 273s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 273s 273s Threshold coefficients: 273s Estimate Std. Error z value 273s 1|2 -1.70920 0.14977 -11.412 273s 2|3 -0.36737 0.06302 -5.830 273s 3|4 -0.06736 0.05734 -1.175 273s 4|5 0.14657 0.05708 2.568 273s 5|6 0.67063 0.07072 9.483 273s > 273s > ######################################################################## 273s > ### clm.fit 273s > ######################################################################## 273s > 273s > ## Example with log-gamma: 273s > fm1 <- clm(rating ~ contact + temp, data=wine, link="log-gamma") 273s Warning message: 273s (-1) Model failed to converge with max|grad| = 9.9099e-05 (tol = 1e-06) 273s > summary(fm1) 273s formula: rating ~ contact + temp 273s data: wine 273s 273s link threshold nobs logLik AIC niter max.grad cond.H 273s log-gamma flexible 72 -85.72 185.44 27(179) 9.91e-05 5.9e+01 273s 273s Coefficients: 273s Estimate Std. Error z value Pr(>|z|) 273s contactyes 0.8614 0.2675 3.220 0.00128 ** 273s tempwarm 1.5072 0.2947 5.114 3.16e-07 *** 273s --- 273s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 273s 273s Link coefficients: 273s Estimate Std. Error z value Pr(>|z|) 273s lambda 0.1615 0.5752 0.281 0.779 273s 273s Threshold coefficients: 273s Estimate Std. Error z value 273s 1|2 -0.8798 0.5003 -1.759 273s 2|3 0.6678 0.3450 1.936 273s 3|4 1.9807 0.3826 5.177 273s 4|5 2.8593 0.4656 6.141 273s > ## get the model frame containing y and X: 273s > mf1 <- update(fm1, method="design") 273s > names(mf1) 273s [1] "y" "y.levels" "X" "offset" "terms" "contrasts" 273s [7] "xlevels" "weights" "doFit" "control" "link" "threshold" 273s [13] "start" "formulas" 273s > res <- clm.fit(mf1$y, mf1$X, link="log-gamma") ## invoking the factor method 273s Changing to 'nlminb' optimizer for flexible link function 273s > coef(res) 273s 1|2 2|3 3|4 4|5 contactyes tempwarm lambda 273s Warning message: 273s (-1) Model failed to converge with max|grad| = 9.9099e-05 (tol = 1e-06) 273s -0.8797774 0.6678307 1.9806826 2.8593125 0.8614400 1.5071959 0.1614741 273s > stopifnot(all.equal(coef(res), coef(fm1))) 273s > 273s > ## Example with Aranda-Ordaz: 273s > fm1 <- clm(rating ~ contact + temp, data=wine, link="Aranda-Ordaz") 273s Changing to 'nlminb' optimizer for flexible link function 273s Warning message: 273s (-1) Model failed to converge with max|grad| = 1.63026e-05 (tol = 1e-06) 273s > mf1 <- update(fm1, method="design") 273s > res <- clm.fit(mf1$y, mf1$X, link="Aranda") ## invoking the factor method 273s Changing to 'nlminb' optimizer for flexible link function 273s Warning message: 273s (-1) Model failed to converge with max|grad| = 1.63026e-05 (tol = 1e-06) 273s > stopifnot(all.equal(coef(res), coef(fm1))) 273s > 273s > 273s BEGIN TEST test.clm.model.matrix.R 274s 274s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 274s Copyright (C) 2024 The R Foundation for Statistical Computing 274s Platform: aarch64-unknown-linux-gnu (64-bit) 274s 274s R is free software and comes with ABSOLUTELY NO WARRANTY. 274s You are welcome to redistribute it under certain conditions. 274s Type 'license()' or 'licence()' for distribution details. 274s 274s R is a collaborative project with many contributors. 274s Type 'contributors()' for more information and 274s 'citation()' on how to cite R or R packages in publications. 274s 274s Type 'demo()' for some demos, 'help()' for on-line help, or 274s 'help.start()' for an HTML browser interface to help. 274s Type 'q()' to quit R. 274s 274s > library(ordinal) 275s > ## source("test.clm.model.matrix.R") 275s > 275s > ## library(devtools) 275s > ## r2path <- "/Users/rhbc/Documents/Rpackages/ordinal/pkg/ordinal" 275s > ## clean_dll(pkg = r2path) 275s > ## load_all(r2path) 275s > 275s > ## Check that get_clmDesign works in standard setting: 275s > fm1 <- clm(rating ~ temp, scale=~contact, nominal=~contact, data=wine) 275s > contr <- c(fm1$contrasts, fm1$S.contrasts, fm1$nom.contrasts) 275s > XX <- ordinal:::get_clmDesign(fm1$model, terms(fm1, "all"), contrasts=contr) 275s > XX2 <- update(fm1, method="design") 275s > (keep <- intersect(names(XX), names(XX2))) 275s [1] "y" "y.levels" "X" "offset" 275s [5] "terms" "contrasts" "xlevels" "weights" 275s [9] "S" "S.terms" "S.off" "S.contrasts" 275s [13] "S.xlevels" "NOM" "nom.terms" "nom.contrasts" 275s [17] "nom.xlevels" 275s > (test <- mapply(function(x, y) isTRUE(all.equal(x, y)), 275s + XX[keep], XX2[keep])) 275s y y.levels X offset terms 275s TRUE TRUE TRUE TRUE TRUE 275s contrasts xlevels weights S S.terms 275s TRUE TRUE TRUE TRUE TRUE 275s S.off S.contrasts S.xlevels NOM nom.terms 275s TRUE TRUE TRUE TRUE TRUE 275s nom.contrasts nom.xlevels 275s TRUE TRUE 275s > stopifnot(all(test)) 275s > 275s > ## Check that get_clmDesign works with singular fit and NAs: 275s > cy <- with(wine, which(temp == "cold" & contact == "yes")) 275s > wine2 <- subset(wine, subset=(!1:nrow(wine) %in% cy)) 275s > wine2[c(9, 15, 46), "rating"] <- NA 275s > fm1 <- clm(rating ~ temp, scale=~contact, nominal=~contact, 275s + data=wine2) 275s Warning message: 275s (1) Hessian is numerically singular: parameters are not uniquely determined 275s In addition: Absolute convergence criterion was met, but relative criterion was not met 275s > contr <- c(fm1$contrasts, fm1$S.contrasts, fm1$nom.contrasts) 275s > XX <- ordinal:::get_clmDesign(fm1$model, terms(fm1, "all"), contrasts=contr) 275s > XX2 <- update(fm1, method="design") 275s > (keep <- intersect(names(XX), names(XX2))) 275s [1] "y" "y.levels" "X" "offset" 275s [5] "terms" "contrasts" "xlevels" "na.action" 275s [9] "weights" "S" "S.terms" "S.off" 275s [13] "S.contrasts" "S.xlevels" "NOM" "nom.terms" 275s [17] "nom.contrasts" "nom.xlevels" 275s > (test <- mapply(function(x, y) isTRUE(all.equal(x, y)), 275s + XX[keep], XX2[keep])) 275s y y.levels X offset terms 275s TRUE TRUE TRUE TRUE TRUE 275s contrasts xlevels na.action weights S 275s TRUE TRUE TRUE TRUE TRUE 275s S.terms S.off S.contrasts S.xlevels NOM 275s TRUE TRUE TRUE TRUE TRUE 275s nom.terms nom.contrasts nom.xlevels 275s TRUE TRUE TRUE 275s > stopifnot(all(test)) 275s > 275s > ## In this situation update and get_clmRho give the same results: 275s > wine2 <- wine 275s > fm1 <- clm(rating ~ temp + contact, data=wine2) ## OK 275s > rho1 <- ordinal:::get_clmRho.clm(fm1) 275s > l1 <- as.list(rho1) 275s > l2 <- as.list(update(fm1, doFit=FALSE)) 275s > (test <- mapply(function(x, y) isTRUE(all.equal(x, y)), 275s + l1, l2[names(l1)])) 275s nlambda link gfun dfun pfun par clm.hess clm.grad 275s TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 275s clm.nll wts fitted has.scale sigma k Soff S 275s TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 275s n.psi o2 o1 B2 B1 275s TRUE TRUE TRUE TRUE TRUE 275s > stopifnot(all(test)) 275s > ## If we modify the data (or other subset, weights, formulae, etc.) 275s > ## used in the model call, the results from update no longer correspond 275s > ## to the elements of the fitted model object. get_clmRho gets it 275s > ## right on the other hand: 275s > wine2[10:13, "rating"] <- NA 275s > l3 <- as.list(ordinal:::get_clmRho.clm(fm1)) 275s > l4 <- as.list(update(fm1, doFit=FALSE)) 275s > (test <- mapply(function(x, y) isTRUE(all.equal(x, y)), 275s + l1, l3)) 275s nlambda link gfun dfun pfun par clm.hess clm.grad 275s TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 275s clm.nll wts fitted has.scale sigma k Soff S 275s TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 275s n.psi o2 o1 B2 B1 275s TRUE TRUE TRUE TRUE TRUE 275s > stopifnot(all(test)) ## same 275s > (test <- mapply(function(x, y) isTRUE(all.equal(x, y)), 275s + l3, l4[names(l3)])) 275s nlambda link gfun dfun pfun par clm.hess clm.grad Warning messages: 275s 1: In model.matrix.default(terms, data = fullmf, contrasts.arg = getContrasts(terms, : 275s non-list contrasts argument ignored 275s 2: In model.matrix.default(terms, data = fullmf, contrasts.arg = getContrasts(terms, : 275s non-list contrasts argument ignored 275s 275s TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 275s clm.nll wts fitted has.scale sigma k Soff S 275s TRUE FALSE FALSE TRUE FALSE TRUE FALSE TRUE 275s n.psi o2 o1 B2 B1 275s TRUE FALSE FALSE FALSE FALSE 275s > stopifnot(sum(!test) == 8) ## not all the same anymore! 275s > ## In conclusion l1, l2, and l3 are identical. l4 is different. 275s > 275s > ################################# 275s > ## Test that checkContrasts give appropriate warnings: 275s > contr <- c(temp="contr.sum", contact="contr.sum") 275s > fm1 <- clm(rating ~ temp + contact, scale=~contact, data=wine) ## OK 275s > fm1 <- clm(rating ~ temp + contact, scale=~contact, data=wine, 275s + contrasts=contr) ## OK 275s > fm1 <- clm(rating ~ temp, scale=~contact, data=wine, 275s + contrasts=contr) ## OK 275s Warning messages: 275s 1: In model.matrix.default(terms, data = fullmf, contrasts.arg = getContrasts(terms, : 275s non-list contrasts argument ignored 275s 2: In model.matrix.default(terms, data = fullmf, contrasts.arg = getContrasts(terms, : 275s non-list contrasts argument ignored 275s Warning messages: 275s 1: variable 'contact' is absent: its contrasts will be ignored 275s 2: In model.matrix.default(terms, data = fullmf, contrasts.arg = getContrasts(terms, : 275s non-list contrasts argument ignored 275s > ## These should give warnings: 275s > fm1 <- clm(rating ~ temp, contrasts=c(contact="contr.sum"), data=wine) 275s > fm1 <- clm(rating ~ temp, contrasts=contr, data=wine) 275s Warning messages: 275s 1: variable 'contact' is absent: its contrasts will be ignored 275s 2: In model.matrix.default(terms, data = fullmf, contrasts.arg = getContrasts(terms, : 275s non-list contrasts argument ignored 275s > fm1 <- clm(rating ~ 1, scale=~contact, contrasts=c(temp="contr.sum"), 275s + data=wine) 275s Warning messages: 275s 1: variable 'temp' is absent: its contrasts will be ignored 275s 2: In model.matrix.default(terms, data = fullmf, contrasts.arg = getContrasts(terms, : 275s non-list contrasts argument ignored 275s 3: In model.matrix.default(terms, data = fullmf, contrasts.arg = getContrasts(terms, : 275s non-list contrasts argument ignored 275s Warning message: 275s variable 'temp' is absent: its contrasts will be ignored 275s > fm1 <- clm(rating ~ 1, scale=~contact, contrasts=list(temp="contr.sum"), 275s + data=wine) 275s > 275s > fm0 <- clm(rating ~ temp + contact, scale=~contact, data=wine) 275s Warning message: 275s variable 'temp' is absent: its contrasts will be ignored 275s > ordinal:::checkContrasts(fm0$S.terms, fm0$contrasts) 275s > ordinal:::checkContrasts(fm0$S.terms, fm0$S.contrasts) 275s > ordinal:::checkContrasts(fm0$terms, fm0$contrasts) 275s > ordinal:::checkContrasts(fm0$terms, fm0$S.contrasts) 275s > 275s > ################################# 275s > ## Check that clm and model.matrix respects contrast settings: 275s > options("contrasts" = c("contr.treatment", "contr.poly")) 275s > fm0 <- clm(rating ~ temp + contact, data=wine) 275s > options("contrasts" = c("contr.sum", "contr.poly")) 275s > fm1 <- clm(rating ~ temp + contact, data=wine) 275s > stopifnot(all(model.matrix(fm0)$X[, 2] %in% c(0, 1))) 275s > stopifnot(all(model.matrix(fm1)$X[, 2] %in% c(1, -1))) 275s > 275s > ################################# 275s > ## Check that model.matrix results do not depend on global contrast 275s > ## setting: 275s > options("contrasts" = c("contr.sum", "contr.poly")) 275s > fm0 <- clm(rating ~ temp + contact, scale=~contact, data=wine) 275s > MM <- model.matrix(fm0) 275s > options("contrasts" = c("contr.treatment", "contr.poly")) 275s > MM2 <- model.matrix(fm0) 275s > for(x in MM) print(head(x)) 275s (Intercept) temp1 contact1 275s 1 1 1 1 275s 2 1 1 1 275s 3 1 1 -1 275s 4 1 1 -1 275s 5 1 -1 1 275s 6 1 -1 1 275s (Intercept) contact1 275s 1 1 1 275s 2 1 1 275s 3 1 -1 275s 4 1 -1 275s 5 1 1 275s 6 1 1 275s > for(x in MM2) print(head(x)) 275s (Intercept) temp1 contact1 275s 1 1 1 1 275s 2 1 1 1 275s 3 1 1 -1 275s 4 1 1 -1 275s 5 1 -1 1 275s 6 1 -1 1 275s (Intercept) contact1 275s 1 1 1 275s 2 1 1 275s 3 1 -1 275s 4 1 -1 275s 5 1 1 275s 6 1 1 275s > stopifnot(all(mapply(all.equal, MM, MM2))) 275s > 275s > ################################# 275s > ## This gave a warning before getContrasts was implemented: 275s > fm0 <- clm(rating ~ temp + contact, scale=~contact, data=wine) 275s > MM <- model.matrix(fm0) 275s > ## > fm0 <- clm(rating ~ temp + contact, scale=~contact, data=wine) 275s > ## > MM <- model.matrix(fm0) 275s > ## Warning message: 275s > ## In model.matrix.default(res$S.terms, data = fullmf, contrasts.arg = getContrasts(res$S.terms, : 275s > ## variable 'temp' is absent, its contrast will be ignored 275s > for(x in MM) print(head(x)) 275s (Intercept) tempwarm contactyes 275s 1 1 0 0 275s 2 1 0 0 275s 3 1 0 1 275s 4 1 0 1 275s 5 1 1 0 275s 6 1 1 0 275s (Intercept) contactyes 275s 1 1 0 275s 2 1 0 275s 3 1 1 275s 4 1 1 275s 5 1 0 275s 6 1 0 275s > 275s > 275s BEGIN TEST test.clm.predict.R 275s 275s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 275s Copyright (C) 2024 The R Foundation for Statistical Computing 275s Platform: aarch64-unknown-linux-gnu (64-bit) 275s 275s R is free software and comes with ABSOLUTELY NO WARRANTY. 275s You are welcome to redistribute it under certain conditions. 275s Type 'license()' or 'licence()' for distribution details. 275s 275s R is a collaborative project with many contributors. 275s Type 'contributors()' for more information and 275s 'citation()' on how to cite R or R packages in publications. 275s 275s Type 'demo()' for some demos, 'help()' for on-line help, or 275s 'help.start()' for an HTML browser interface to help. 275s Type 'q()' to quit R. 275s 275s > library(ordinal) 276s > ## source("test.clm.predict.R") 276s > 276s > ## library(devtools) 276s > ## r2path <- "/Users/rhbc/Documents/Rpackages/ordinal/pkg/ordinal" 276s > ## clean_dll(pkg = r2path) 276s > ## load_all(r2path) 276s > 276s > cy <- with(wine, which(temp == "cold" & contact == "yes")) 276s > options("contrasts" = c("contr.treatment", "contr.poly")) 276s > getOption("contrasts") 276s [1] "contr.treatment" "contr.poly" 276s > 276s > ## Example model 276s > 276s > wine1.clm <- clm(rating ~ temp*contact, subset = -cy, data = wine) 276s > summary(wine1.clm) 276s formula: rating ~ temp * contact 276s data: wine 276s subset: -cy 276s 276s link threshold nobs logLik AIC niter max.grad cond.H 276s logit flexible 54 -65.47 142.93 6(0) 2.80e-12 2.9e+01 276s 276s Coefficients: (1 not defined because of singularities) 276s Estimate Std. Error z value Pr(>|z|) 276s tempwarm 2.2892 0.7192 3.183 0.00146 ** 276s contactyes 1.6505 0.6698 2.464 0.01374 * 276s tempwarm:contactyes NA NA NA NA 276s --- 276s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 276s 276s Threshold coefficients: 276s Estimate Std. Error z value 276s 1|2 -1.3971 0.5728 -2.439 276s 2|3 1.1349 0.5262 2.157 276s 3|4 3.3351 0.6987 4.774 276s 4|5 4.7924 0.7996 5.994 276s > names(wine1.clm) 276s [1] "aliased" "alpha" "beta" "call" 276s [5] "coefficients" "cond.H" "contrasts" "control" 276s [9] "convergence" "df.residual" "edf" "fitted.values" 276s [13] "formula" "formulas" "gradient" "Hessian" 276s [17] "info" "link" "logLik" "maxGradient" 276s [21] "message" "model" "n" "niter" 276s [25] "nobs" "start" "terms" "Theta" 276s [29] "threshold" "tJac" "vcov" "xlevels" 276s [33] "y" "y.levels" 276s > 276s > wine.clm <- clm(rating~temp*contact, data=wine) 276s > summary(wine.clm) 276s formula: rating ~ temp * contact 276s data: wine 276s 276s link threshold nobs logLik AIC niter max.grad cond.H 276s logit flexible 72 -86.42 186.83 6(0) 5.22e-12 5.1e+01 276s 276s Coefficients: 276s Estimate Std. Error z value Pr(>|z|) 276s tempwarm 2.3212 0.7009 3.311 0.000928 *** 276s contactyes 1.3475 0.6604 2.041 0.041300 * 276s tempwarm:contactyes 0.3595 0.9238 0.389 0.697129 276s --- 276s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 276s 276s Threshold coefficients: 276s Estimate Std. Error z value 276s 1|2 -1.4113 0.5454 -2.588 276s 2|3 1.1436 0.5097 2.244 276s 3|4 3.3771 0.6382 5.292 276s 4|5 4.9420 0.7509 6.581 276s > names(wine.clm) 276s [1] "aliased" "alpha" "beta" "call" 276s [5] "coefficients" "cond.H" "contrasts" "control" 276s [9] "convergence" "df.residual" "edf" "fitted.values" 276s [13] "formula" "formulas" "gradient" "Hessian" 276s [17] "info" "link" "logLik" "maxGradient" 276s [21] "message" "model" "n" "niter" 276s [25] "nobs" "start" "terms" "Theta" 276s [29] "threshold" "tJac" "vcov" "xlevels" 276s [33] "y" "y.levels" 276s > ## Make sure the same elements are present with a rank deficient model 276s > ## fit: 276s > stopifnot(all(names(wine1.clm) == names(wine.clm))) 276s > 276s > ## With treatment contrasts: 276s > options("contrasts" = c("contr.treatment", "contr.poly")) 276s > wine.clm <- clm(rating~temp*contact, data=wine) 276s > coef(summary(wine.clm)) 276s Estimate Std. Error z value Pr(>|z|) 276s 1|2 -1.4112620 0.5453532 -2.5877943 9.659266e-03 276s 2|3 1.1435537 0.5096555 2.2437776 2.484671e-02 276s 3|4 3.3770825 0.6381617 5.2918913 1.210578e-07 276s 4|5 4.9419823 0.7509113 6.5813133 4.663108e-11 276s tempwarm 2.3211843 0.7009479 3.3114931 9.279953e-04 276s contactyes 1.3474604 0.6603557 2.0405072 4.129984e-02 276s tempwarm:contactyes 0.3595489 0.9238188 0.3891985 6.971293e-01 276s > head(model.matrix(wine.clm)$X) 276s (Intercept) tempwarm contactyes tempwarm:contactyes 276s 1 1 0 0 0 276s 2 1 0 0 0 276s 3 1 0 1 0 276s 4 1 0 1 0 276s 5 1 1 0 0 276s 6 1 1 0 0 276s > wine.clm$contrasts 276s $temp 276s [1] "contr.treatment" 276s 276s $contact 276s [1] "contr.treatment" 276s 276s > head(pred1 <- predict(wine.clm)$fit) 276s [1] 0.56229641 0.20864908 0.43467309 0.08938852 0.19028226 0.19028226 276s > 276s > ## With sum contrasts: 276s > options("contrasts" = c("contr.sum", "contr.poly")) 276s > wine.clm <- clm(rating~temp*contact, data=wine) 276s > coef(summary(wine.clm)) 276s Estimate Std. Error z value Pr(>|z|) 276s 1|2 -3.33547153 0.5253364 -6.3492103 2.164231e-10 276s 2|3 -0.78065590 0.2945538 -2.6503003 8.042025e-03 276s 3|4 1.45287292 0.3367529 4.3143590 1.600667e-05 276s 4|5 3.01777269 0.4813097 6.2699186 3.612370e-10 276s temp1 -1.25047935 0.2641023 -4.7348292 2.192396e-06 276s contact1 -0.76361743 0.2380971 -3.2071683 1.340485e-03 276s temp1:contact1 0.08988722 0.2309547 0.3891985 6.971293e-01 276s > head(model.matrix(wine.clm)$X) 276s (Intercept) temp1 contact1 temp1:contact1 276s 1 1 1 1 1 276s 2 1 1 1 1 276s 3 1 1 -1 -1 276s 4 1 1 -1 -1 276s 5 1 -1 1 -1 276s 6 1 -1 1 -1 276s > wine.clm$contrasts 276s $temp 276s [1] "contr.sum" 276s 276s $contact 276s [1] "contr.sum" 276s 276s > head(pred2 <- predict(wine.clm)$fit) 276s [1] 0.56229641 0.20864908 0.43467309 0.08938852 0.19028226 0.19028226 276s > 276s > ## Mixture of sum and treatment contrasts: 276s > options("contrasts" = c("contr.treatment", "contr.poly")) 276s > wine.clm <- clm(rating~temp*contact, data=wine, 276s + contrasts=list(temp="contr.sum")) 276s > coef(summary(wine.clm)) 276s Estimate Std. Error z value Pr(>|z|) 276s 1|2 -2.57185410 0.5227165 -4.92016984 8.646915e-07 276s 2|3 -0.01703847 0.3611634 -0.04717662 9.623725e-01 276s 3|4 2.21649036 0.4529312 4.89365773 9.897892e-07 276s 4|5 3.78139013 0.5957919 6.34683010 2.197966e-10 276s temp1 -1.16059213 0.3504740 -3.31149309 9.279953e-04 276s contactyes 1.52723487 0.4761942 3.20716830 1.340485e-03 276s temp1:contactyes -0.17977444 0.4619094 -0.38919847 6.971293e-01 276s > head(model.matrix(wine.clm)$X) 276s (Intercept) temp1 contactyes temp1:contactyes 276s 1 1 1 0 0 276s 2 1 1 0 0 276s 3 1 1 1 1 276s 4 1 1 1 1 276s 5 1 -1 0 0 276s 6 1 -1 0 0 276s > wine.clm$contrasts 276s $temp 276s [1] "contr.sum" 276s 276s $contact 276s [1] "contr.treatment" 276s 276s > head(pred3 <- predict(wine.clm)$fit) 276s [1] 0.56229641 0.20864908 0.43467309 0.08938852 0.19028226 0.19028226 276s > 276s > stopifnot(isTRUE(all.equal(pred1, pred2))) 276s > stopifnot(isTRUE(all.equal(pred1, pred3))) 276s > 276s > ################################# 276s > ### Now for a rank deficient fit: 276s > ################################# 276s > 276s > cy <- with(wine, which(temp == "cold" & contact == "yes")) 276s > options("contrasts" = c("contr.treatment", "contr.poly")) 276s > wine1.clm <- clm(rating ~ temp*contact, subset = -cy, data = wine) 276s > coef(summary(wine1.clm)) 276s Estimate Std. Error z value Pr(>|z|) 276s 1|2 -1.397134 0.5727918 -2.439164 1.472127e-02 276s 2|3 1.134907 0.5261653 2.156940 3.101038e-02 276s 3|4 3.335090 0.6986647 4.773521 1.810331e-06 276s 4|5 4.792428 0.7995580 5.993846 2.049352e-09 276s tempwarm 2.289221 0.7191705 3.183140 1.456870e-03 276s contactyes 1.650538 0.6698484 2.464047 1.373782e-02 276s tempwarm:contactyes NA NA NA NA 276s > attributes(model.matrix(wine1.clm)$X)$contrasts 276s $temp 276s [1] "contr.treatment" 276s 276s $contact 276s [1] "contr.treatment" 276s 276s > wine1.clm$contrasts 276s $temp 276s [1] "contr.treatment" 276s 276s $contact 276s [1] "contr.treatment" 276s 276s > head(pred4 <- predict(wine1.clm)$fit) 276s [1] 0.5584719 0.2088699 0.1843854 0.1843854 0.2988733 0.2988733 276s > 276s > options("contrasts" = c("contr.sum", "contr.poly")) 276s > wine1.clm <- clm(rating ~ temp*contact, subset = -cy, data = wine) 276s > attributes(model.matrix(wine1.clm)$X)$contrasts 276s $temp 276s [1] "contr.sum" 276s 276s $contact 276s [1] "contr.sum" 276s 276s > options("contrasts" = c("contr.treatment", "contr.poly")) 276s > attributes(model.matrix(wine1.clm)$X)$contrasts 276s $temp 276s [1] "contr.sum" 276s 276s $contact 276s [1] "contr.sum" 276s 276s > ## Notice that the contrasts change in the attributes of the fit!!! 276s > coef(summary(wine1.clm)) 276s Estimate Std. Error z value Pr(>|z|) 276s 1|2 -3.3670128 0.6149672 -5.475110 4.372411e-08 276s 2|3 -0.8349725 0.4231096 -1.973419 4.844787e-02 276s 3|4 1.3652108 0.4310181 3.167409 1.538037e-03 276s 4|5 2.8225483 0.5190089 5.438343 5.377826e-08 276s temp1 -1.1446104 0.3595853 -3.183140 1.456870e-03 276s contact1 -0.8252689 0.3349242 -2.464047 1.373782e-02 276s temp1:contact1 NA NA NA NA 276s > wine1.clm$contrasts 276s $temp 276s [1] "contr.sum" 276s 276s $contact 276s [1] "contr.sum" 276s 276s > head(pred5 <- predict(wine1.clm)$fit) 276s [1] 0.5584719 0.2088699 0.1843854 0.1843854 0.2988733 0.2988733 276s > 276s > head(cbind(pred4, pred5)) 276s pred4 pred5 276s [1,] 0.5584719 0.5584719 276s [2,] 0.2088699 0.2088699 276s [3,] 0.1843854 0.1843854 276s [4,] 0.1843854 0.1843854 276s [5,] 0.2988733 0.2988733 276s [6,] 0.2988733 0.2988733 276s > stopifnot(isTRUE(all.equal(pred4, pred5))) 276s > 276s > options("contrasts" = c("contr.treatment", "contr.poly")) 276s > wine1.clm <- clm(rating ~ temp*contact, subset = -cy, data = wine, 276s + contrasts=list(temp="contr.sum")) 276s > coef(summary(wine1.clm)) 276s Estimate Std. Error z value Pr(>|z|) 276s 1|2 -2.54174387 0.5792622 -4.38789851 1.144512e-05 276s 2|3 -0.00970353 0.3737929 -0.02595964 9.792895e-01 276s 3|4 2.19047975 0.4965589 4.41131906 1.027428e-05 276s 4|5 3.64781729 0.6257007 5.82997171 5.543677e-09 276s temp1 -1.14461036 0.3595853 -3.18314035 1.456870e-03 276s contactyes 1.65053789 0.6698484 2.46404685 1.373782e-02 276s temp1:contactyes NA NA NA NA 276s > head(model.matrix(wine1.clm)$X) 276s (Intercept) temp1 contactyes temp1:contactyes 276s 1 1 1 0 0 276s 2 1 1 0 0 276s 5 1 -1 0 0 276s 6 1 -1 0 0 276s 7 1 -1 1 -1 276s 8 1 -1 1 -1 276s > attributes(model.matrix(wine1.clm)$X)$contrasts 276s $temp 276s [1] "contr.sum" 276s 276s $contact 276s [1] "contr.treatment" 276s 276s > wine1.clm$contrasts 276s $temp 276s [1] "contr.sum" 276s 276s $contact 276s [1] "contr.treatment" 276s 276s > head(pred6 <- predict(wine1.clm)$fit) 276s [1] 0.5584719 0.2088699 0.1843854 0.1843854 0.2988733 0.2988733 276s > 276s > head(cbind(pred4, pred5, pred6)) 276s pred4 pred5 pred6 276s [1,] 0.5584719 0.5584719 0.5584719 276s [2,] 0.2088699 0.2088699 0.2088699 276s [3,] 0.1843854 0.1843854 0.1843854 276s [4,] 0.1843854 0.1843854 0.1843854 276s [5,] 0.2988733 0.2988733 0.2988733 276s [6,] 0.2988733 0.2988733 0.2988733 276s > stopifnot(isTRUE(all.equal(pred4, pred6))) 276s > ################################################################## 276s > 276s > ## Compare equality of fitted values for models with different contrasts: 276s > options("contrasts" = c("contr.treatment", "contr.poly")) 276s > fm1 <- clm(rating ~ temp + contact, data=wine) 276s > fitted(fm1) 276s [1] 0.57064970 0.19229094 0.44305990 0.09582084 0.20049402 0.20049402 276s [7] 0.27378469 0.27378469 0.20679013 0.57064970 0.05354601 0.44305990 276s [13] 0.20141572 0.50157554 0.27378469 0.36359581 0.57064970 0.19229094 276s [19] 0.44305990 0.37764614 0.07562701 0.07562701 0.36359581 0.36359581 276s [25] 0.19229094 0.57064970 0.44305990 0.37764614 0.50157554 0.20141572 276s [31] 0.27378469 0.30420994 0.57064970 0.19229094 0.09582084 0.44305990 276s [37] 0.50157554 0.50157554 0.30420994 0.30420994 0.19229094 0.57064970 276s [43] 0.44305990 0.37764614 0.20141572 0.20049402 0.27378469 0.36359581 276s [49] 0.20679013 0.20679013 0.37764614 0.37764614 0.20141572 0.50157554 276s [55] 0.05380128 0.30420994 0.57064970 0.57064970 0.37764614 0.44305990 276s [61] 0.50157554 0.50157554 0.30420994 0.36359581 0.20679013 0.57064970 276s [67] 0.44305990 0.37764614 0.50157554 0.20141572 0.36359581 0.36359581 276s > options("contrasts" = c("contr.sum", "contr.poly")) 276s > fm2 <- clm(rating ~ temp + contact, data=wine) 276s > fitted(fm2) 276s [1] 0.57064970 0.19229094 0.44305990 0.09582084 0.20049402 0.20049402 276s [7] 0.27378469 0.27378469 0.20679013 0.57064970 0.05354601 0.44305990 276s [13] 0.20141572 0.50157554 0.27378469 0.36359581 0.57064970 0.19229094 276s [19] 0.44305990 0.37764614 0.07562701 0.07562701 0.36359581 0.36359581 276s [25] 0.19229094 0.57064970 0.44305990 0.37764614 0.50157554 0.20141572 276s [31] 0.27378469 0.30420994 0.57064970 0.19229094 0.09582084 0.44305990 276s [37] 0.50157554 0.50157554 0.30420994 0.30420994 0.19229094 0.57064970 276s [43] 0.44305990 0.37764614 0.20141572 0.20049402 0.27378469 0.36359581 276s [49] 0.20679013 0.20679013 0.37764614 0.37764614 0.20141572 0.50157554 276s [55] 0.05380128 0.30420994 0.57064970 0.57064970 0.37764614 0.44305990 276s [61] 0.50157554 0.50157554 0.30420994 0.36359581 0.20679013 0.57064970 276s [67] 0.44305990 0.37764614 0.50157554 0.20141572 0.36359581 0.36359581 276s > options("contrasts" = c("contr.treatment", "contr.poly")) 276s > fm3 <- clm(rating ~ temp + contact, data=wine, 276s + contrasts=list(contact="contr.sum")) 276s > fitted(fm3) 276s [1] 0.57064970 0.19229094 0.44305990 0.09582084 0.20049402 0.20049402 276s [7] 0.27378469 0.27378469 0.20679013 0.57064970 0.05354601 0.44305990 276s [13] 0.20141572 0.50157554 0.27378469 0.36359581 0.57064970 0.19229094 276s [19] 0.44305990 0.37764614 0.07562701 0.07562701 0.36359581 0.36359581 276s [25] 0.19229094 0.57064970 0.44305990 0.37764614 0.50157554 0.20141572 276s [31] 0.27378469 0.30420994 0.57064970 0.19229094 0.09582084 0.44305990 276s [37] 0.50157554 0.50157554 0.30420994 0.30420994 0.19229094 0.57064970 276s [43] 0.44305990 0.37764614 0.20141572 0.20049402 0.27378469 0.36359581 276s [49] 0.20679013 0.20679013 0.37764614 0.37764614 0.20141572 0.50157554 276s [55] 0.05380128 0.30420994 0.57064970 0.57064970 0.37764614 0.44305990 276s [61] 0.50157554 0.50157554 0.30420994 0.36359581 0.20679013 0.57064970 276s [67] 0.44305990 0.37764614 0.50157554 0.20141572 0.36359581 0.36359581 276s > stopifnot(isTRUE(all.equal(fitted(fm1), fitted(fm2)))) 276s > stopifnot(isTRUE(all.equal(fitted(fm1), fitted(fm3)))) 276s > 276s > ################################################################## 276s > ## Compare equality of fitted values for models with different 276s > ## contrasts in face of aliased coefficients: 276s > options("contrasts" = c("contr.treatment", "contr.poly")) 276s > cy <- with(wine, which(temp == "cold" & contact == "yes")) 276s > Wine <- subset(wine, subset=!(temp == "cold" & contact == "yes")) 276s > fm1 <- clm(rating ~ temp + contact, data=Wine) 276s > options("contrasts" = c("contr.sum", "contr.poly")) 276s > fm2 <- clm(rating ~ temp + contact, data=Wine) 276s > options("contrasts" = c("contr.treatment", "contr.poly")) 276s > fm3 <- clm(rating ~ temp + contact, data=Wine, 276s + contrasts=list(contact="contr.sum")) 276s > 276s > stopifnot(isTRUE(all.equal(fitted(fm1), fitted(fm2)))) 276s > stopifnot(isTRUE(all.equal(fitted(fm1), fitted(fm3)))) 276s > stopifnot(isTRUE(all.equal(predict(fm1)$fit, predict(fm2)$fit))) 276s > stopifnot(isTRUE(all.equal(predict(fm1)$fit, predict(fm3)$fit))) 276s > 276s > ################################# 276s > ## Does this also happen if the wine data has changed? 276s > options("contrasts" = c("contr.treatment", "contr.poly")) 276s > Wine <- subset(wine, subset=!(temp == "cold" & contact == "yes")) 276s > fm1 <- clm(rating ~ temp + contact, data=Wine) 276s > fit1 <- fitted(fm1) 276s > pred1 <- predict(fm1)$fit 276s > Wine <- wine 276s > pred2 <- predict(fm1)$fit 276s > stopifnot(isTRUE(all.equal(fit1, pred1))) 276s > stopifnot(isTRUE(all.equal(fit1, pred2))) 276s > 276s > ## What if weights, say, is an expression? 276s > ## Notice that updating the model object changes it: 276s > set.seed(123) 276s > fm1 <- clm(rating ~ temp + contact, data=wine, 276s + weights=runif(nrow(wine), .5, 1.5)) 276s > fm2 <- update(fm1) 276s > stopifnot(isTRUE(all.equal(fitted(fm1), predict(fm1)$fit))) 276s > stopifnot(!isTRUE(all.equal(fitted(fm1), fitted(fm2)))) 276s > 276s > ################################# 276s > ## Test equality of fits and predictions of models with: 276s > ## 'x + I(x^2)' and 'poly(x, 2)': 276s > ## December 25th 2014, RHBC. 276s > data(wine) 276s > set.seed(1) 276s > x <- rnorm(nrow(wine), sd=2) + as.numeric(wine$rating) 276s > range(x) 276s [1] -1.429400 7.803236 276s > 276s > ## Comparison of 'x + I(x^2)' and 'poly(x, 2)': 276s > fm3 <- clm(rating ~ temp + x + I(x^2), data=wine) 276s > fm4 <- clm(rating ~ temp + poly(x, 2), data=wine) 276s > ## Same model fits, but different parameterizations: 276s > stopifnot( 276s + !isTRUE(all.equal(coef(fm3), coef(fm4), check.names=FALSE)) 276s + ) 276s > stopifnot(isTRUE(all.equal(logLik(fm3), logLik(fm4)))) 276s > newData <- expand.grid(temp = levels(wine$temp), 276s + x=seq(-1, 7, 3)) 276s > predict(fm3, newdata=newData)$fit 276s 1 2 3 4 5 276s 1 0.206057293 0.56152859 0.2029812 0.0245885 0.004844463 276s 2 0.036289668 0.28766182 0.5031703 0.1404155 0.032462707 276s 3 0.147105364 0.53988789 0.2693657 0.0363691 0.007271946 276s 4 0.024413857 0.21711772 0.5192073 0.1912002 0.048060899 276s 5 0.035397238 0.28292433 0.5050762 0.1433185 0.033283705 276s 6 0.005296054 0.05815716 0.3400568 0.4047024 0.191787585 276s > predict(fm4, newdata=newData)$fit 276s 1 2 3 4 5 276s 1 0.206057293 0.56152859 0.2029812 0.0245885 0.004844463 276s 2 0.036289668 0.28766182 0.5031703 0.1404155 0.032462707 276s 3 0.147105364 0.53988789 0.2693657 0.0363691 0.007271946 276s 4 0.024413857 0.21711772 0.5192073 0.1912002 0.048060899 276s 5 0.035397238 0.28292433 0.5050762 0.1433185 0.033283705 276s 6 0.005296054 0.05815716 0.3400568 0.4047024 0.191787585 276s > stopifnot(isTRUE(all.equal(fitted(fm3), fitted(fm4)))) 276s > stopifnot(isTRUE( 276s + all.equal(predict(fm3, newdata=newData)$fit, 276s + predict(fm4, newdata=newData)$fit))) 276s > ################################# 276s > 276s BEGIN TEST test.clm.profile.R 276s 276s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 276s Copyright (C) 2024 The R Foundation for Statistical Computing 276s Platform: aarch64-unknown-linux-gnu (64-bit) 276s 276s R is free software and comes with ABSOLUTELY NO WARRANTY. 276s You are welcome to redistribute it under certain conditions. 276s Type 'license()' or 'licence()' for distribution details. 276s 276s R is a collaborative project with many contributors. 276s Type 'contributors()' for more information and 276s 'citation()' on how to cite R or R packages in publications. 276s 276s Type 'demo()' for some demos, 'help()' for on-line help, or 276s 'help.start()' for an HTML browser interface to help. 276s Type 'q()' to quit R. 276s 276s > library(ordinal) 277s > 277s > ## Testing that the profile remains the same - that the model object 277s > ## is not 'distorted' by update(object/fitted, doFit=FALSE) 277s > set.seed(1234) 277s > wts <- runif(nrow(wine), 0, 2) 277s > fm3 <- clm(rating ~ temp + contact, data=wine, 277s + weights=wts) 277s > pr <- profile(fm3) 277s > 277s > set.seed(1234) 277s > fm3 <- clm(rating ~ temp + contact, data=wine, 277s + weights=runif(nrow(wine), 0, 2)) 277s > pr3 <- profile(fm3) 277s > ## > set.seed(1234) 277s > ## > fm3 <- clm(rating ~ temp + contact, data=wine, 277s > ## + weights=runif(nrow(wine), 0, 2)) 277s > ## > pr3 <- profile(fm3) 277s > ## Warning messages: 277s > ## 1: In profile.clm.beta(fitted, which.beta, alpha, max.steps, nsteps, : 277s > ## profile may be unreliable for tempwarm because only 1 277s > ## steps were taken down 277s > ## 2: In profile.clm.beta(fitted, which.beta, alpha, max.steps, nsteps, : 277s > ## profile may be unreliable for tempwarm because only 1 277s > ## steps were taken up 277s > ## 3: In profile.clm.beta(fitted, which.beta, alpha, max.steps, nsteps, : 277s > ## profile may be unreliable for contactyes because only 1 277s > ## steps were taken down 277s > ## 4: In profile.clm.beta(fitted, which.beta, alpha, max.steps, nsteps, : 277s > ## profile may be unreliable for contactyes because only 1 277s > ## steps were taken up 277s > ## 277s > stopifnot(isTRUE(all.equal(pr, pr3, check.attributes=FALSE))) 277s > stopifnot( 277s + isTRUE(all.equal(pr$tempwarm[, "lroot"], pr3$tempwarm[, "lroot"])), 277s + isTRUE(all.equal(pr$contactyes[, "lroot"], pr3$contactyes[, "lroot"]))) 277s > 277s BEGIN TEST test.clm.single.anova.R 277s 277s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 277s Copyright (C) 2024 The R Foundation for Statistical Computing 277s Platform: aarch64-unknown-linux-gnu (64-bit) 277s 277s R is free software and comes with ABSOLUTELY NO WARRANTY. 277s You are welcome to redistribute it under certain conditions. 277s Type 'license()' or 'licence()' for distribution details. 277s 277s R is a collaborative project with many contributors. 277s Type 'contributors()' for more information and 277s 'citation()' on how to cite R or R packages in publications. 277s 277s Type 'demo()' for some demos, 'help()' for on-line help, or 277s 'help.start()' for an HTML browser interface to help. 277s Type 'q()' to quit R. 277s 277s > # test.clm.single.anova.R 277s > 277s > library(ordinal) 278s > 278s > # WRE says "using if(requireNamespace("pkgname")) is preferred, if possible." 278s > # even in tests: 278s > assertError <- function(expr, ...) 278s + if(requireNamespace("tools")) tools::assertError(expr, ...) else invisible() 278s > assertWarning <- function(expr, ...) 278s + if(requireNamespace("tools")) tools::assertWarning(expr, ...) else invisible() 278s > 278s > fm <- clm(rating ~ temp * contact, scale=~contact, data=wine) 278s > 278s > anova(fm, type="I") 278s Type I Analysis of Deviance Table with Wald chi-square tests 278s 278s Df Chisq Pr(>Chisq) 278s temp 1 17.1046 3.538e-05 *** 278s contact 1 9.1574 0.002477 ** 278s temp:contact 1 0.1097 0.740512 278s --- 278s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 278s > anova(fm, type="II") 278s Type II Analysis of Deviance Table with Wald chi-square tests 278s 278s Df Chisq Pr(>Chisq) 278s temp 1 17.1046 3.538e-05 *** 278s contact 1 9.1574 0.002477 ** 278s temp:contact 1 0.1097 0.740512 278s --- 278s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 278s > anova(fm, type="III") 278s Type III Analysis of Deviance Table with Wald chi-square tests 278s 278s Df Chisq Pr(>Chisq) 278s temp 1 9.5681 0.00198 ** 278s contact 1 4.1830 0.04083 * 278s temp:contact 1 0.1097 0.74051 278s --- 278s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 278s > anova(fm, type=1) 278s Type I Analysis of Deviance Table with Wald chi-square tests 278s 278s Df Chisq Pr(>Chisq) 278s temp 1 17.1046 3.538e-05 *** 278s contact 1 9.1574 0.002477 ** 278s temp:contact 1 0.1097 0.740512 278s --- 278s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 278s > anova(fm, type=2) 278s Type II Analysis of Deviance Table with Wald chi-square tests 278s 278s Df Chisq Pr(>Chisq) 278s temp 1 17.1046 3.538e-05 *** 278s contact 1 9.1574 0.002477 ** 278s temp:contact 1 0.1097 0.740512 278s --- 278s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 278s > anova(fm, type=3) 278s Type III Analysis of Deviance Table with Wald chi-square tests 278s 278s Df Chisq Pr(>Chisq) 278s temp 1 9.5681 0.00198 ** 278s contact 1 4.1830 0.04083 * 278s temp:contact 1 0.1097 0.74051 278s --- 278s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 278s > anova(fm, type="1") 278s Type I Analysis of Deviance Table with Wald chi-square tests 278s 278s Df Chisq Pr(>Chisq) 278s temp 1 17.1046 3.538e-05 *** 278s contact 1 9.1574 0.002477 ** 278s temp:contact 1 0.1097 0.740512 278s --- 278s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 278s > anova(fm, type="2") 278s Type II Analysis of Deviance Table with Wald chi-square tests 278s 278s Df Chisq Pr(>Chisq) 278s temp 1 17.1046 3.538e-05 *** 278s contact 1 9.1574 0.002477 ** 278s temp:contact 1 0.1097 0.740512 278s --- 278s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 278s > anova(fm, type="3") 278s Type III Analysis of Deviance Table with Wald chi-square tests 278s 278s Df Chisq Pr(>Chisq) 278s temp 1 9.5681 0.00198 ** 278s contact 1 4.1830 0.04083 * 278s temp:contact 1 0.1097 0.74051 278s --- 278s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 278s > anova(fm, type="marginal") 278s Marginal Analysis of Deviance Table with Wald chi-square tests 278s 278s Df Chisq Pr(>Chisq) 278s temp 1 9.5681 0.00198 ** 278s contact 1 4.1830 0.04083 * 278s temp:contact 1 0.1097 0.74051 278s --- 278s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 278s > 278s > # Nominal effects: 278s > fm <- clm(rating ~ temp, nominal=~contact, data=wine) 278s > anova(fm) 278s Type I Analysis of Deviance Table with Wald chi-square tests 278s 278s Df Chisq Pr(>Chisq) 278s temp 1 22.166 2.501e-06 *** 278s --- 278s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 278s > 278s > # Flexible links: 278s > fm1 <- clm(rating ~ temp + contact, link="log-gamma", data=wine) 278s Changing to 'nlminb' optimizer for flexible link function 278s Warning message: 278s (-1) Model failed to converge with max|grad| = 9.92664e-05 (tol = 1e-06) 278s > anova(fm1, type=1) 278s Type I Analysis of Deviance Table with Wald chi-square tests 278s 278s Df Chisq Pr(>Chisq) 278s temp 1 26.150 3.16e-07 *** 278s contact 1 10.369 0.001282 ** 278s --- 278s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 278s > anova(fm1, type=2) 278s Type II Analysis of Deviance Table with Wald chi-square tests 278s 278s Df Chisq Pr(>Chisq) 278s temp 1 26.150 3.16e-07 *** 278s contact 1 10.369 0.001282 ** 278s --- 278s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 278s > anova(fm1, type=3) 278s Type III Analysis of Deviance Table with Wald chi-square tests 278s 278s Df Chisq Pr(>Chisq) 278s temp 1 26.150 3.16e-07 *** 278s contact 1 10.369 0.001282 ** 278s --- 278s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 278s > 278s > # Equivalence of tests irrespective of contrasts: 278s > fm1 <- clm(SURENESS ~ PRODID * SOUPFREQ, data=soup) 279s > # summary(fm1) 279s > (an1 <- anova(fm1, type=3)) 279s Type III Analysis of Deviance Table with Wald chi-square tests 279s 279s Df Chisq Pr(>Chisq) 279s PRODID 5 72.5901 2.959e-14 *** 279s SOUPFREQ 2 1.8132 0.4039 279s PRODID:SOUPFREQ 10 8.5837 0.5720 279s --- 279s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 279s > fm2 <- clm(SURENESS ~ PRODID * SOUPFREQ, data=soup, 279s + contrasts = list(SOUPFREQ = "contr.sum", PRODID = "contr.SAS")) 279s > # summary(fm2) 279s > anova(fm1, fm2) 279s Likelihood ratio tests of cumulative link models: 279s 279s formula: link: threshold: 279s fm1 SURENESS ~ PRODID * SOUPFREQ logit flexible 279s fm2 SURENESS ~ PRODID * SOUPFREQ logit flexible 279s 279s no.par AIC logLik LR.stat df Pr(>Chisq) 279s fm1 22 5388 -2672 279s fm2 22 5388 -2672 0 0 279s > (an2 <- anova(fm2, type=3)) 279s Type III Analysis of Deviance Table with Wald chi-square tests 279s 279s Df Chisq Pr(>Chisq) 279s PRODID 5 72.5901 2.959e-14 *** 279s SOUPFREQ 2 1.8132 0.4039 279s PRODID:SOUPFREQ 10 8.5837 0.5720 279s --- 279s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 279s > stopifnot( 279s + isTRUE(all.equal(an1, an2, check.attributes=FALSE)) 279s + ) 279s > 279s > 279s > # Aliased coefficients: 279s > fm1 <- clm(SURENESS ~ PRODID * DAY, data=soup) 279s > anova(fm1, type=1) 279s Type I Analysis of Deviance Table with Wald chi-square tests 279s 279s Df Chisq Pr(>Chisq) 279s PRODID 5 185.2017 < 2e-16 *** 279s DAY 1 4.1131 0.04255 * 279s PRODID:DAY 4 5.1186 0.27534 279s --- 279s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 279s > anova(fm1, type=2) 279s Type II Analysis of Deviance Table with Wald chi-square tests 279s 279s Df Chisq Pr(>Chisq) 279s PRODID 5 181.5967 < 2e-16 *** 279s DAY 1 4.1131 0.04255 * 279s PRODID:DAY 4 5.1186 0.27534 279s --- 279s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 279s > anova(fm1, type=3) 279s Missing cells for: PRODID3:DAY2. 279s Interpret type III hypotheses with care. 279s Type III Analysis of Deviance Table with Wald chi-square tests 279s 279s Df Chisq Pr(>Chisq) 279s PRODID 5 76.3722 4.81e-15 *** 279s DAY 1 10.1485 0.001444 ** 279s PRODID:DAY 4 5.1186 0.275344 279s --- 279s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 279s > 279s > # Aliased term (due to nominal effects): 279s > fm <- clm(rating ~ temp * contact, nominal=~contact, data=wine) 279s > anova(fm, type=1) 279s Type I Analysis of Deviance Table with Wald chi-square tests 279s 279s Df Chisq Pr(>Chisq) 279s temp 1 22.066 2.634e-06 *** 279s contact 279s temp:contact 1 0.250 0.6171 279s --- 279s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 279s > anova(fm, type=2) 279s Type II Analysis of Deviance Table with Wald chi-square tests 279s 279s Df Chisq Pr(>Chisq) 279s temp 1 22.066 2.634e-06 *** 279s contact 279s temp:contact 1 0.250 0.6171 279s --- 279s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 279s > anova(fm, type=3) 279s Type III Analysis of Deviance Table with Wald chi-square tests 279s 279s Df Chisq Pr(>Chisq) 279s temp 1 9.6335 0.001911 ** 279s contact 279s temp:contact 1 0.2500 0.617071 279s --- 279s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 279s > 279s > # model with all NA in vcov(object): 279s > fm <- clm(rating ~ temp * contact, nominal=~contact, scale=~contact, data=wine) 279s > assertError(anova(fm, type=1)) # error 279s Warning message: 279s (1) Hessian is numerically singular: parameters are not uniquely determined 279s In addition: Absolute and relative convergence criteria were met 279s Loading required namespace: tools 279s > assertError(anova(fm, type=2)) # error 279s > assertError(anova(fm, type=3)) # error 279s > all(is.na(vcov(fm))) 279s [1] TRUE 279s > 279s BEGIN TEST test.general.R 279s 279s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 279s Copyright (C) 2024 The R Foundation for Statistical Computing 279s Platform: aarch64-unknown-linux-gnu (64-bit) 279s 279s R is free software and comes with ABSOLUTELY NO WARRANTY. 279s You are welcome to redistribute it under certain conditions. 279s Type 'license()' or 'licence()' for distribution details. 279s 279s R is a collaborative project with many contributors. 279s Type 'contributors()' for more information and 279s 'citation()' on how to cite R or R packages in publications. 279s 279s Type 'demo()' for some demos, 'help()' for on-line help, or 279s 'help.start()' for an HTML browser interface to help. 279s Type 'q()' to quit R. 279s 279s > 279s > txt <- citation("ordinal") 279s > stopifnot(as.logical(grep("year", txt))) 279s > 279s BEGIN TEST test.makeThresholds.R 279s 279s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 279s Copyright (C) 2024 The R Foundation for Statistical Computing 279s Platform: aarch64-unknown-linux-gnu (64-bit) 279s 279s R is free software and comes with ABSOLUTELY NO WARRANTY. 279s You are welcome to redistribute it under certain conditions. 279s Type 'license()' or 'licence()' for distribution details. 279s 279s R is a collaborative project with many contributors. 279s Type 'contributors()' for more information and 279s 'citation()' on how to cite R or R packages in publications. 279s 279s Type 'demo()' for some demos, 'help()' for on-line help, or 279s 'help.start()' for an HTML browser interface to help. 279s Type 'q()' to quit R. 279s 279s > # test.makeThresholds.R 279s > 279s > library(ordinal) 281s > 281s > # Prvious bug which is now fixed: 281s > res <- ordinal:::makeThresholds(letters[1:3], "symmetric") 281s > stopifnot(length(res$alpha.names) == res$nalpha) 281s > # length(res$alpha.names) used to be 4 281s > 281s > # Real data example: 281s > wine <- within(wine, { 281s + rating_comb3b <- rating 281s + levels(rating_comb3b) <- c("1-2", "1-2", "3", "4-5", "4-5") 281s + }) 281s > wine$rating_comb3b[1] <- "4-5" # Need to remove the zero here to avoid inf MLE 281s > ftable(rating_comb3b ~ temp + contact, data=wine) 281s rating_comb3b 1-2 3 4-5 281s temp contact 281s cold no 12 5 1 281s yes 8 8 2 281s warm no 5 8 5 281s yes 1 5 12 281s > 281s > fm.comb3_c <- clm(rating_comb3b ~ contact, #scale=~contact, 281s + threshold = "symmetric", data=wine) # no error 281s > 281s BEGIN TEST test.sign.R 281s 281s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 281s Copyright (C) 2024 The R Foundation for Statistical Computing 281s Platform: aarch64-unknown-linux-gnu (64-bit) 281s 281s R is free software and comes with ABSOLUTELY NO WARRANTY. 281s You are welcome to redistribute it under certain conditions. 281s Type 'license()' or 'licence()' for distribution details. 281s 281s R is a collaborative project with many contributors. 281s Type 'contributors()' for more information and 281s 'citation()' on how to cite R or R packages in publications. 281s 281s Type 'demo()' for some demos, 'help()' for on-line help, or 281s 'help.start()' for an HTML browser interface to help. 281s Type 'q()' to quit R. 281s 281s > # test.sign.R 281s > 281s > # Test the use of sign.location and sign.nominal in clm.control(): 281s > 281s > library(ordinal) 281s > 281s > fm1 <- clm(rating ~ temp + contact, data=wine) 281s > fm2 <- clm(rating ~ temp + contact, data=wine, 281s + sign.location="positive") 281s > # dput(names(fm1)) 281s > keep <- c("aliased", "alpha", "cond.H", 281s + "contrasts", "convergence", "df.residual", "edf", 281s + "fitted.values", "formula", "formulas", "gradient", 281s + "info", "link", "logLik", "maxGradient", "message", "model", 281s + "n", "niter", "nobs", "start", "terms", "Theta", "threshold", 281s + "tJac", "xlevels", "y", "y.levels") 281s > check <- mapply(function(x, y) isTRUE(all.equal(x, y)), fm1[keep], fm2[keep]) 281s > stopifnot(all(check)) 281s > stopifnot(isTRUE(all.equal( 281s + fm1$beta, - fm2$beta 281s + ))) 281s > 281s > fm1 <- clm(rating ~ temp, nominal=~ contact, data=wine) 281s > fm2 <- clm(rating ~ temp, nominal=~ contact, data=wine, 281s + sign.nominal="negative") 281s > keep <- c("aliased", "beta", "cond.H", 281s + "contrasts", "convergence", "df.residual", "edf", 281s + "fitted.values", "formula", "formulas", "gradient", 281s + "info", "link", "logLik", "maxGradient", "message", "model", 281s + "n", "niter", "nobs", "start", "terms", "Theta", "threshold", 281s + "tJac", "xlevels", "y", "y.levels") 281s > # check <- mapply(function(x, y) isTRUE(all.equal(x, y)), fm1, fm2) 281s > check <- mapply(function(x, y) isTRUE(all.equal(x, y)), fm1[keep], fm2[keep]) 281s > stopifnot(all(check)) 281s > stopifnot(isTRUE(all.equal( 281s + fm1$alpha[5:8], -fm2$alpha[5:8] 281s + ))) 281s > 281s > 281s > fm1 <- clm(rating ~ temp, nominal=~ contact, data=wine) 281s > fm2 <- clm(rating ~ temp, nominal=~ contact, data=wine, 281s + sign.nominal="negative", sign.location="positive") 281s > keep <- c("aliased", "cond.H", 281s + "contrasts", "convergence", "df.residual", "edf", 281s + "fitted.values", "formula", "formulas", "gradient", 281s + "info", "link", "logLik", "maxGradient", "message", "model", 281s + "n", "niter", "nobs", "start", "terms", "Theta", "threshold", 281s + "tJac", "xlevels", "y", "y.levels") 281s > # check <- mapply(function(x, y) isTRUE(all.equal(x, y)), fm1, fm2) 281s > check <- mapply(function(x, y) isTRUE(all.equal(x, y)), fm1[keep], fm2[keep]) 281s > stopifnot(all(check)) 281s > stopifnot( 281s + isTRUE(all.equal(fm1$alpha[5:8], -fm2$alpha[5:8])), 281s + isTRUE(all.equal(fm1$beta, -fm2$beta)) 281s + ) 281s > 281s > # Check predict method: 281s > newData <- with(wine, expand.grid(temp=levels(temp), contact=levels(contact))) 281s > (p1 <- predict(fm1, newdata=newData)) 281s $fit 281s 1 2 3 4 5 281s 1 0.210312404 0.56637121 0.1953950 0.0185460 0.009375394 281s 2 0.020998377 0.19781391 0.5182972 0.1577343 0.105156202 281s 3 0.050301839 0.38380275 0.4329644 0.1065821 0.026348960 281s 4 0.004247588 0.05393811 0.2862121 0.4040930 0.251509196 281s 281s > (p2 <- predict(fm2, newdata=newData)) 281s $fit 281s 1 2 3 4 5 281s 1 0.210312404 0.56637121 0.1953950 0.0185460 0.009375394 281s 2 0.020998377 0.19781391 0.5182972 0.1577343 0.105156202 281s 3 0.050301839 0.38380275 0.4329644 0.1065821 0.026348960 281s 4 0.004247588 0.05393811 0.2862121 0.4040930 0.251509196 281s 281s > stopifnot(isTRUE(all.equal(p1, p2))) 281s > 281s > stopifnot(isTRUE( 281s + all.equal(predict(fm1, newdata=wine, se=TRUE, interval=TRUE), 281s + predict(fm2, newdata=wine, se=TRUE, interval=TRUE)) 281s + )) 281s > 281s > # Check profile and confint methods: 281s > confint.default(fm1) 281s 2.5 % 97.5 % 281s 1|2.(Intercept) -2.4250844 -0.2210024 281s 2|3.(Intercept) 0.3158056 2.1770814 281s 3|4.(Intercept) 2.2642614 4.8358258 281s 4|5.(Intercept) 2.9738888 6.3466053 281s 1|2.contactyes -3.8921464 0.6620280 281s 2|3.contactyes -2.6692032 -0.3539315 281s 3|4.contactyes -2.9464535 -0.4030579 281s 4|5.contactyes -2.8077520 0.7065061 281s tempwarm 1.4703720 3.5677176 281s > confint.default(fm2) 281s 2.5 % 97.5 % 281s 1|2.(Intercept) -2.4250844 -0.2210024 281s 2|3.(Intercept) 0.3158056 2.1770814 281s 3|4.(Intercept) 2.2642614 4.8358258 281s 4|5.(Intercept) 2.9738888 6.3466053 281s 1|2.contactyes -0.6620280 3.8921464 281s 2|3.contactyes 0.3539315 2.6692032 281s 3|4.contactyes 0.4030579 2.9464535 281s 4|5.contactyes -0.7065061 2.8077520 281s tempwarm -3.5677176 -1.4703720 281s > 281s > stopifnot( 281s + isTRUE(all.equal(confint(fm1), -confint(fm2)[, 2:1, drop=FALSE], 281s + check.attributes=FALSE)) 281s + ) 281s > 281s > fm1 <- clm(rating ~ temp + contact, data=wine) 281s > fm2 <- clm(rating ~ temp + contact, data=wine, 281s + sign.location="positive") 281s > pr1 <- profile(fm1) 281s > pr2 <- profile(fm2) 281s > stopifnot( 281s + isTRUE(all.equal(confint(fm1), - confint(fm2)[, 2:1], check.attributes=FALSE)) 281s + ) 281s > 281s > 281s BEGIN TEST test0weights.R 282s 282s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 282s Copyright (C) 2024 The R Foundation for Statistical Computing 282s Platform: aarch64-unknown-linux-gnu (64-bit) 282s 282s R is free software and comes with ABSOLUTELY NO WARRANTY. 282s You are welcome to redistribute it under certain conditions. 282s Type 'license()' or 'licence()' for distribution details. 282s 282s R is a collaborative project with many contributors. 282s Type 'contributors()' for more information and 282s 'citation()' on how to cite R or R packages in publications. 282s 282s Type 'demo()' for some demos, 'help()' for on-line help, or 282s 'help.start()' for an HTML browser interface to help. 282s Type 'q()' to quit R. 282s 282s > library(ordinal) 283s > options(contrasts = c("contr.treatment", "contr.poly")) 283s > ## library(devtools) 283s > ## r2path <- "/Users/rhbc/Documents/Rpackages/ordinal/pkg/ordinal" 283s > ## clean_dll(pkg = r2path) 283s > ## load_all(r2path) 283s > 283s > ## one zero weight: 283s > data(wine, package="ordinal") 283s > wts <- rep(1, nrow(wine)) 283s > wine$rating 283s [1] 2 3 3 4 4 4 5 5 1 2 1 3 2 3 5 4 2 3 3 2 5 5 4 4 3 2 3 2 3 2 5 3 2 3 4 3 3 3 283s [39] 3 3 3 2 3 2 2 4 5 4 1 1 2 2 2 3 2 3 2 2 2 3 3 3 3 4 1 2 3 2 3 2 4 4 283s Levels: 1 < 2 < 3 < 4 < 5 283s > wts[1] <- 0 283s > fm1 <- clm(rating ~ contact + temp, data=wine, weights=wts) 283s > fm1 283s formula: rating ~ contact + temp 283s data: wine 283s 283s link threshold nobs logLik AIC niter max.grad cond.H 283s logit flexible 71 -85.92 183.84 6(0) 3.44e-12 2.7e+01 283s 283s Coefficients: 283s contactyes tempwarm 283s 1.511 2.482 283s 283s Threshold coefficients: 283s 1|2 2|3 3|4 4|5 283s -1.295 1.220 3.437 4.975 283s > fm1$n ## 72 283s [1] 72 283s > fm1$nobs ## 71 283s [1] 71 283s > confint(fm1) 283s 2.5 % 97.5 % 283s contactyes 0.5951066 2.478924 283s tempwarm 1.4856829 3.577621 283s > plot(profile(fm1)) 283s > plot(slice(fm1), 5) 283s > convergence(fm1) 283s nobs logLik niter max.grad cond.H logLik.Error 283s 71 -85.92 6(0) 3.44e-12 2.7e+01 <1e-10 283s 283s Estimate Std.Err Gradient Error Cor.Dec Sig.Dig 283s 1|2 -1.295 0.5220 7.57e-13 7.84e-14 12 13 283s 2|3 1.220 0.4436 2.65e-12 -1.27e-13 12 13 283s 3|4 3.437 0.6014 -3.44e-12 -7.18e-13 11 12 283s 4|5 4.975 0.7341 -5.44e-14 -7.00e-13 11 12 283s contactyes 1.511 0.4785 1.54e-13 -1.96e-13 12 13 283s tempwarm 2.482 0.5303 -4.01e-13 -4.94e-13 12 13 283s 283s Eigen values of Hessian: 283s 21.7419 18.5476 10.4115 5.2426 4.0755 0.8013 283s 283s Convergence message from clm: 283s (0) successful convergence 283s In addition: Absolute and relative convergence criteria were met 283s 283s > drop1(fm1, test="Chi") 283s Single term deletions 283s 283s Model: 283s rating ~ contact + temp 283s Df AIC LRT Pr(>Chi) 283s 183.84 283s contact 1 192.54 10.698 0.001072 ** 283s temp 1 208.07 26.234 3.024e-07 *** 283s --- 283s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 283s > add1(fm1, scope=~.^2, test="Chi") 283s Single term additions 283s 283s Model: 283s rating ~ contact + temp 283s Df AIC LRT Pr(>Chi) 283s 183.84 283s contact:temp 1 185.66 0.18256 0.6692 283s > ## clm_anova(fm1) 283s > pred <- predict(fm1, newdata=wine) ## OK 283s > step.fm1 <- step(fm1, trace=0) 283s > fitted(fm1) 283s [1] 0.19683278 0.44514183 0.09677403 0.20147980 0.20147980 0.27261558 283s [7] 0.27261558 0.21497073 0.55705124 0.05699435 0.44514183 0.19814731 283s [13] 0.50160837 0.27261558 0.36288756 0.55705124 0.19683278 0.44514183 283s [19] 0.37073110 0.07640020 0.07640020 0.36288756 0.36288756 0.19683278 283s [25] 0.55705124 0.44514183 0.37073110 0.50160837 0.19814731 0.27261558 283s [31] 0.30572865 0.55705124 0.19683278 0.09677403 0.44514183 0.50160837 283s [37] 0.50160837 0.30572865 0.30572865 0.19683278 0.55705124 0.44514183 283s [43] 0.37073110 0.19814731 0.20147980 0.27261558 0.36288756 0.21497073 283s [49] 0.21497073 0.37073110 0.37073110 0.19814731 0.50160837 0.05374460 283s [55] 0.30572865 0.55705124 0.55705124 0.37073110 0.44514183 0.50160837 283s [61] 0.50160837 0.30572865 0.36288756 0.21497073 0.55705124 0.44514183 283s [67] 0.37073110 0.50160837 0.19814731 0.36288756 0.36288756 283s > dim(model.matrix(fm1)$X) 283s [1] 72 3 283s > dim(model.matrix(fm1, "B")$B1) 283s [1] 71 6 283s > mf <- update(fm1, method="model.frame") 283s > str(mf) 283s 'data.frame': 72 obs. of 4 variables: 283s $ rating : Ord.factor w/ 5 levels "1"<"2"<"3"<"4"<..: 2 3 3 4 4 4 5 5 1 2 ... 283s $ contact : Factor w/ 2 levels "no","yes": 1 1 2 2 1 1 2 2 1 1 ... 283s $ temp : Factor w/ 2 levels "cold","warm": 1 1 1 1 2 2 2 2 1 1 ... 283s $ (weights): num 0 1 1 1 1 1 1 1 1 1 ... 283s - attr(*, "terms")=Classes 'terms', 'formula' language rating ~ contact + temp 283s .. ..- attr(*, "variables")= language list(rating, contact, temp) 283s .. ..- attr(*, "factors")= int [1:3, 1:2] 0 1 0 0 0 1 283s .. .. ..- attr(*, "dimnames")=List of 2 283s .. .. .. ..$ : chr [1:3] "rating" "contact" "temp" 283s .. .. .. ..$ : chr [1:2] "contact" "temp" 283s .. ..- attr(*, "term.labels")= chr [1:2] "contact" "temp" 283s .. ..- attr(*, "order")= int [1:2] 1 1 283s .. ..- attr(*, "intercept")= int 1 283s .. ..- attr(*, "response")= int 1 283s .. ..- attr(*, ".Environment")= 283s .. ..- attr(*, "predvars")= language list(rating, contact, temp) 283s .. ..- attr(*, "dataClasses")= Named chr [1:4] "ordered" "factor" "factor" "numeric" 283s .. .. ..- attr(*, "names")= chr [1:4] "rating" "contact" "temp" "(weights)" 283s > wts <- mf$wts 283s > dim(model.matrix(fm1)$X[wts > 0, , drop=FALSE]) 283s [1] 0 3 283s > 283s > fm1b <- clm(rating ~ temp, scale=~contact, data=wine, weights=wts) 283s > summary(fm1b) 283s formula: rating ~ temp 283s scale: ~contact 283s data: wine 283s 283s link threshold nobs logLik AIC niter max.grad cond.H 283s logit flexible 72 -91.92 195.83 8(0) 1.57e-09 5.6e+01 283s 283s Coefficients: 283s Estimate Std. Error z value Pr(>|z|) 283s tempwarm 2.1690 0.5527 3.924 8.69e-05 *** 283s --- 283s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 283s 283s log-scale coefficients: 283s Estimate Std. Error z value Pr(>|z|) 283s contactyes -0.1222 0.2775 -0.44 0.66 283s 283s Threshold coefficients: 283s Estimate Std. Error z value 283s 1|2 -1.8957 0.4756 -3.986 283s 2|3 0.3668 0.3442 1.066 283s 3|4 2.2483 0.5932 3.790 283s 4|5 3.5393 0.8336 4.246 283s > pr <- profile(fm1b) 283s > confint(pr) 283s 2.5 % 97.5 % 283s tempwarm 1.2122036 3.4033767 283s sca.contactyes -0.6721766 0.4156449 283s > plot(pr, 1) 283s > fm1c <- clm(rating ~ temp, nominal=~contact, data=wine, weights=wts) 283s > summary(fm1c) 283s formula: rating ~ temp 283s nominal: ~contact 283s data: wine 283s 283s link threshold nobs logLik AIC niter max.grad cond.H 283s logit flexible 72 -86.21 190.42 6(0) 1.64e-10 4.8e+01 283s 283s Coefficients: 283s Estimate Std. Error z value Pr(>|z|) 283s tempwarm 2.519 0.535 4.708 2.5e-06 *** 283s --- 283s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 283s 283s Threshold coefficients: 283s Estimate Std. Error z value 283s 1|2.(Intercept) -1.3230 0.5623 -2.353 283s 2|3.(Intercept) 1.2464 0.4748 2.625 283s 3|4.(Intercept) 3.5500 0.6560 5.411 283s 4|5.(Intercept) 4.6602 0.8604 5.416 283s 1|2.contactyes -1.6151 1.1618 -1.390 283s 2|3.contactyes -1.5116 0.5906 -2.559 283s 3|4.contactyes -1.6748 0.6488 -2.581 283s 4|5.contactyes -1.0506 0.8965 -1.172 283s > pr <- profile(fm1c) 283s > confint(pr) 283s 2.5 % 97.5 % 283s tempwarm 1.516862 3.629098 283s > plot(pr, 1) 283s > 283s > ## nominal.test(fm1) 283s > ## scale.test(fm1) 283s > 283s > ## zero out an entire response category: 283s > wts2 <- 1 * with(wine, rating != "2") 283s > fm2 <- clm(rating ~ contact + temp, data=wine, weights=wts2) 283s > fm2 283s formula: rating ~ contact + temp 283s data: wine 283s 283s link threshold nobs logLik AIC niter max.grad cond.H 283s logit flexible 50 -46.76 103.52 7(0) 3.55e-13 4.2e+01 283s 283s Coefficients: 283s contactyes tempwarm 283s 1.593 3.062 283s 283s Threshold coefficients: 283s 1|3 3|4 4|5 283s -0.5173 3.6238 5.3657 283s > fm2$n ## 72 283s [1] 72 283s > fm2$nobs ## 50 283s [1] 50 283s > ## Dimension of X and B1, B2 differ: 283s > dim(model.matrix(fm2)$X) 283s [1] 72 3 283s > dim(model.matrix(fm2, "B")$B1) 283s [1] 50 5 283s > ## Cannot directly evaluate predictions on the original data: 283s > try(predict(fm2, newdata=wine), silent=TRUE)[1] 283s [1] "Error in predict.clm(fm2, newdata = wine) : \n response factor 'rating' has new levels\n" 283s > confint(fm2) 283s 2.5 % 97.5 % 283s contactyes 0.4216272 2.876550 283s tempwarm 1.5970977 5.026527 283s > profile(fm2) 283s $contactyes 283s lroot par.vals.1|3 par.vals.3|4 par.vals.4|5 par.vals.contactyes 283s 1 3.4747852 -1.448538968 2.255543944 3.804439509 -0.447374822 283s 2 3.0276372 -1.308493024 2.407453551 3.967827135 -0.192380808 283s 3 2.5822211 -1.174976592 2.565043880 4.140537415 0.062613207 283s 4 2.1395315 -1.048101582 2.728199207 4.322490592 0.317607222 283s 5 1.7005507 -0.927983229 2.896810974 4.513576014 0.572601236 283s 6 1.2662317 -0.814738724 3.070776301 4.713647671 0.827595251 283s 7 0.8374817 -0.708483160 3.249996208 4.922519451 1.082589265 283s 8 0.4151468 -0.609322477 3.434373593 5.139960291 1.337583280 283s 9 0.0000000 -0.517343412 3.623810880 5.365689290 1.592577294 283s 10 -0.4072702 -0.432600941 3.818207180 5.599370818 1.847571309 283s 11 -0.8060673 -0.355104205 4.017454848 5.840609731 2.102565323 283s 12 -1.1958918 -0.284802472 4.221435388 6.088946911 2.357559338 283s 13 -1.5763436 -0.221573075 4.430015019 6.343855637 2.612553352 283s 14 -1.9471215 -0.165213368 4.643040370 6.604739566 2.867547367 283s 15 -2.3080198 -0.115438462 4.860335061 6.870933284 3.122541381 283s 16 -2.6589228 -0.071885700 5.081697900 7.141706504 3.377535396 283s 17 -2.9997972 -0.034125762 5.306903276 7.416272839 3.632529410 283s 18 -3.3306833 -0.001679093 5.535703885 7.693803770 3.887523425 283s par.vals.tempwarm 283s 1 2.840981986 283s 2 2.848907417 283s 3 2.863086150 283s 4 2.883227511 283s 5 2.909025226 283s 6 2.940155181 283s 7 2.976272850 283s 8 3.017010511 283s 9 3.061974244 283s 10 3.110740675 283s 11 3.162853507 283s 12 3.217819929 283s 13 3.275107380 283s 14 3.334141312 283s 15 3.394304942 283s 16 3.454942107 283s 17 3.515364293 283s 18 3.574862708 283s 283s $tempwarm 283s lroot par.vals.1|3 par.vals.3|4 par.vals.4|5 par.vals.contactyes 283s 1 3.4300164 -1.3083735 1.7272573 3.1899360 1.3296606 283s 2 2.8813858 -1.1550431 1.9737448 3.4740817 1.3627908 283s 3 2.3491188 -1.0148529 2.2280703 3.7683888 1.3992293 283s 4 1.8354355 -0.8881411 2.4904988 4.0722937 1.4379639 283s 5 1.3422735 -0.7751174 2.7612331 4.3850175 1.4778669 283s 6 0.8712358 -0.6758159 3.0403898 4.7055883 1.5177348 283s 7 0.4235444 -0.5900448 3.3279674 5.0328829 1.5563515 283s 8 0.0000000 -0.5173434 3.6238109 5.3656893 1.5925773 283s 9 -0.3990485 -0.4569595 3.9275814 5.7027863 1.6254526 283s 10 -0.7737184 -0.4078590 4.2387443 6.0430310 1.6542958 283s 11 -1.1245809 -0.3687765 4.5565843 6.3854348 1.6787668 283s 12 -1.4526173 -0.3383014 4.8802522 6.7292117 1.6988730 283s 13 -1.7591420 -0.3149843 5.2088333 7.0737893 1.7149136 283s 14 -2.0457031 -0.2974396 5.5414220 7.4187857 1.7273842 283s 15 -2.3139760 -0.2844232 5.8771833 7.7639689 1.7368704 283s 16 -2.5656664 -0.2748765 6.2153929 8.1092106 1.7439599 283s 17 -2.8024328 -0.2679376 6.5554528 8.4544482 1.7491850 283s 18 -3.0258332 -0.2629290 6.8968876 8.7996559 1.7529951 283s 19 -3.2372944 -0.2593326 7.2393314 9.1448275 1.7557514 283s 20 -3.4380992 -0.2567600 7.5825083 9.4899654 1.7577335 283s par.vals.tempwarm 283s 1 0.6468007 283s 2 0.9918255 283s 3 1.3368503 283s 4 1.6818751 283s 5 2.0268999 283s 6 2.3719247 283s 7 2.7169495 283s 8 3.0619742 283s 9 3.4069990 283s 10 3.7520238 283s 11 4.0970486 283s 12 4.4420734 283s 13 4.7870982 283s 14 5.1321230 283s 15 5.4771478 283s 16 5.8221726 283s 17 6.1671974 283s 18 6.5122222 283s 19 6.8572470 283s 20 7.2022718 283s 283s attr(,"original.fit") 283s formula: rating ~ contact + temp 283s data: wine 283s 283s link threshold nobs logLik AIC niter max.grad cond.H 283s logit flexible 50 -46.76 103.52 7(0) 3.55e-13 4.2e+01 283s 283s Coefficients: 283s contactyes tempwarm 283s 1.593 3.062 283s 283s Threshold coefficients: 283s 1|3 3|4 4|5 283s -0.5173 3.6238 5.3657 283s attr(,"class") 283s [1] "profile.clm" 283s > plot(slice(fm2), 5) 283s > step.fm2 <- step(fm2, trace=0) 283s > fitted(fm2) 283s [1] 0.60053892 0.77590129 0.09349820 0.27230685 0.27230685 0.32934749 283s [7] 0.32934749 0.37347364 0.10813631 0.77590129 0.60973967 0.32934749 283s [13] 0.40771198 0.60053892 0.77590129 0.09081575 0.09081575 0.40771198 283s [19] 0.40771198 0.60053892 0.77590129 0.60973967 0.32934749 0.25729874 283s [25] 0.60053892 0.09349820 0.77590129 0.60973967 0.60973967 0.25729874 283s [31] 0.25729874 0.60053892 0.77590129 0.27230685 0.32934749 0.40771198 283s [37] 0.37347364 0.37347364 0.60973967 0.25729874 0.77590129 0.60973967 283s [43] 0.60973967 0.25729874 0.40771198 0.37347364 0.77590129 0.60973967 283s [49] 0.40771198 0.40771198 283s > ## Scale and nominal effects: 283s > fm2b <- clm(rating ~ temp, scale=~contact, data=wine, weights=wts2) 283s > summary(fm2b) 283s formula: rating ~ temp 283s scale: ~contact 283s data: wine 283s 283s link threshold nobs logLik AIC niter max.grad cond.H 283s logit flexible 50 -50.35 110.71 9(0) 2.51e-08 1.2e+02 283s 283s Coefficients: 283s Estimate Std. Error z value Pr(>|z|) 283s tempwarm 2.667 1.059 2.519 0.0118 * 283s --- 283s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 283s 283s log-scale coefficients: 283s Estimate Std. Error z value Pr(>|z|) 283s contactyes -0.09812 0.38836 -0.253 0.801 283s 283s Threshold coefficients: 283s Estimate Std. Error z value 283s 1|3 -1.2009 0.5033 -2.386 283s 3|4 2.3219 1.0427 2.227 283s 4|5 3.7986 1.3876 2.738 283s > pr <- profile(fm2b) 283s > confint(pr) 283s 2.5 % 97.5 % 283s tempwarm 1.1319929 6.0851931 283s sca.contactyes -0.8403892 0.7190847 283s > plot(pr, 1) 283s > fm2c <- clm(rating ~ temp, nominal=~contact, data=wine, weights=wts2) 283s > summary(fm2c) 283s formula: rating ~ temp 283s nominal: ~contact 283s data: wine 283s 283s link threshold nobs logLik AIC niter max.grad cond.H 283s logit flexible 50 -46.36 106.72 7(0) 1.22e-12 4.8e+01 283s 283s Coefficients: 283s Estimate Std. Error z value Pr(>|z|) 283s tempwarm 3.1100 0.8529 3.646 0.000266 *** 283s --- 283s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 283s 283s Threshold coefficients: 283s Estimate Std. Error z value 283s 1|3.(Intercept) -0.4250 0.6381 -0.666 283s 3|4.(Intercept) 3.6911 0.9505 3.883 283s 4|5.(Intercept) 4.8968 1.1001 4.451 283s 1|3.contactyes -1.8993 1.2128 -1.566 283s 3|4.contactyes -1.7003 0.7432 -2.288 283s 4|5.contactyes -0.9153 0.9243 -0.990 283s > pr <- profile(fm2c) 283s > confint(pr) 283s 2.5 % 97.5 % 283s tempwarm 1.623761 5.102185 283s > plot(pr, 1) 283s > pred <- predict(fm2c, newdata=wine[!names(wine) %in% "rating"]) 283s > pred <- predict(fm2b, newdata=wine[!names(wine) %in% "rating"]) 283s > 283s > ## nominal.test(fm2) 283s > ## scale.test(fm2) 283s > 283s > ## Different data sets (error): 283s > try(anova(fm1, fm2), silent=TRUE)[1] ## OK 283s [1] "Error in anova.clm(fm1, fm2) : \n models were not all fitted to the same dataset\n" 283s > 283s > ## Test clm.fit: 283s > wts2 <- 1 * with(wine, rating != "2") 283s > mf2 <- update(fm2, method="design") 283s > fm3 <- with(mf2, clm.fit(y, X, weights=wts)) 283s > 283s > ################################# 283s > 283s BEGIN TEST testAnova.clm2.R 283s 283s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 283s Copyright (C) 2024 The R Foundation for Statistical Computing 283s Platform: aarch64-unknown-linux-gnu (64-bit) 283s 283s R is free software and comes with ABSOLUTELY NO WARRANTY. 283s You are welcome to redistribute it under certain conditions. 283s Type 'license()' or 'licence()' for distribution details. 283s 283s R is a collaborative project with many contributors. 283s Type 'contributors()' for more information and 283s 'citation()' on how to cite R or R packages in publications. 283s 283s Type 'demo()' for some demos, 'help()' for on-line help, or 283s 'help.start()' for an HTML browser interface to help. 283s Type 'q()' to quit R. 283s 283s > library(ordinal) 284s > options(contrasts = c("contr.treatment", "contr.poly")) 284s > 284s > ## More manageable data set: 284s > (tab26 <- with(soup, table("Product" = PROD, "Response" = SURENESS))) 284s Response 284s Product 1 2 3 4 5 6 284s Ref 132 161 65 41 121 219 284s Test 96 99 50 57 156 650 284s > dimnames(tab26)[[2]] <- c("Sure", "Not Sure", "Guess", "Guess", "Not Sure", "Sure") 284s > dat26 <- expand.grid(sureness = as.factor(1:6), prod = c("Ref", "Test")) 284s > dat26$wghts <- c(t(tab26)) 284s > m1 <- clm(sureness ~ prod, scale = ~prod, data = dat26, 284s + weights = wghts, link = "logit") 284s > 284s > ## anova 284s > m2 <- update(m1, scale = ~1) 284s > anova(m1, m2) 284s Likelihood ratio tests of cumulative link models: 284s 284s formula: scale: link: threshold: 284s m2 sureness ~ prod ~1 logit flexible 284s m1 sureness ~ prod ~prod logit flexible 284s 284s no.par AIC logLik LR.stat df Pr(>Chisq) 284s m2 6 5392.7 -2690.3 284s m1 7 5389.5 -2687.7 5.1749 1 0.02292 * 284s --- 284s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 284s > mN1 <- clm(sureness ~ 1, nominal = ~prod, data = dat26, 284s + link = "logit") 284s > anova(m1, mN1) 284s Likelihood ratio tests of cumulative link models: 284s 284s formula: nominal: scale: link: threshold: 284s m1 sureness ~ prod ~1 ~prod logit flexible 284s mN1 sureness ~ 1 ~prod ~1 logit flexible 284s 284s no.par AIC logLik LR.stat df Pr(>Chisq) 284s m1 7 5389.489 -2687.745 284s mN1 10 63.002 -21.501 5332.5 3 < 2.2e-16 *** 284s --- 284s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 284s > anova(m1, m2, mN1) 284s Likelihood ratio tests of cumulative link models: 284s 284s formula: nominal: scale: link: threshold: 284s m2 sureness ~ prod ~1 ~1 logit flexible 284s m1 sureness ~ prod ~1 ~prod logit flexible 284s mN1 sureness ~ 1 ~prod ~1 logit flexible 284s 284s no.par AIC logLik LR.stat df Pr(>Chisq) 284s m2 6 5392.664 -2690.332 284s m1 7 5389.489 -2687.745 5.1749 1 0.02292 * 284s mN1 10 63.002 -21.501 5332.4869 3 < 2e-16 *** 284s --- 284s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 284s > 284s > ## dropterm 284s > if(require(MASS)) { 284s + dropterm(m1, test = "Chi") 284s + mB1 <- clm(SURENESS ~ PROD + GENDER + SOUPTYPE, 284s + scale = ~ COLD, data = soup, link = "probit") 284s + dropterm(mB1, test = "Chi") # or 284s + 284s + ## addterm 284s + addterm(mB1, scope = ~.^2, test = "Chi") 284s + ## addterm(mB1, scope = ~ . + AGEGROUP + SOUPFREQ, 284s + ## test = "Chi", which = "location") 284s + ## addterm(mB1, scope = ~ . + GENDER + SOUPTYPE, 284s + ## test = "Chi", which = "scale") 284s + 284s + ## Fit model from polr example: 284s + ## data(housing, package = "MASS") 284s + 284s + fm1 <- clm(Sat ~ Infl + Type + Cont, weights = Freq, data = housing) 284s + ## addterm(fm1, ~ Infl + Type + Cont, test= "Chisq", which = "scale") 284s + dropterm(fm1, test = "Chisq") 284s + fm2 <- update(fm1, scale =~ Cont) 284s + fm3 <- update(fm1, formula =~.-Cont, nominal =~ Cont) 284s + anova(fm1, fm2, fm3) 284s + } 284s Loading required package: MASS 285s Likelihood ratio tests of cumulative link models: 285s 285s formula: nominal: scale: link: threshold: 285s fm1 Sat ~ Infl + Type + Cont ~1 ~1 logit flexible 285s fm2 Sat ~ Infl + Type + Cont ~1 ~Cont logit flexible 285s fm3 Sat ~ Infl + Type ~Cont ~1 logit flexible 285s 285s no.par AIC logLik LR.stat df Pr(>Chisq) 285s fm1 8 3495.1 -1739.6 285s fm2 9 3491.5 -1736.7 5.6559 1 0.0174 * 285s fm3 9 3494.7 -1738.4 -3.2113 0 285s --- 285s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 285s > 285s > 285s BEGIN TEST testCLM.R 285s 285s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 285s Copyright (C) 2024 The R Foundation for Statistical Computing 285s Platform: aarch64-unknown-linux-gnu (64-bit) 285s 285s R is free software and comes with ABSOLUTELY NO WARRANTY. 285s You are welcome to redistribute it under certain conditions. 285s Type 'license()' or 'licence()' for distribution details. 285s 285s R is a collaborative project with many contributors. 285s Type 'contributors()' for more information and 285s 'citation()' on how to cite R or R packages in publications. 285s 285s Type 'demo()' for some demos, 'help()' for on-line help, or 285s 'help.start()' for an HTML browser interface to help. 285s Type 'q()' to quit R. 285s 285s > library(ordinal) 286s > options(contrasts = c("contr.treatment", "contr.poly")) 286s > ## library(devtools) 286s > ## r2path <- "/Users/rhbc/Documents/Rpackages/ordinal/pkg/ordinal" 286s > ## clean_dll(pkg = r2path) 286s > ## load_all(r2path) 286s > 286s > ## More manageable data set: 286s > data(soup, package="ordinal") 286s > (tab26 <- with(soup, table("Product" = PROD, "Response" = SURENESS))) 286s Response 286s Product 1 2 3 4 5 6 286s Ref 132 161 65 41 121 219 286s Test 96 99 50 57 156 650 286s > dimnames(tab26)[[2]] <- c("Sure", "Not Sure", "Guess", "Guess", "Not Sure", "Sure") 286s > dat26 <- expand.grid(sureness = as.factor(1:6), prod = c("Ref", "Test")) 286s > dat26$wghts <- c(t(tab26)) 286s > m1 <- clm(sureness ~ prod, scale = ~prod, data = dat26, 286s + weights = wghts, link = "logit") 286s > ## print, summary, vcov, logLik, AIC: 286s > m1 286s formula: sureness ~ prod 286s scale: ~prod 286s data: dat26 286s 286s link threshold nobs logLik AIC niter max.grad cond.H 286s logit flexible 1847 -2687.74 5389.49 8(1) 5.09e-07 1.0e+02 286s 286s Coefficients: 286s prodTest 286s 1.296 286s 286s log-scale coefficients: 286s prodTest 286s 0.148 286s 286s Threshold coefficients: 286s 1|2 2|3 3|4 4|5 5|6 286s -1.4913 -0.4522 -0.1072 0.1634 0.8829 286s > summary(m1) 286s formula: sureness ~ prod 286s scale: ~prod 286s data: dat26 286s 286s link threshold nobs logLik AIC niter max.grad cond.H 286s logit flexible 1847 -2687.74 5389.49 8(1) 5.09e-07 1.0e+02 286s 286s Coefficients: 286s Estimate Std. Error z value Pr(>|z|) 286s prodTest 1.296 0.119 10.89 <2e-16 *** 286s --- 286s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 286s 286s log-scale coefficients: 286s Estimate Std. Error z value Pr(>|z|) 286s prodTest 0.1480 0.0651 2.273 0.023 * 286s --- 286s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 286s 286s Threshold coefficients: 286s Estimate Std. Error z value 286s 1|2 -1.49126 0.09215 -16.183 286s 2|3 -0.45218 0.07182 -6.296 286s 3|4 -0.10721 0.06995 -1.533 286s 4|5 0.16337 0.07025 2.325 286s 5|6 0.88291 0.07957 11.096 286s > vcov(m1) 286s 1|2 2|3 3|4 4|5 5|6 286s 1|2 0.0084917417 0.0046258673 0.0038492096 0.003316006 0.002036170 286s 2|3 0.0046258673 0.0051586967 0.0044974099 0.004099300 0.003352323 286s 3|4 0.0038492096 0.0044974099 0.0048935739 0.004528181 0.003948048 286s 4|5 0.0033160059 0.0040993002 0.0045281811 0.004935721 0.004489054 286s 5|6 0.0020361699 0.0033523229 0.0039480481 0.004489054 0.006331523 286s prodTest 0.0009111749 0.0031074167 0.0039832831 0.004738959 0.007064828 286s prodTest -0.0024312129 -0.0007825923 -0.0001820514 0.000338977 0.001989991 286s prodTest prodTest 286s 1|2 0.0009111749 -0.0024312129 286s 2|3 0.0031074167 -0.0007825923 286s 3|4 0.0039832831 -0.0001820514 286s 4|5 0.0047389591 0.0003389770 286s 5|6 0.0070648284 0.0019899912 286s prodTest 0.0141687135 0.0045752922 286s prodTest 0.0045752922 0.0042385585 286s > 286s > logLik(m1) 286s 'log Lik.' -2687.745 (df=7) 286s > ll.m1 <- structure(-2687.74456343981, df = 7L, nobs = 1847, 286s + class = "logLik") 286s > stopifnot(all.equal(logLik(m1), ll.m1)) 286s > 286s > AIC(m1) 286s [1] 5389.489 286s > 286s > coef(m1) 286s 1|2 2|3 3|4 4|5 5|6 prodTest prodTest 286s -1.4912570 -0.4521846 -0.1072083 0.1633653 0.8829135 1.2958776 0.1479862 286s > cm1 <- c(-1.49125702755587, -0.45218462707814, -0.107208315524318, 0.163365282774162, 286s + 0.88291347877514, 1.29587762626394, 0.147986162902775) 286s > stopifnot(all.equal(as.vector(coef(m1)), cm1)) 286s > 286s > coef(summary(m1)) 286s Estimate Std. Error z value Pr(>|z|) 286s 1|2 -1.4912570 0.09215065 -16.182817 6.667319e-59 286s 2|3 -0.4521846 0.07182407 -6.295726 3.059652e-10 286s 3|4 -0.1072083 0.06995408 -1.532553 1.253861e-01 286s 4|5 0.1633653 0.07025469 2.325329 2.005437e-02 286s 5|6 0.8829135 0.07957087 11.095938 1.312749e-28 286s prodTest 1.2958776 0.11903241 10.886763 1.332938e-27 286s prodTest 0.1479862 0.06510421 2.273066 2.302222e-02 286s > csm1 <- structure(c(-1.49125702755587, -0.45218462707814, -0.107208315524318, 286s + 0.163365282774162, 0.88291347877514, 1.29587762626394, 0.147986162902775, 286s + 0.0921506468161812, 0.0718240681909781, 0.069954084652323, 0.0702546879687391, 286s + 0.0795708692869622, 0.119032405993894, 0.065104213008022, -16.1828167145758, 286s + -6.2957256316336, -1.53255261729392, 2.32532927691394, 11.0959385851501, 286s + 10.8867632762999, 2.27306584421104, 6.66732036748908e-59, 3.05965144996025e-10, 286s + 0.125386123756898, 0.0200543599621069, 1.31274723412040e-28, 286s + 1.33293711602276e-27, 0.0230222123418036), .Dim = c(7L, 4L), .Dimnames = list( 286s + c("1|2", "2|3", "3|4", "4|5", "5|6", "prodTest", "prodTest" 286s + ), c("Estimate", "Std. Error", "z value", "Pr(>|z|)"))) 286s > stopifnot(all.equal(coef(summary(m1)), csm1)) 286s > 286s > ## link functions: 286s > m2 <- update(m1, link = "probit") 286s > m3 <- update(m1, link = "cloglog") 286s > 286s > m4 <- update(m1, link = "loglog") 286s > m5 <- update(m1, link = "cauchit", start = coef(m1)) 286s > ## m6 <- update(m1, link = "Aranda-Ordaz", lambda = 1) 286s > ## m7 <- update(m1, link = "Aranda-Ordaz") 286s > ## m8 <- update(m1, link = "log-gamma", lambda = 1) 286s > ## m9 <- update(m1, link = "log-gamma") 286s > ## nominal effects: 286s > mN1 <- clm(sureness ~ 1, nominal = ~ prod, data = dat26, 286s + weights = wghts) 286s > anova(m1, mN1) 286s Likelihood ratio tests of cumulative link models: 286s 286s formula: nominal: scale: link: threshold: 286s m1 sureness ~ prod ~1 ~prod logit flexible 286s mN1 sureness ~ 1 ~prod ~1 logit flexible 286s 286s no.par AIC logLik LR.stat df Pr(>Chisq) 286s m1 7 5389.5 -2687.7 286s mN1 10 5390.1 -2685.1 5.3755 3 0.1463 286s > ## optimizer / method: 286s > update(m1, scale = ~ 1, method = "Newton") 286s formula: sureness ~ prod 286s scale: ~1 286s data: dat26 286s 286s link threshold nobs logLik AIC niter max.grad cond.H 286s logit flexible 1847 -2690.33 5392.66 6(1) 3.21e-12 1.1e+02 286s 286s Coefficients: 286s prodTest 286s 1.144 286s 286s Threshold coefficients: 286s 1|2 2|3 3|4 4|5 5|6 286s -1.4050 -0.4247 -0.1013 0.1508 0.8126 286s > update(m1, scale = ~ 1, method = "ucminf") 286s formula: sureness ~ prod 286s scale: ~1 286s data: dat26 286s 286s link threshold nobs logLik AIC niter max.grad cond.H 286s logit flexible 1847 -2690.33 5392.66 19(0) 1.26e-08 1.1e+02 286s 286s Coefficients: 286s prodTest 286s 1.144 286s 286s Threshold coefficients: 286s 1|2 2|3 3|4 4|5 5|6 286s -1.4050 -0.4247 -0.1013 0.1508 0.8126 286s > update(m1, scale = ~ 1, method = "nlminb") 286s formula: sureness ~ prod 286s scale: ~1 286s data: dat26 286s 286s link threshold nobs logLik AIC niter max.grad cond.H 286s logit flexible 1847 -2690.33 5392.66 56(43) 4.13e-03 1.1e+02 286s 286s Coefficients: 286s prodTest 286s 1.144 286s 286s Threshold coefficients: 286s 1|2 2|3 3|4 4|5 5|6 286s -1.4050 -0.4247 -0.1013 0.1508 0.8126 286s > update(m1, scale = ~ 1, method = "optim") 286s Warning message: 286s (-1) Model failed to converge with max|grad| = 0.00413248 (tol = 1e-06) 286s formula: sureness ~ prod 286s scale: ~1 286s data: dat26 286s 286s link threshold nobs logLik AIC niter max.grad cond.H 286s logit flexible 1847 -2690.33 5392.66 44(12) 4.73e-03 1.1e+02 286s 286s Coefficients: 286s prodTest 286s 1.144 286s 286s Threshold coefficients: 286s 1|2 2|3 3|4 4|5 5|6 286s -1.4050 -0.4247 -0.1013 0.1508 0.8126 286s > update(m1, scale = ~ 1, method = "model.frame") 286s sureness prod (weights) 286s 1 1 Ref 132 286s 2 2 Ref 161 286s 3 3 Ref 65 286s 4 4 Ref 41 286s 5 5 Ref 121 286s 6 Warning message: 286s (-1) Model failed to converge with max|grad| = 0.00472568 (tol = 1e-06) 286s 6 Ref 219 286s 7 1 Test 96 286s 8 2 Test 99 286s 9 3 Test 50 286s 10 4 Test 57 286s 11 5 Test 156 286s 12 6 Test 650 286s > update(m1, ~.-prod, scale = ~ 1, 286s + nominal = ~ prod, method = "model.frame") 286s sureness prod (weights) 286s 1 1 Ref 132 286s 2 2 Ref 161 286s 3 3 Ref 65 286s 4 4 Ref 41 286s 5 5 Ref 121 286s 6 6 Ref 219 286s 7 1 Test 96 286s 8 2 Test 99 286s 9 3 Test 50 286s 10 4 Test 57 286s 11 5 Test 156 286s 12 6 Test 650 286s > ## threshold functions 286s > mT1 <- update(m1, threshold = "symmetric") 286s > mT2 <- update(m1, threshold = "equidistant") 286s > anova(m1, mT1, mT2) 286s Likelihood ratio tests of cumulative link models: 286s 286s formula: scale: link: threshold: 286s mT2 sureness ~ prod ~prod logit equidistant 286s mT1 sureness ~ prod ~prod logit symmetric 286s m1 sureness ~ prod ~prod logit flexible 286s 286s no.par AIC logLik LR.stat df Pr(>Chisq) 286s mT2 4 5585.6 -2788.8 286s mT1 5 5407.8 -2698.9 179.806 1 < 2.2e-16 *** 286s m1 7 5389.5 -2687.7 22.271 2 1.459e-05 *** 286s --- 286s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 286s > 286s > ## Extend example from polr in package MASS: 286s > ## Fit model from polr example: 286s > if(require(MASS)) { 286s + fm1 <- clm(Sat ~ Infl + Type + Cont, weights = Freq, data = housing) 286s + fm1 286s + summary(fm1) 286s + ## With probit link: 286s + summary(update(fm1, link = "probit")) 286s + ## Allow scale to depend on Cont-variable 286s + summary(fm2 <- update(fm1, scale =~ Cont)) 286s + summary(fm3 <- update(fm1, location =~.-Cont, nominal =~ Cont)) 286s + summary(fm4 <- update(fm2, location =~.-Cont, nominal =~ Cont)) 286s + anova(fm1, fm2, fm3, fm4) 286s + ## which seems to improve the fit 286s + } 286s Loading required package: MASS 286s Likelihood ratio tests of cumulative link models: 286s 286s formula: nominal: scale: link: threshold: 286s fm1 Sat ~ Infl + Type + Cont ~1 ~1 logit flexible 286s fm2 Sat ~ Infl + Type + Cont ~1 ~Cont logit flexible 286s fm3 Sat ~ Infl + Type + Cont ~Cont ~1 logit flexible 286s fm4 Sat ~ Infl + Type + Cont ~Cont ~Cont logit flexible 286s 286s no.par AIC logLik LR.stat df Pr(>Chisq) 286s fm1 8 3495.1 -1739.6 286s fm2 9 3491.5 -1736.7 5.6559 1 0.01740 * 286s fm3 9 3494.7 -1738.4 -3.2113 0 286s fm4 10 3492.5 -1736.2 4.2190 1 0.03997 * 286s --- 286s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 286s > 286s > ################################# 286s > ## Better handling of ill-defined variance-covariance matrix of the 286s > ## parameters in summary methods for clm and clmm objects: 286s > dat26.2 <- data.frame(sureness = as.factor(1:12), 286s + prod = rep(c("One", "Two", "Three"),each=4)) 286s > fm1 <- clm(sureness ~ prod, ~prod, data = dat26.2) 286s Warning message: 286s (1) Hessian is numerically singular: parameters are not uniquely determined 286s In addition: Absolute convergence criterion was met, but relative criterion was not met 286s > fm1 286s formula: sureness ~ prod 286s scale: ~prod 286s data: dat26.2 286s 286s link threshold nobs logLik AIC niter max.grad cond.H 286s logit flexible 12 -16.64 63.27 33(14) 6.18e-07 2.0e+12 286s 286s Coefficients: 286s prodThree prodTwo 286s 90.72 46.65 286s 286s log-scale coefficients: 286s prodThree prodTwo 286s -0.11719 -0.09167 286s 286s Threshold coefficients: 286s 1|2 2|3 3|4 4|5 5|6 6|7 7|8 286s -1.099e+00 8.725e-16 1.099e+00 2.441e+01 4.564e+01 4.665e+01 4.765e+01 286s 8|9 9|10 10|11 11|12 286s 6.888e+01 8.975e+01 9.072e+01 9.170e+01 286s > summary(fm1) 286s formula: sureness ~ prod 286s scale: ~prod 286s data: dat26.2 286s 286s link threshold nobs logLik AIC niter max.grad cond.H 286s logit flexible 12 -16.64 63.27 33(14) 6.18e-07 2.0e+12 286s 286s Coefficients: 286s Estimate Std. Error z value Pr(>|z|) 286s prodThree 90.72 NA NA NA 286s prodTwo 46.65 NA NA NA 286s 286s log-scale coefficients: 286s Estimate Std. Error z value Pr(>|z|) 286s prodThree -0.11719 NA NA NA 286s prodTwo -0.09167 NA NA NA 286s 286s Threshold coefficients: 286s Estimate Std. Error z value 286s 1|2 -1.099e+00 NA NA 286s 2|3 8.725e-16 NA NA 286s 3|4 1.099e+00 NA NA 286s 4|5 2.441e+01 NA NA 286s 5|6 4.564e+01 NA NA 286s 6|7 4.665e+01 NA NA 286s 7|8 4.765e+01 NA NA 286s 8|9 6.888e+01 NA NA 286s 9|10 8.975e+01 NA NA 286s 10|11 9.072e+01 NA NA 286s 11|12 9.170e+01 NA NA 286s > summary(fm1, corr = 1) 286s formula: sureness ~ prod 286s scale: ~prod 286s data: dat26.2 286s 286s link threshold nobs logLik AIC niter max.grad cond.H 286s logit flexible 12 -16.64 63.27 33(14) 6.18e-07 2.0e+12 286s 286s Coefficients: 286s Estimate Std. Error z value Pr(>|z|) 286s prodThree 90.72 NA NA NA 286s prodTwo 46.65 NA NA NA 286s 286s log-scale coefficients: 286s Estimate Std. Error z value Pr(>|z|) 286s prodThree -0.11719 NA NA NA 286s prodTwo -0.09167 NA NA NA 286s 286s Threshold coefficients: 286s Estimate Std. Error z value 286s 1|2 -1.099e+00 NA NA 286s 2|3 8.725e-16 NA NA 286s 3|4 1.099e+00 NA NA 286s 4|5 2.441e+01 NA NA 286s 5|6 4.564e+01 NA NA 286s 6|7 4.665e+01 NA NA 286s 7|8 4.765e+01 NA NA 286s 8|9 6.888e+01 NA NA 286s 9|10 8.975e+01 NA NA 286s 10|11 9.072e+01 NA NA 286s 11|12 9.170e+01 NA NA 286s > ## fm1$Hessian 286s > ## sl1 <- slice(fm1, 13) 286s > ## fitted(fm1) 286s > ## convergence(fm1) 286s > ## eigen(fm1$Hessian)$values 286s > ## sqrt(diag(solve(fm1$Hessian))) 286s > ## sqrt(diag(ginv(fm1$Hessian))) 286s > 286s > ################################# 286s > ## Missing values: 286s > ## Bug-report from Jonathan Williams 286s > ## , 18 March 2010 12:42 286s > data(soup, package = "ordinal") 286s > soup$SURENESS[10] <- NA 286s > c1a <- clm(ordered(SURENESS)~PROD, data=soup); summary(c1a) 286s formula: ordered(SURENESS) ~ PROD 286s data: soup 286s 286s link threshold nobs logLik AIC niter max.grad cond.H 286s logit flexible 1846 -2688.71 5389.43 6(1) 2.87e-12 1.1e+02 286s 286s Coefficients: 286s Estimate Std. Error z value Pr(>|z|) 286s PRODTest 1.14251 0.08931 12.79 <2e-16 *** 286s --- 286s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 286s 286s Threshold coefficients: 286s Estimate Std. Error z value 286s 1|2 -1.40460 0.08174 -17.184 286s 2|3 -0.42733 0.06965 -6.135 286s 3|4 -0.10357 0.06884 -1.505 286s 4|5 0.14862 0.06898 2.155 286s 5|6 0.81063 0.07185 11.282 286s (1 observation deleted due to missingness) 286s > c2a <- clm(ordered(SURENESS)~PROD, scale = ~PROD, data=soup) 286s Warning message: 286s In summary.clm(fm1, corr = 1) : Correlation matrix is unavailable 286s > summary(c2a) 286s formula: ordered(SURENESS) ~ PROD 286s scale: ~PROD 286s data: soup 286s 286s link threshold nobs logLik AIC niter max.grad cond.H 286s logit flexible 1846 -2686.16 5386.32 8(1) 4.81e-07 1.0e+02 286s 286s Coefficients: 286s Estimate Std. Error z value Pr(>|z|) 286s PRODTest 1.293 0.119 10.87 <2e-16 *** 286s --- 286s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 286s 286s log-scale coefficients: 286s Estimate Std. Error z value Pr(>|z|) 286s PRODTest 0.14711 0.06514 2.258 0.0239 * 286s --- 286s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 286s 286s Threshold coefficients: 286s Estimate Std. Error z value 286s 1|2 -1.49041 0.09219 -16.166 286s 2|3 -0.45478 0.07189 -6.326 286s 3|4 -0.10961 0.07000 -1.566 286s 4|5 0.16104 0.07029 2.291 286s 5|6 0.88052 0.07959 11.064 286s (1 observation deleted due to missingness) 286s > c3a <- clm(ordered(SURENESS)~1, scale = ~PROD, data=soup) 286s > summary(c3a) 286s formula: ordered(SURENESS) ~ 1 286s scale: ~PROD 286s data: soup 286s 286s link threshold nobs logLik AIC niter max.grad cond.H 286s logit flexible 1846 -2769.95 5551.91 10(1) 9.20e-13 6.9e+01 286s 286s log-scale coefficients: 286s Estimate Std. Error z value Pr(>|z|) 286s PRODTest -0.15478 0.06683 -2.316 0.0206 * 286s --- 286s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 286s 286s Threshold coefficients: 286s Estimate Std. Error z value 286s 1|2 -1.85565 0.08111 -22.878 286s 2|3 -0.98626 0.05260 -18.752 286s 3|4 -0.70743 0.04676 -15.129 286s 4|5 -0.49243 0.04393 -11.208 286s 5|6 0.06504 0.04653 1.398 286s (1 observation deleted due to missingness) 286s > data(soup, package = "ordinal") 286s > soup$PROD[1] <- NA 286s > c1a <- clm(ordered(SURENESS)~PROD, data=soup) 286s > summary(c1a) 286s formula: ordered(SURENESS) ~ PROD 286s data: soup 286s 286s link threshold nobs logLik AIC niter max.grad cond.H 286s logit flexible 1846 -2689.15 5390.30 6(1) 2.85e-12 1.1e+02 286s 286s Coefficients: 286s Estimate Std. Error z value Pr(>|z|) 286s PRODTest 1.14774 0.08932 12.85 <2e-16 *** 286s --- 286s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 286s 286s Threshold coefficients: 286s Estimate Std. Error z value 286s 1|2 -1.40278 0.08171 -17.167 286s 2|3 -0.42216 0.06962 -6.064 286s 3|4 -0.09849 0.06882 -1.431 286s 4|5 0.15373 0.06898 2.229 286s 5|6 0.81613 0.07188 11.353 286s (1 observation deleted due to missingness) 286s > c2a <- clm(ordered(SURENESS)~PROD, scale = ~PROD, data=soup) 286s > summary(c2a) 286s formula: ordered(SURENESS) ~ PROD 286s scale: ~PROD 286s data: soup 286s 286s link threshold nobs logLik AIC niter max.grad cond.H 286s logit flexible 1846 -2686.51 5387.03 8(1) 5.41e-07 1.0e+02 286s 286s Coefficients: 286s Estimate Std. Error z value Pr(>|z|) 286s PRODTest 1.3009 0.1192 10.91 <2e-16 *** 286s --- 286s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 286s 286s log-scale coefficients: 286s Estimate Std. Error z value Pr(>|z|) 286s PRODTest 0.1494 0.0651 2.295 0.0217 * 286s --- 286s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 286s 286s Threshold coefficients: 286s Estimate Std. Error z value 286s 1|2 -1.48982 0.09217 -16.163 286s 2|3 -0.44981 0.07186 -6.260 286s 3|4 -0.10441 0.07000 -1.492 286s 4|5 0.16655 0.07031 2.369 286s 5|6 0.88740 0.07969 11.136 286s (1 observation deleted due to missingness) 286s > c3a <- clm(ordered(SURENESS)~1, scale = ~PROD, data=soup) 286s > summary(c3a) 286s formula: ordered(SURENESS) ~ 1 286s scale: ~PROD 286s data: soup 286s 286s link threshold nobs logLik AIC niter max.grad cond.H 286s logit flexible 1846 -2771.22 5554.43 10(1) 7.39e-13 6.9e+01 286s 286s log-scale coefficients: 286s Estimate Std. Error z value Pr(>|z|) 286s PRODTest -0.15330 0.06689 -2.292 0.0219 * 286s --- 286s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 286s 286s Threshold coefficients: 286s Estimate Std. Error z value 286s 1|2 -1.85700 0.08108 -22.903 286s 2|3 -0.98437 0.05252 -18.742 286s 3|4 -0.70562 0.04673 -15.100 286s 4|5 -0.49061 0.04395 -11.163 286s 5|6 0.06723 0.04667 1.441 286s (1 observation deleted due to missingness) 286s > soup$SURENESS[10] <- NA 286s > c1a <- clm(ordered(SURENESS)~PROD, data=soup) 286s > summary(c1a) 286s formula: ordered(SURENESS) ~ PROD 286s data: soup 286s 286s link threshold nobs logLik AIC niter max.grad cond.H 286s logit flexible 1845 -2687.53 5387.07 6(1) 2.82e-12 1.1e+02 286s 286s Coefficients: 286s Estimate Std. Error z value Pr(>|z|) 286s PRODTest 1.14581 0.08934 12.82 <2e-16 *** 286s --- 286s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 286s 286s Threshold coefficients: 286s Estimate Std. Error z value 286s 1|2 -1.40237 0.08175 -17.155 286s 2|3 -0.42475 0.06968 -6.096 286s 3|4 -0.10080 0.06887 -1.464 286s 4|5 0.15158 0.06902 2.196 286s 5|6 0.81421 0.07191 11.322 286s (2 observations deleted due to missingness) 286s > c2a <- clm(ordered(SURENESS)~PROD, scale = ~PROD, data=soup) 286s > summary(c2a) 286s formula: ordered(SURENESS) ~ PROD 286s scale: ~PROD 286s data: soup 286s 286s link threshold nobs logLik AIC niter max.grad cond.H 286s logit flexible 1845 -2684.93 5383.86 8(1) 5.12e-07 1.0e+02 286s 286s Coefficients: 286s Estimate Std. Error z value Pr(>|z|) 286s PRODTest 1.2979 0.1192 10.89 <2e-16 *** 286s --- 286s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 286s 286s log-scale coefficients: 286s Estimate Std. Error z value Pr(>|z|) 286s PRODTest 0.14853 0.06514 2.28 0.0226 * 286s --- 286s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 286s 286s Threshold coefficients: 286s Estimate Std. Error z value 286s 1|2 -1.48896 0.09222 -16.147 286s 2|3 -0.45241 0.07192 -6.290 286s 3|4 -0.10681 0.07004 -1.525 286s 4|5 0.16422 0.07034 2.335 286s 5|6 0.88500 0.07970 11.104 286s (2 observations deleted due to missingness) 286s > c3a <- clm(ordered(SURENESS)~1, scale = ~PROD, data=soup) 286s > summary(c3a) 286s formula: ordered(SURENESS) ~ 1 286s scale: ~PROD 286s data: soup 286s 286s link threshold nobs logLik AIC niter max.grad cond.H 286s logit flexible 1845 -2769.23 5550.46 10(1) 1.07e-12 6.9e+01 286s 286s log-scale coefficients: 286s Estimate Std. Error z value Pr(>|z|) 286s PRODTest -0.15410 0.06688 -2.304 0.0212 * 286s --- 286s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 286s 286s Threshold coefficients: 286s Estimate Std. Error z value 286s 1|2 -1.85563 0.08111 -22.877 286s 2|3 -0.98586 0.05259 -18.745 286s 3|4 -0.70689 0.04676 -15.116 286s 4|5 -0.49176 0.04395 -11.188 286s 5|6 0.06616 0.04661 1.419 286s (2 observations deleted due to missingness) 286s > 286s > ## na.actions: 286s > c4a <- clm(ordered(SURENESS)~PROD, scale = ~PROD, data=soup, 286s + na.action=na.omit) 286s > summary(c4a) 286s formula: ordered(SURENESS) ~ PROD 286s scale: ~PROD 286s data: soup 286s 286s link threshold nobs logLik AIC niter max.grad cond.H 286s logit flexible 1845 -2684.93 5383.86 8(1) 5.12e-07 1.0e+02 286s 286s Coefficients: 286s Estimate Std. Error z value Pr(>|z|) 286s PRODTest 1.2979 0.1192 10.89 <2e-16 *** 286s --- 286s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 286s 286s log-scale coefficients: 286s Estimate Std. Error z value Pr(>|z|) 286s PRODTest 0.14853 0.06514 2.28 0.0226 * 286s --- 286s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 286s 286s Threshold coefficients: 286s Estimate Std. Error z value 286s 1|2 -1.48896 0.09222 -16.147 286s 2|3 -0.45241 0.07192 -6.290 286s 3|4 -0.10681 0.07004 -1.525 286s 4|5 0.16422 0.07034 2.335 286s 5|6 0.88500 0.07970 11.104 286s (2 observations deleted due to missingness) 286s > 286s > tC1 <- try(clm(ordered(SURENESS)~PROD, scale = ~PROD, data=soup, 286s + na.action=na.fail), silent = TRUE) 286s > stopifnot(inherits(tC1, "try-error")) 286s > 286s > c4a <- clm(ordered(SURENESS)~PROD, scale = ~PROD, data=soup, 286s + na.action=na.exclude) 286s > summary(c4a) 286s formula: ordered(SURENESS) ~ PROD 286s scale: ~PROD 286s data: soup 286s 286s link threshold nobs logLik AIC niter max.grad cond.H 286s logit flexible 1845 -2684.93 5383.86 8(1) 5.12e-07 1.0e+02 286s 286s Coefficients: 286s Estimate Std. Error z value Pr(>|z|) 286s PRODTest 1.2979 0.1192 10.89 <2e-16 *** 286s --- 286s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 286s 286s log-scale coefficients: 286s Estimate Std. Error z value Pr(>|z|) 286s PRODTest 0.14853 0.06514 2.28 0.0226 * 286s --- 286s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 286s 286s Threshold coefficients: 286s Estimate Std. Error z value 286s 1|2 -1.48896 0.09222 -16.147 286s 2|3 -0.45241 0.07192 -6.290 286s 3|4 -0.10681 0.07004 -1.525 286s 4|5 0.16422 0.07034 2.335 286s 5|6 0.88500 0.07970 11.104 286s (2 observations deleted due to missingness) 286s > 286s > tC2 <- try(clm(ordered(SURENESS)~PROD, scale = ~PROD, data=soup, 286s + na.action=na.pass), silent = TRUE) 286s > stopifnot(inherits(tC2, "try-error")) 286s > 286s > ## Subset: 286s > data(soup, package="ordinal") 286s > c4a <- clm(ordered(SURENESS)~PROD, scale = ~PROD, data=soup, 286s + subset = 1:100) 286s > c4a <- clm(ordered(SURENESS)~1, scale = ~PROD, data=soup, 286s + subset = 1:100) 286s > c4a <- clm(ordered(SURENESS)~PROD, data=soup, 286s + subset = 1:100) 286s > c4a <- clm(ordered(SURENESS)~1, data=soup, 286s + subset = 1:100) 286s > 286s > ## Offset: 286s > data(soup, package = "ordinal") 286s > set.seed(290980) 286s > offs <- runif(nrow(soup)) 286s > c4a <- clm(ordered(SURENESS)~PROD + offset(offs), 286s + scale = ~PROD, data=soup, subset = 1:100) 286s > summary(c4a) 286s formula: ordered(SURENESS) ~ PROD + offset(offs) 286s scale: ~PROD 286s data: soup 286s subset: 1:100 286s 286s link threshold nobs logLik AIC niter max.grad cond.H 286s logit flexible 100 -139.58 293.17 9(2) 1.41e-07 2.0e+02 286s 286s Coefficients: 286s Estimate Std. Error z value Pr(>|z|) 286s PRODTest 2.4410 0.7091 3.443 0.000576 *** 286s --- 286s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 286s 286s log-scale coefficients: 286s Estimate Std. Error z value Pr(>|z|) 286s PRODTest 0.5105 0.2671 1.911 0.056 . 286s --- 286s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 286s 286s Threshold coefficients: 286s Estimate Std. Error z value 286s 1|2 -1.0470 0.4019 -2.605 286s 2|3 0.4213 0.3106 1.356 286s 3|4 0.5488 0.3106 1.767 286s 4|5 0.9217 0.3162 2.915 286s 5|6 2.0775 0.4062 5.114 286s > 286s > c4a <- clm(ordered(SURENESS)~PROD + offset(offs), 286s + scale = ~PROD + offset(offs), data=soup, subset = 1:100) 286s > summary(c4a) 286s formula: ordered(SURENESS) ~ PROD + offset(offs) 286s scale: ~PROD + offset(offs) 286s data: soup 286s subset: 1:100 286s 286s link threshold nobs logLik AIC niter max.grad cond.H 286s logit flexible 100 -143.12 300.24 9(2) 5.32e-09 1.9e+02 286s 286s Coefficients: 286s Estimate Std. Error z value Pr(>|z|) 286s PRODTest 3.344 1.020 3.277 0.00105 ** 286s --- 286s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 286s 286s log-scale coefficients: 286s Estimate Std. Error z value Pr(>|z|) 286s PRODTest 0.4412 0.2753 1.603 0.109 286s 286s Threshold coefficients: 286s Estimate Std. Error z value 286s 1|2 -2.09797 0.62565 -3.353 286s 2|3 0.06671 0.46874 0.142 286s 3|4 0.25559 0.46525 0.549 286s 4|5 0.80178 0.46743 1.715 286s 5|6 2.46041 0.59193 4.157 286s > 286s > off2 <- offs 286s > c4a <- clm(ordered(SURENESS)~PROD + offset(offs), 286s + scale = ~PROD + offset(off2), data=soup, subset = 1:100) 286s > summary(c4a) 286s formula: ordered(SURENESS) ~ PROD + offset(offs) 286s scale: ~PROD + offset(off2) 286s data: soup 286s subset: 1:100 286s 286s link threshold nobs logLik AIC niter max.grad cond.H 286s logit flexible 100 -143.12 300.24 9(2) 5.32e-09 1.9e+02 286s 286s Coefficients: 286s Estimate Std. Error z value Pr(>|z|) 286s PRODTest 3.344 1.020 3.277 0.00105 ** 286s --- 286s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 286s 286s log-scale coefficients: 286s Estimate Std. Error z value Pr(>|z|) 286s PRODTest 0.4412 0.2753 1.603 0.109 286s 286s Threshold coefficients: 286s Estimate Std. Error z value 286s 1|2 -2.09797 0.62565 -3.353 286s 2|3 0.06671 0.46874 0.142 286s 3|4 0.25559 0.46525 0.549 286s 4|5 0.80178 0.46743 1.715 286s 5|6 2.46041 0.59193 4.157 286s > 286s > c4a <- clm(ordered(SURENESS)~PROD, 286s + scale = ~PROD + offset(offs), data=soup, subset = 1:100) 286s > summary(c4a) 286s formula: ordered(SURENESS) ~ PROD 286s scale: ~PROD + offset(offs) 286s data: soup 286s subset: 1:100 286s 287s link threshold nobs logLik AIC niter max.grad cond.H 287s logit flexible 100 -142.15 298.31 10(2) 7.69e-10 1.8e+02 287s 287s Coefficients: 287s Estimate Std. Error z value Pr(>|z|) 287s PRODTest 3.283 1.016 3.231 0.00123 ** 287s --- 287s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 287s 287s log-scale coefficients: 287s Estimate Std. Error z value Pr(>|z|) 287s PRODTest 0.4263 0.2801 1.522 0.128 287s 287s Threshold coefficients: 287s Estimate Std. Error z value 287s 1|2 -2.4698 0.6308 -3.915 287s 2|3 -0.2916 0.4668 -0.625 287s 3|4 -0.1005 0.4628 -0.217 287s 4|5 0.4484 0.4638 0.967 287s 5|6 2.1036 0.5864 3.587 287s > 287s > ## data as matrix: 287s > dat26M <- as.matrix(dat26) 287s > m1 <- clm(sureness ~ prod, scale = ~prod, data = dat26, 287s + weights = wghts, link = "logit") 287s > summary(m1) 287s formula: sureness ~ prod 287s scale: ~prod 287s data: dat26 287s 287s link threshold nobs logLik AIC niter max.grad cond.H 287s logit flexible 1847 -2687.74 5389.49 8(1) 5.09e-07 1.0e+02 287s 287s Coefficients: 287s Estimate Std. Error z value Pr(>|z|) 287s prodTest 1.296 0.119 10.89 <2e-16 *** 287s --- 287s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 287s 287s log-scale coefficients: 287s Estimate Std. Error z value Pr(>|z|) 287s prodTest 0.1480 0.0651 2.273 0.023 * 287s --- 287s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 287s 287s Threshold coefficients: 287s Estimate Std. Error z value 287s 1|2 -1.49126 0.09215 -16.183 287s 2|3 -0.45218 0.07182 -6.296 287s 3|4 -0.10721 0.06995 -1.533 287s 4|5 0.16337 0.07025 2.325 287s 5|6 0.88291 0.07957 11.096 287s > 287s > ## data in enclosing environment: 287s > attach(soup) 287s > m1 <- clm(SURENESS ~ PROD, scale = ~PROD) 287s > summary(m1) 287s formula: SURENESS ~ PROD 287s scale: ~PROD 287s 287s link threshold nobs logLik AIC niter max.grad cond.H 287s logit flexible 1847 -2687.74 5389.49 8(1) 5.09e-07 1.0e+02 287s 287s Coefficients: 287s Estimate Std. Error z value Pr(>|z|) 287s PRODTest 1.296 0.119 10.89 <2e-16 *** 287s --- 287s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 287s 287s log-scale coefficients: 287s Estimate Std. Error z value Pr(>|z|) 287s PRODTest 0.1480 0.0651 2.273 0.023 * 287s --- 287s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 287s 287s Threshold coefficients: 287s Estimate Std. Error z value 287s 1|2 -1.49126 0.09215 -16.183 287s 2|3 -0.45218 0.07182 -6.296 287s 3|4 -0.10721 0.06995 -1.533 287s 4|5 0.16337 0.07025 2.325 287s 5|6 0.88291 0.07957 11.096 287s > detach(soup) 287s > 287s > ################################################################## 287s > ### Parameter estimates were not correct with large scale effects due 287s > ### to end cut-points being \pm 100. This is not enough for 287s > ### location-scale model, but seems to be for location only models. 287s > ### Bug report from Ioannis Kosmidis : 287s > 287s > ### A 2x3 contigency table that will give a large estimated value of 287s > ### zeta 287s > x <- rep(0:1, each = 3) 287s > response <- factor(rep(c(1, 2, 3), times = 2)) 287s > freq <- c(1, 11, 1, 13, 1, 14) 287s > totals <- rep(tapply(freq, x, sum), each = 3) 287s > Dat <- data.frame(response, x, freq) 287s > 287s > ### Fitting a cumulative link model with dispersion effects 287s > modClm <- clm(response ~ x, scale = ~ x, weights = freq, data = Dat, 287s + control = clm.control(grtol = 1e-10, convTol = 1e-10)) 287s > summary(modClm) 287s formula: response ~ x 287s scale: ~x 287s data: Dat 287s 287s link threshold nobs logLik AIC niter max.grad cond.H 287s logit flexible 41 -29.98 67.96 10(3) 9.23e-10 2.4e+02 287s 287s Coefficients: 287s Estimate Std. Error z value Pr(>|z|) 287s x 2.485 13.168 0.189 0.85 287s 287s log-scale coefficients: 287s Estimate Std. Error z value Pr(>|z|) 287s x 3.548 1.023 3.468 0.000524 *** 287s --- 287s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 287s 287s Threshold coefficients: 287s Estimate Std. Error z value 287s 1|2 -2.485 1.041 -2.387 287s 2|3 2.485 1.041 2.387 287s > ### The maximized log-likelihood for this saturated model should be 287s > sum(freq*log(freq/totals)) 287s [1] -29.97808 287s > # > sum(freq*log(freq/totals)) 287s > # [1] -29.97808 287s > ### but apparently clm fails to maximixe the log-likelihood 287s > modClm$logLik 287s [1] -29.97808 287s > # > modClm$logLik 287s > # [1] -30.44452 287s > stopifnot(isTRUE(all.equal(sum(freq*log(freq/totals)), modClm$logLik))) 287s > 287s > ### The estimates reported by clm are 287s > coef(modClm) 287s 1|2 2|3 x x 287s -2.484907 2.484907 2.484907 3.547588 287s > coef.res <- structure(c(-2.48490664104217, 2.48490665578163, 287s + 2.48490659188594, 287s + 3.54758796387530), .Names = c("1|2", "2|3", 287s + "x", "x")) 287s > stopifnot(isTRUE(all.equal(coef.res, coef(modClm)))) 287s > # > modClm$coefficients 287s > # 1|2 2|3 x x 287s > # -2.297718 2.297038 1.239023 2.834285 287s > ### while they should be (from my own software) 287s > # 1|2 2|3 x disp.x 287s > #-2.484907 2.484907 2.484907 3.547588 287s > convergence(modClm) 287s nobs logLik niter max.grad cond.H logLik.Error 287s 41 -29.98 10(3) 9.23e-10 2.4e+02 <1e-10 287s 287s Estimate Std.Err Gradient Error Cor.Dec Sig.Dig 287s 1|2 -2.485 1.041 3.50e-10 5.32e-10 8 9 287s 2|3 2.485 1.041 -1.60e-10 -5.32e-10 8 9 287s x 2.485 13.168 -1.90e-10 -3.54e-08 7 8 287s x 3.548 1.023 -9.23e-10 -1.55e-09 8 9 287s 287s Eigen values of Hessian: 287s 1.374792 0.855786 0.785151 0.005766 287s 287s Convergence message from clm: 287s (0) successful convergence 287s In addition: Absolute and relative convergence criteria were met 287s 287s > 287s > ################################################################## 287s > 287s autopkgtest [19:28:12]: test run-unit-test: -----------------------] 288s autopkgtest [19:28:13]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 288s run-unit-test PASS 288s autopkgtest [19:28:13]: test pkg-r-autopkgtest: preparing testbed 485s autopkgtest [19:31:30]: testbed dpkg architecture: arm64 485s autopkgtest [19:31:30]: testbed apt version: 2.7.12 485s autopkgtest [19:31:30]: @@@@@@@@@@@@@@@@@@@@ test bed setup 485s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 486s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 486s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [474 kB] 486s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3657 kB] 486s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 486s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [646 kB] 486s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 486s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 486s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 486s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4013 kB] 486s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 486s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.5 kB] 486s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 488s Fetched 9065 kB in 2s (5323 kB/s) 488s Reading package lists... 491s Reading package lists... 492s Building dependency tree... 492s Reading state information... 492s Calculating upgrade... 492s The following packages will be REMOVED: 492s libglib2.0-0 libssl3 492s The following NEW packages will be installed: 492s libglib2.0-0t64 libssl3t64 xdg-user-dirs 492s The following packages have been kept back: 492s curl 492s The following packages will be upgraded: 492s gir1.2-glib-2.0 libglib2.0-data libtirpc-common openssl readline-common 492s ubuntu-minimal ubuntu-standard 492s 7 upgraded, 3 newly installed, 2 to remove and 1 not upgraded. 492s Need to get 4613 kB of archives. 492s After this operation, 211 kB of additional disk space will be used. 492s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gir1.2-glib-2.0 arm64 2.79.3-3ubuntu5 [182 kB] 493s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-0t64 arm64 2.79.3-3ubuntu5 [1527 kB] 493s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB] 493s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB] 493s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-data all 2.79.3-3ubuntu5 [46.6 kB] 493s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc-common all 1.3.4+ds-1.1 [8018 B] 493s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 readline-common all 8.2-3.1 [56.4 kB] 493s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-minimal arm64 1.536 [10.7 kB] 493s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-user-dirs arm64 0.18-1 [18.1 kB] 493s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-standard arm64 1.536 [10.7 kB] 494s Fetched 4613 kB in 1s (5645 kB/s) 494s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74758 files and directories currently installed.) 494s Preparing to unpack .../gir1.2-glib-2.0_2.79.3-3ubuntu5_arm64.deb ... 494s Unpacking gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 494s dpkg: libglib2.0-0:arm64: dependency problems, but removing anyway as you requested: 494s udisks2 depends on libglib2.0-0 (>= 2.77.0). 494s shared-mime-info depends on libglib2.0-0 (>= 2.75.3). 494s python3-gi depends on libglib2.0-0 (>= 2.77.0). 494s python3-dbus depends on libglib2.0-0 (>= 2.16.0). 494s netplan.io depends on libglib2.0-0 (>= 2.70.0). 494s netplan-generator depends on libglib2.0-0 (>= 2.70.0). 494s libxmlb2:arm64 depends on libglib2.0-0 (>= 2.54.0). 494s libvolume-key1:arm64 depends on libglib2.0-0 (>= 2.18.0). 494s libudisks2-0:arm64 depends on libglib2.0-0 (>= 2.75.3). 494s libqrtr-glib0:arm64 depends on libglib2.0-0 (>= 2.56). 494s libqmi-proxy depends on libglib2.0-0 (>= 2.30.0). 494s libqmi-glib5:arm64 depends on libglib2.0-0 (>= 2.54.0). 494s libpolkit-gobject-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 494s libpolkit-agent-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 494s libnetplan0:arm64 depends on libglib2.0-0 (>= 2.75.3). 494s libmm-glib0:arm64 depends on libglib2.0-0 (>= 2.62.0). 494s libmbim-proxy depends on libglib2.0-0 (>= 2.56). 494s libmbim-glib4:arm64 depends on libglib2.0-0 (>= 2.56). 494s libjson-glib-1.0-0:arm64 depends on libglib2.0-0 (>= 2.75.3). 494s libjcat1:arm64 depends on libglib2.0-0 (>= 2.75.3). 494s libgusb2:arm64 depends on libglib2.0-0 (>= 2.75.3). 494s libgudev-1.0-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 494s libgirepository-1.0-1:arm64 depends on libglib2.0-0 (>= 2.79.0). 494s libfwupd2:arm64 depends on libglib2.0-0 (>= 2.79.0). 494s libblockdev3:arm64 depends on libglib2.0-0 (>= 2.42.2). 494s libblockdev-utils3:arm64 depends on libglib2.0-0 (>= 2.75.3). 494s libblockdev-swap3:arm64 depends on libglib2.0-0 (>= 2.42.2). 494s libblockdev-part3:arm64 depends on libglib2.0-0 (>= 2.42.2). 494s libblockdev-nvme3:arm64 depends on libglib2.0-0 (>= 2.42.2). 494s libblockdev-mdraid3:arm64 depends on libglib2.0-0 (>= 2.42.2). 494s libblockdev-loop3:arm64 depends on libglib2.0-0 (>= 2.42.2). 494s libblockdev-fs3:arm64 depends on libglib2.0-0 (>= 2.42.2). 494s libblockdev-crypto3:arm64 depends on libglib2.0-0 (>= 2.42.2). 494s fwupd depends on libglib2.0-0 (>= 2.79.0). 494s bolt depends on libglib2.0-0 (>= 2.56.0). 494s 494s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74758 files and directories currently installed.) 494s Removing libglib2.0-0:arm64 (2.79.2-1~ubuntu1) ... 494s Selecting previously unselected package libglib2.0-0t64:arm64. 494s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74733 files and directories currently installed.) 494s Preparing to unpack .../libglib2.0-0t64_2.79.3-3ubuntu5_arm64.deb ... 494s libglib2.0-0t64.preinst: Removing /var/lib/dpkg/info/libglib2.0-0:arm64.postrm to avoid loss of /usr/share/glib-2.0/schemas/gschemas.compiled... 494s removed '/var/lib/dpkg/info/libglib2.0-0:arm64.postrm' 494s Unpacking libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ... 494s Preparing to unpack .../openssl_3.0.13-0ubuntu1_arm64.deb ... 494s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ... 495s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 495s wget depends on libssl3 (>= 3.0.0). 495s u-boot-tools depends on libssl3 (>= 3.0.0). 495s tnftp depends on libssl3 (>= 3.0.0). 495s tcpdump depends on libssl3 (>= 3.0.0). 495s systemd-resolved depends on libssl3 (>= 3.0.0). 495s systemd depends on libssl3 (>= 3.0.0). 495s sudo depends on libssl3 (>= 3.0.0). 495s sbsigntool depends on libssl3 (>= 3.0.0). 495s rsync depends on libssl3 (>= 3.0.0). 495s python3-cryptography depends on libssl3 (>= 3.0.0). 495s openssh-server depends on libssl3 (>= 3.0.10). 495s openssh-client depends on libssl3 (>= 3.0.10). 495s mtd-utils depends on libssl3 (>= 3.0.0). 495s mokutil depends on libssl3 (>= 3.0.0). 495s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 495s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 495s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 495s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 495s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 495s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 495s libnvme1 depends on libssl3 (>= 3.0.0). 495s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 495s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 495s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 495s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 495s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 495s kmod depends on libssl3 (>= 3.0.0). 495s dhcpcd-base depends on libssl3 (>= 3.0.0). 495s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 495s 495s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74758 files and directories currently installed.) 495s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 495s Selecting previously unselected package libssl3t64:arm64. 495s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74747 files and directories currently installed.) 495s Preparing to unpack .../0-libssl3t64_3.0.13-0ubuntu1_arm64.deb ... 495s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ... 495s Preparing to unpack .../1-libglib2.0-data_2.79.3-3ubuntu5_all.deb ... 495s Unpacking libglib2.0-data (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 495s Preparing to unpack .../2-libtirpc-common_1.3.4+ds-1.1_all.deb ... 495s Unpacking libtirpc-common (1.3.4+ds-1.1) over (1.3.4+ds-1build1) ... 495s Preparing to unpack .../3-readline-common_8.2-3.1_all.deb ... 495s Unpacking readline-common (8.2-3.1) over (8.2-3) ... 495s Preparing to unpack .../4-ubuntu-minimal_1.536_arm64.deb ... 495s Unpacking ubuntu-minimal (1.536) over (1.535) ... 495s Selecting previously unselected package xdg-user-dirs. 495s Preparing to unpack .../5-xdg-user-dirs_0.18-1_arm64.deb ... 495s Unpacking xdg-user-dirs (0.18-1) ... 495s Preparing to unpack .../6-ubuntu-standard_1.536_arm64.deb ... 495s Unpacking ubuntu-standard (1.536) over (1.535) ... 495s Setting up ubuntu-minimal (1.536) ... 495s Setting up xdg-user-dirs (0.18-1) ... 495s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ... 495s Setting up libtirpc-common (1.3.4+ds-1.1) ... 495s Setting up ubuntu-standard (1.536) ... 495s Setting up libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ... 495s No schema files found: doing nothing. 495s Setting up libglib2.0-data (2.79.3-3ubuntu5) ... 495s Setting up gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) ... 495s Setting up openssl (3.0.13-0ubuntu1) ... 495s Setting up readline-common (8.2-3.1) ... 495s Processing triggers for man-db (2.12.0-3) ... 496s Processing triggers for install-info (7.1-3) ... 496s Processing triggers for libc-bin (2.39-0ubuntu2) ... 496s Reading package lists... 496s Building dependency tree... 496s Reading state information... 497s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 497s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 498s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 498s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 498s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 499s Reading package lists... 499s Reading package lists... 499s Building dependency tree... 499s Reading state information... 500s Calculating upgrade... 500s The following packages have been kept back: 500s curl 500s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 500s Reading package lists... 500s Building dependency tree... 500s Reading state information... 501s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 504s Reading package lists... 505s Building dependency tree... 505s Reading state information... 505s Starting pkgProblemResolver with broken count: 0 505s Starting 2 pkgProblemResolver with broken count: 0 505s Done 506s The following additional packages will be installed: 506s build-essential cpp cpp-13 cpp-13-aarch64-linux-gnu cpp-aarch64-linux-gnu 506s curl dctrl-tools fontconfig fontconfig-config fonts-dejavu-core 506s fonts-dejavu-mono g++ g++-13 g++-13-aarch64-linux-gnu g++-aarch64-linux-gnu 506s gcc gcc-13 gcc-13-aarch64-linux-gnu gcc-aarch64-linux-gnu gfortran 506s gfortran-13 gfortran-13-aarch64-linux-gnu gfortran-aarch64-linux-gnu 506s icu-devtools libasan8 libatomic1 libblas-dev libblas3 libbz2-dev 506s libc-dev-bin libc6-dev libcairo2 libcc1-0 libcrypt-dev libcurl4t64 506s libdatrie1 libdeflate0 libfontconfig1 libgcc-13-dev libgfortran-13-dev 506s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhwasan0 libice6 506s libicu-dev libisl23 libitm1 libjbig0 libjpeg-dev libjpeg-turbo8 506s libjpeg-turbo8-dev libjpeg8 libjpeg8-dev liblapack-dev liblapack3 liblerc4 506s liblsan0 liblzma-dev libmpc3 libncurses-dev libnlopt0 libnsl-dev 506s libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils 506s libpaper1 libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3 506s libpixman-1-0 libpkgconf3 libpng-dev libpng16-16t64 libpsl5t64 506s libreadline-dev libreadline8t64 libsharpyuv0 libsm6 libstdc++-13-dev 506s libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-dev libtirpc3t64 libtk8.6 506s libtsan2 libubsan1 libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 506s libxss1 libxt6t64 linux-libc-dev littler pkg-config pkg-r-autopkgtest 506s pkgconf pkgconf-bin r-base-core r-base-dev r-cran-boot r-cran-brio 506s r-cran-callr r-cran-cli r-cran-crayon r-cran-desc r-cran-diffobj 506s r-cran-digest r-cran-evaluate r-cran-fansi r-cran-fs r-cran-glue 506s r-cran-jsonlite r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-lme4 506s r-cran-magrittr r-cran-mass r-cran-matrix r-cran-minqa r-cran-nlme 506s r-cran-nloptr r-cran-nnet r-cran-numderiv r-cran-ordinal r-cran-pillar 506s r-cran-pkgbuild r-cran-pkgconfig r-cran-pkgkitten r-cran-pkgload 506s r-cran-praise r-cran-processx r-cran-ps r-cran-r6 r-cran-rcpp 506s r-cran-rcppeigen r-cran-rematch2 r-cran-rlang r-cran-rprojroot 506s r-cran-statmod r-cran-testthat r-cran-tibble r-cran-ucminf r-cran-utf8 506s r-cran-vctrs r-cran-waldo r-cran-withr r-cran-xtable rpcsvc-proto unzip 506s x11-common xdg-utils zip zlib1g-dev 506s Suggested packages: 506s cpp-doc gcc-13-locales cpp-13-doc debtags gcc-13-doc gcc-multilib 506s manpages-dev autoconf automake libtool flex bison gdb gcc-doc 506s gdb-aarch64-linux-gnu gfortran-doc gfortran-13-doc libcoarrays-dev 506s liblapack-doc glibc-doc icu-doc liblzma-doc ncurses-doc readline-doc 506s libstdc++-13-doc tcl8.6 tk8.6 elpa-ess r-doc-info | r-doc-pdf r-mathlib 506s r-base-html texlive-base texlive-latex-base texlive-plain-generic 506s texlive-fonts-recommended texlive-fonts-extra texlive-extra-utils 506s texlive-latex-recommended texlive-latex-extra texinfo r-cran-covr 506s r-cran-spelling r-cran-rstudioapi r-cran-knitr r-cran-rmarkdown 506s r-cran-getopt r-cran-bit64 r-cran-dbi r-cran-dplyr r-cran-formattable 506s r-cran-ggplot2 r-cran-nanotime r-cran-palmerpenguins r-cran-scales 506s r-cran-stringi r-cran-survival r-cran-units r-cran-vdiffr r-cran-inline 506s r-cran-bench r-cran-blob r-cran-here r-cran-hms r-cran-htmltools 506s r-cran-purrr r-cran-tidyr r-cran-plm r-cran-zoo 506s Recommended packages: 506s bzip2-doc manpages manpages-dev libc-devtools libpng-tools r-recommended 506s r-doc-html r-cran-covr r-cran-cliapp r-cran-mockery r-cran-htmltools 506s r-cran-htmlwidgets r-cran-knitr r-cran-rmarkdown r-cran-rstudioapi 506s r-cran-whoami r-cran-gh r-cran-spelling r-cran-ggplot2 r-cran-unitizer 506s r-cran-dbi r-cran-dplyr r-cran-rsqlite r-cran-httr r-cran-r.rsp r-cran-sf 506s r-cran-lintr r-cran-tidyverse r-cran-lubridate r-cran-cpp11 r-cran-bitops 506s r-cran-mathjaxr r-cran-mockr r-cran-remotes r-cran-codetools r-cran-curl 506s r-cran-webfakes r-cran-pingr r-cran-usethis r-cran-shiny r-cran-xml2 506s r-cran-data.table r-cran-formattable r-cran-bit64 r-cran-generics 506s r-cran-pkgdown r-cran-zeallot libfile-mimeinfo-perl libnet-dbus-perl 506s libx11-protocol-perl x11-utils x11-xserver-utils 506s The following packages will be REMOVED: 506s libcurl4 libpng16-16 libpsl5 libreadline8 libtirpc3 506s The following NEW packages will be installed: 506s autopkgtest-satdep build-essential cpp cpp-13 cpp-13-aarch64-linux-gnu 506s cpp-aarch64-linux-gnu dctrl-tools fontconfig fontconfig-config 506s fonts-dejavu-core fonts-dejavu-mono g++ g++-13 g++-13-aarch64-linux-gnu 506s g++-aarch64-linux-gnu gcc gcc-13 gcc-13-aarch64-linux-gnu 506s gcc-aarch64-linux-gnu gfortran gfortran-13 gfortran-13-aarch64-linux-gnu 506s gfortran-aarch64-linux-gnu icu-devtools libasan8 libatomic1 libblas-dev 506s libblas3 libbz2-dev libc-dev-bin libc6-dev libcairo2 libcc1-0 libcrypt-dev 506s libcurl4t64 libdatrie1 libdeflate0 libfontconfig1 libgcc-13-dev 506s libgfortran-13-dev libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b 506s libhwasan0 libice6 libicu-dev libisl23 libitm1 libjbig0 libjpeg-dev 506s libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev liblapack-dev 506s liblapack3 liblerc4 liblsan0 liblzma-dev libmpc3 libncurses-dev libnlopt0 506s libnsl-dev libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 506s libpaper-utils libpaper1 libpcre2-16-0 libpcre2-32-0 libpcre2-dev 506s libpcre2-posix3 libpixman-1-0 libpkgconf3 libpng-dev libpng16-16t64 506s libpsl5t64 libreadline-dev libreadline8t64 libsharpyuv0 libsm6 506s libstdc++-13-dev libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-dev 506s libtirpc3t64 libtk8.6 libtsan2 libubsan1 libwebp7 libxcb-render0 libxcb-shm0 506s libxft2 libxrender1 libxss1 libxt6t64 linux-libc-dev littler pkg-config 506s pkg-r-autopkgtest pkgconf pkgconf-bin r-base-core r-base-dev r-cran-boot 506s r-cran-brio r-cran-callr r-cran-cli r-cran-crayon r-cran-desc r-cran-diffobj 506s r-cran-digest r-cran-evaluate r-cran-fansi r-cran-fs r-cran-glue 506s r-cran-jsonlite r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-lme4 506s r-cran-magrittr r-cran-mass r-cran-matrix r-cran-minqa r-cran-nlme 506s r-cran-nloptr r-cran-nnet r-cran-numderiv r-cran-ordinal r-cran-pillar 506s r-cran-pkgbuild r-cran-pkgconfig r-cran-pkgkitten r-cran-pkgload 506s r-cran-praise r-cran-processx r-cran-ps r-cran-r6 r-cran-rcpp 506s r-cran-rcppeigen r-cran-rematch2 r-cran-rlang r-cran-rprojroot 506s r-cran-statmod r-cran-testthat r-cran-tibble r-cran-ucminf r-cran-utf8 506s r-cran-vctrs r-cran-waldo r-cran-withr r-cran-xtable rpcsvc-proto unzip 506s x11-common xdg-utils zip zlib1g-dev 506s The following packages will be upgraded: 506s curl 506s 1 upgraded, 162 newly installed, 5 to remove and 0 not upgraded. 506s Need to get 163 MB/163 MB of archives. 506s After this operation, 482 MB of additional disk space will be used. 506s Get:1 /tmp/autopkgtest.7IB1w2/2-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [740 B] 506s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpsl5t64 arm64 0.21.2-1.1 [57.4 kB] 506s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 curl arm64 8.5.0-2ubuntu7 [222 kB] 506s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcurl4t64 arm64 8.5.0-2ubuntu7 [332 kB] 506s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpng16-16t64 arm64 1.6.43-3 [185 kB] 506s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libreadline8t64 arm64 8.2-3.1 [153 kB] 506s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.1 [83.5 kB] 506s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libc-dev-bin arm64 2.39-0ubuntu2 [19.7 kB] 506s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 linux-libc-dev arm64 6.8.0-11.11 [1569 kB] 507s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libcrypt-dev arm64 1:4.4.36-4 [136 kB] 507s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc-dev arm64 1.3.4+ds-1.1 [201 kB] 507s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libnsl-dev arm64 1.3.0-3 [71.9 kB] 507s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 rpcsvc-proto arm64 1.4.2-0ubuntu6 [65.4 kB] 507s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libc6-dev arm64 2.39-0ubuntu2 [1596 kB] 507s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libisl23 arm64 0.26-3 [713 kB] 507s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libmpc3 arm64 1.3.1-1 [55.3 kB] 507s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [10.3 MB] 507s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13 arm64 13.2.0-17ubuntu2 [1028 B] 507s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [5316 B] 507s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 cpp arm64 4:13.2.0-7ubuntu1 [22.4 kB] 507s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libcc1-0 arm64 14-20240303-1ubuntu1 [44.7 kB] 507s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 507s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libitm1 arm64 14-20240303-1ubuntu1 [27.7 kB] 507s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libatomic1 arm64 14-20240303-1ubuntu1 [11.4 kB] 507s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 libasan8 arm64 14-20240303-1ubuntu1 [2919 kB] 507s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 liblsan0 arm64 14-20240303-1ubuntu1 [1282 kB] 507s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libtsan2 arm64 14-20240303-1ubuntu1 [2687 kB] 507s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libubsan1 arm64 14-20240303-1ubuntu1 [1151 kB] 507s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 libhwasan0 arm64 14-20240303-1ubuntu1 [1597 kB] 507s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 libgcc-13-dev arm64 13.2.0-17ubuntu2 [2464 kB] 507s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [20.1 MB] 508s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13 arm64 13.2.0-17ubuntu2 [467 kB] 508s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [1198 B] 508s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 gcc arm64 4:13.2.0-7ubuntu1 [5018 B] 508s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libstdc++-13-dev arm64 13.2.0-17ubuntu2 [2322 kB] 508s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [11.7 MB] 508s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13 arm64 13.2.0-17ubuntu2 [14.4 kB] 508s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 g++-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [962 B] 508s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 g++ arm64 4:13.2.0-7ubuntu1 [1082 B] 508s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 build-essential arm64 12.10ubuntu1 [4932 B] 508s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 dctrl-tools arm64 2.24-3build2 [65.2 kB] 508s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 508s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 508s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 508s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 508s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig arm64 2.15.0-1ubuntu1 [190 kB] 508s Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 508s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran-13-dev arm64 13.2.0-17ubuntu2 [478 kB] 508s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [10.8 MB] 508s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran-13 arm64 13.2.0-17ubuntu2 [10.3 kB] 508s Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [1022 B] 508s Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran arm64 4:13.2.0-7ubuntu1 [1164 B] 508s Get:53 http://ftpmaster.internal/ubuntu noble/main arm64 icu-devtools arm64 74.2-1ubuntu1 [209 kB] 508s Get:54 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 508s Get:55 http://ftpmaster.internal/ubuntu noble/main arm64 libblas-dev arm64 3.12.0-3 [111 kB] 508s Get:56 http://ftpmaster.internal/ubuntu noble/main arm64 libbz2-dev arm64 1.0.8-5ubuntu1 [35.8 kB] 508s Get:57 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB] 508s Get:58 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB] 508s Get:59 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B] 508s Get:60 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] 508s Get:61 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB] 508s Get:62 http://ftpmaster.internal/ubuntu noble/main arm64 libdatrie1 arm64 0.2.13-3 [21.7 kB] 508s Get:63 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 508s Get:64 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 508s Get:65 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 508s Get:66 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 508s Get:67 http://ftpmaster.internal/ubuntu noble/main arm64 libice6 arm64 2:1.0.10-1build2 [41.7 kB] 508s Get:68 http://ftpmaster.internal/ubuntu noble/main arm64 libicu-dev arm64 74.2-1ubuntu1 [11.9 MB] 509s Get:69 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 509s Get:70 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8-dev arm64 2.1.5-2ubuntu1 [304 kB] 509s Get:71 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 509s Get:72 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8-dev arm64 8c-2ubuntu11 [1484 B] 509s Get:73 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-dev arm64 8c-2ubuntu11 [1482 B] 509s Get:74 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 509s Get:75 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack-dev arm64 3.12.0-3 [4293 kB] 509s Get:76 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] 509s Get:77 http://ftpmaster.internal/ubuntu noble/main arm64 libncurses-dev arm64 6.4+20240113-1ubuntu1 [385 kB] 509s Get:78 http://ftpmaster.internal/ubuntu noble/main arm64 libthai-data all 0.1.29-2 [158 kB] 509s Get:79 http://ftpmaster.internal/ubuntu noble/main arm64 libthai0 arm64 0.1.29-2 [18.1 kB] 509s Get:80 http://ftpmaster.internal/ubuntu noble/main arm64 libpango-1.0-0 arm64 1.51.0+ds-4 [226 kB] 509s Get:81 http://ftpmaster.internal/ubuntu noble/main arm64 libpangoft2-1.0-0 arm64 1.51.0+ds-4 [41.2 kB] 509s Get:82 http://ftpmaster.internal/ubuntu noble/main arm64 libpangocairo-1.0-0 arm64 1.51.0+ds-4 [27.6 kB] 509s Get:83 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper1 arm64 1.1.29 [13.1 kB] 509s Get:84 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper-utils arm64 1.1.29 [8480 B] 509s Get:85 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-16-0 arm64 10.42-4ubuntu1 [195 kB] 509s Get:86 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-32-0 arm64 10.42-4ubuntu1 [183 kB] 509s Get:87 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-posix3 arm64 10.42-4ubuntu1 [6654 B] 509s Get:88 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-dev arm64 10.42-4ubuntu1 [679 kB] 509s Get:89 http://ftpmaster.internal/ubuntu noble/main arm64 libpkgconf3 arm64 1.8.1-2 [31.2 kB] 509s Get:90 http://ftpmaster.internal/ubuntu noble/main arm64 zlib1g-dev arm64 1:1.3.dfsg-3ubuntu1 [895 kB] 509s Get:91 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpng-dev arm64 1.6.43-3 [267 kB] 509s Get:92 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libreadline-dev arm64 8.2-3.1 [177 kB] 509s Get:93 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB] 509s Get:94 http://ftpmaster.internal/ubuntu noble/main arm64 libsm6 arm64 2:1.2.3-1build2 [16.1 kB] 509s Get:95 http://ftpmaster.internal/ubuntu noble/main arm64 libtcl8.6 arm64 8.6.13+dfsg-2 [980 kB] 509s Get:96 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] 509s Get:97 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB] 509s Get:98 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB] 509s Get:99 http://ftpmaster.internal/ubuntu noble/main arm64 libxft2 arm64 2.3.6-1 [43.3 kB] 509s Get:100 http://ftpmaster.internal/ubuntu noble/main arm64 libxss1 arm64 1:1.2.3-1build2 [8252 B] 509s Get:101 http://ftpmaster.internal/ubuntu noble/main arm64 libtk8.6 arm64 8.6.13-2 [760 kB] 509s Get:102 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libxt6t64 arm64 1:1.2.1-1.2 [168 kB] 509s Get:103 http://ftpmaster.internal/ubuntu noble/main arm64 zip arm64 3.0-13 [172 kB] 510s Get:104 http://ftpmaster.internal/ubuntu noble/main arm64 unzip arm64 6.0-28ubuntu3 [171 kB] 510s Get:105 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 510s Get:106 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 r-base-core arm64 4.3.3-2build1 [26.8 MB] 510s Get:107 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-littler arm64 0.3.19-1 [93.4 kB] 510s Get:108 http://ftpmaster.internal/ubuntu noble/universe arm64 littler all 0.3.19-1 [2472 B] 510s Get:109 http://ftpmaster.internal/ubuntu noble/main arm64 pkgconf-bin arm64 1.8.1-2 [20.4 kB] 510s Get:110 http://ftpmaster.internal/ubuntu noble/main arm64 pkgconf arm64 1.8.1-2 [16.7 kB] 510s Get:111 http://ftpmaster.internal/ubuntu noble/main arm64 pkg-config arm64 1.8.1-2 [7170 B] 510s Get:112 http://ftpmaster.internal/ubuntu noble/main arm64 liblzma-dev arm64 5.4.5-0.3 [209 kB] 510s Get:113 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 r-base-dev all 4.3.3-2build1 [4334 B] 510s Get:114 http://ftpmaster.internal/ubuntu noble/universe arm64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 510s Get:115 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-boot all 1.3-30-1 [619 kB] 510s Get:116 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-brio arm64 1.1.4-1 [37.7 kB] 510s Get:117 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-ps arm64 1.7.6-1 [313 kB] 510s Get:118 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-r6 all 2.5.1-1 [99.0 kB] 510s Get:119 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-processx arm64 3.8.3-1 [345 kB] 510s Get:120 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-callr all 3.7.3-2 [425 kB] 510s Get:121 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-cli arm64 3.6.2-1 [1377 kB] 510s Get:122 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-crayon all 1.5.2-1 [164 kB] 510s Get:123 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-desc all 1.4.3-1 [359 kB] 510s Get:124 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-diffobj arm64 0.3.5-1 [1116 kB] 511s Get:125 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-digest arm64 0.6.34-1 [182 kB] 511s Get:126 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-evaluate all 0.23-1 [90.2 kB] 511s Get:127 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-fansi arm64 1.0.5-1 [616 kB] 511s Get:128 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-fs arm64 1.6.3+dfsg-1 [227 kB] 511s Get:129 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-glue arm64 1.7.0-1 [154 kB] 511s Get:130 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-jsonlite arm64 1.8.8+dfsg-1 [441 kB] 511s Get:131 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lattice arm64 0.22-5-1 [1342 kB] 511s Get:132 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rlang arm64 1.1.3-1 [1663 kB] 511s Get:133 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] 511s Get:134 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-matrix arm64 1.6-5-1 [3776 kB] 511s Get:135 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-mass arm64 7.3-60.0.1-1 [1119 kB] 511s Get:136 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-nlme arm64 3.1.164-1 [2259 kB] 511s Get:137 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pkgkitten all 0.2.3-1 [25.1 kB] 511s Get:138 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rcpp arm64 1.0.12-1 [1971 kB] 511s Get:139 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-minqa arm64 1.2.6-1 [107 kB] 511s Get:140 http://ftpmaster.internal/ubuntu noble/universe arm64 libnlopt0 arm64 2.7.1-5build2 [174 kB] 511s Get:141 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-magrittr arm64 2.0.3-1 [154 kB] 511s Get:142 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pkgbuild all 1.4.3-1 [209 kB] 511s Get:143 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rprojroot all 2.0.4-1 [124 kB] 511s Get:144 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-withr all 2.5.0-1 [225 kB] 511s Get:145 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pkgload all 1.3.4-1 [207 kB] 511s Get:146 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-praise all 1.0.0-4build1 [20.3 kB] 511s Get:147 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-utf8 arm64 1.2.4-1 [140 kB] 511s Get:148 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-vctrs arm64 0.6.5-1 [1327 kB] 511s Get:149 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pillar all 1.9.0+dfsg-1 [464 kB] 511s Get:150 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB] 511s Get:151 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-tibble arm64 3.2.1+dfsg-2 [415 kB] 511s Get:152 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rematch2 all 2.1.2-2build1 [46.5 kB] 511s Get:153 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-waldo all 0.5.2-1build1 [120 kB] 511s Get:154 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-testthat arm64 3.2.1-1 [1678 kB] 511s Get:155 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-nloptr arm64 2.0.3-1 [375 kB] 511s Get:156 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rcppeigen arm64 0.3.3.9.4-1 [1180 kB] 511s Get:157 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-statmod arm64 1.5.0-1 [294 kB] 511s Get:158 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lme4 arm64 1.1-35.1-4 [4116 kB] 511s Get:159 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-nnet arm64 7.3-19-2 [111 kB] 511s Get:160 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-numderiv all 2016.8-1.1-3 [115 kB] 511s Get:161 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-ucminf arm64 1.2.1-1 [34.8 kB] 511s Get:162 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-ordinal arm64 2023.12-4-1 [1263 kB] 511s Get:163 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-xtable all 1:1.8-4-2 [689 kB] 512s Preconfiguring packages ... 513s Fetched 163 MB in 5s (30.4 MB/s) 513s dpkg: libpsl5:arm64: dependency problems, but removing anyway as you requested: 513s wget depends on libpsl5 (>= 0.16.0). 513s libcurl4:arm64 depends on libpsl5 (>= 0.16.0). 513s libcurl3-gnutls:arm64 depends on libpsl5 (>= 0.16.0). 513s 513s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74774 files and directories currently installed.) 513s Removing libpsl5:arm64 (0.21.2-1build1) ... 513s Selecting previously unselected package libpsl5t64:arm64. 513s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74769 files and directories currently installed.) 513s Preparing to unpack .../libpsl5t64_0.21.2-1.1_arm64.deb ... 513s Unpacking libpsl5t64:arm64 (0.21.2-1.1) ... 513s Preparing to unpack .../curl_8.5.0-2ubuntu7_arm64.deb ... 513s Unpacking curl (8.5.0-2ubuntu7) over (8.5.0-2ubuntu2) ... 513s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74775 files and directories currently installed.) 513s Removing libcurl4:arm64 (8.5.0-2ubuntu2) ... 513s Selecting previously unselected package libcurl4t64:arm64. 513s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74770 files and directories currently installed.) 513s Preparing to unpack .../libcurl4t64_8.5.0-2ubuntu7_arm64.deb ... 513s Unpacking libcurl4t64:arm64 (8.5.0-2ubuntu7) ... 513s dpkg: libpng16-16:arm64: dependency problems, but removing anyway as you requested: 513s libplymouth5:arm64 depends on libpng16-16 (>= 1.6.2). 513s libfreetype6:arm64 depends on libpng16-16 (>= 1.6.2-1). 513s 513s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74776 files and directories currently installed.) 513s Removing libpng16-16:arm64 (1.6.43-1) ... 513s Selecting previously unselected package libpng16-16t64:arm64. 513s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74766 files and directories currently installed.) 513s Preparing to unpack .../libpng16-16t64_1.6.43-3_arm64.deb ... 513s Unpacking libpng16-16t64:arm64 (1.6.43-3) ... 513s dpkg: libreadline8:arm64: dependency problems, but removing anyway as you requested: 513s parted depends on libreadline8 (>= 6.0). 513s libpython3.12-stdlib:arm64 depends on libreadline8 (>= 7.0~beta). 513s gpgsm depends on libreadline8 (>= 6.0). 513s gpgconf depends on libreadline8 (>= 6.0). 513s gpg depends on libreadline8 (>= 6.0). 513s gawk depends on libreadline8 (>= 6.0). 513s fdisk depends on libreadline8 (>= 6.0). 513s 513s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74777 files and directories currently installed.) 513s Removing libreadline8:arm64 (8.2-3) ... 513s Selecting previously unselected package libreadline8t64:arm64. 513s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74765 files and directories currently installed.) 513s Preparing to unpack .../libreadline8t64_8.2-3.1_arm64.deb ... 513s Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' 513s Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' 513s Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' 513s Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' 513s Unpacking libreadline8t64:arm64 (8.2-3.1) ... 513s dpkg: libtirpc3:arm64: dependency problems, but removing anyway as you requested: 513s lsof depends on libtirpc3 (>= 1.0.2). 513s libpython3.12-stdlib:arm64 depends on libtirpc3 (>= 1.0.2). 513s libnss-nisplus:arm64 depends on libtirpc3 (>= 1.0.2). 513s libnsl2:arm64 depends on libtirpc3 (>= 1.0.2). 513s iproute2 depends on libtirpc3 (>= 1.0.2). 513s 513s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74785 files and directories currently installed.) 513s Removing libtirpc3:arm64 (1.3.4+ds-1build1) ... 513s Selecting previously unselected package libtirpc3t64:arm64. 513s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74779 files and directories currently installed.) 513s Preparing to unpack .../000-libtirpc3t64_1.3.4+ds-1.1_arm64.deb ... 513s Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' 513s Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' 513s Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.1) ... 513s Selecting previously unselected package libc-dev-bin. 513s Preparing to unpack .../001-libc-dev-bin_2.39-0ubuntu2_arm64.deb ... 513s Unpacking libc-dev-bin (2.39-0ubuntu2) ... 513s Selecting previously unselected package linux-libc-dev:arm64. 514s Preparing to unpack .../002-linux-libc-dev_6.8.0-11.11_arm64.deb ... 514s Unpacking linux-libc-dev:arm64 (6.8.0-11.11) ... 514s Selecting previously unselected package libcrypt-dev:arm64. 514s Preparing to unpack .../003-libcrypt-dev_1%3a4.4.36-4_arm64.deb ... 514s Unpacking libcrypt-dev:arm64 (1:4.4.36-4) ... 514s Selecting previously unselected package libtirpc-dev:arm64. 514s Preparing to unpack .../004-libtirpc-dev_1.3.4+ds-1.1_arm64.deb ... 514s Unpacking libtirpc-dev:arm64 (1.3.4+ds-1.1) ... 514s Selecting previously unselected package libnsl-dev:arm64. 514s Preparing to unpack .../005-libnsl-dev_1.3.0-3_arm64.deb ... 514s Unpacking libnsl-dev:arm64 (1.3.0-3) ... 514s Selecting previously unselected package rpcsvc-proto. 514s Preparing to unpack .../006-rpcsvc-proto_1.4.2-0ubuntu6_arm64.deb ... 514s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ... 514s Selecting previously unselected package libc6-dev:arm64. 514s Preparing to unpack .../007-libc6-dev_2.39-0ubuntu2_arm64.deb ... 514s Unpacking libc6-dev:arm64 (2.39-0ubuntu2) ... 514s Selecting previously unselected package libisl23:arm64. 514s Preparing to unpack .../008-libisl23_0.26-3_arm64.deb ... 514s Unpacking libisl23:arm64 (0.26-3) ... 514s Selecting previously unselected package libmpc3:arm64. 514s Preparing to unpack .../009-libmpc3_1.3.1-1_arm64.deb ... 514s Unpacking libmpc3:arm64 (1.3.1-1) ... 514s Selecting previously unselected package cpp-13-aarch64-linux-gnu. 514s Preparing to unpack .../010-cpp-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 514s Unpacking cpp-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 514s Selecting previously unselected package cpp-13. 514s Preparing to unpack .../011-cpp-13_13.2.0-17ubuntu2_arm64.deb ... 514s Unpacking cpp-13 (13.2.0-17ubuntu2) ... 514s Selecting previously unselected package cpp-aarch64-linux-gnu. 514s Preparing to unpack .../012-cpp-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 514s Unpacking cpp-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 514s Selecting previously unselected package cpp. 514s Preparing to unpack .../013-cpp_4%3a13.2.0-7ubuntu1_arm64.deb ... 514s Unpacking cpp (4:13.2.0-7ubuntu1) ... 514s Selecting previously unselected package libcc1-0:arm64. 514s Preparing to unpack .../014-libcc1-0_14-20240303-1ubuntu1_arm64.deb ... 514s Unpacking libcc1-0:arm64 (14-20240303-1ubuntu1) ... 514s Selecting previously unselected package libgomp1:arm64. 514s Preparing to unpack .../015-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 514s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 514s Selecting previously unselected package libitm1:arm64. 514s Preparing to unpack .../016-libitm1_14-20240303-1ubuntu1_arm64.deb ... 514s Unpacking libitm1:arm64 (14-20240303-1ubuntu1) ... 514s Selecting previously unselected package libatomic1:arm64. 514s Preparing to unpack .../017-libatomic1_14-20240303-1ubuntu1_arm64.deb ... 514s Unpacking libatomic1:arm64 (14-20240303-1ubuntu1) ... 514s Selecting previously unselected package libasan8:arm64. 514s Preparing to unpack .../018-libasan8_14-20240303-1ubuntu1_arm64.deb ... 514s Unpacking libasan8:arm64 (14-20240303-1ubuntu1) ... 515s Selecting previously unselected package liblsan0:arm64. 515s Preparing to unpack .../019-liblsan0_14-20240303-1ubuntu1_arm64.deb ... 515s Unpacking liblsan0:arm64 (14-20240303-1ubuntu1) ... 515s Selecting previously unselected package libtsan2:arm64. 515s Preparing to unpack .../020-libtsan2_14-20240303-1ubuntu1_arm64.deb ... 515s Unpacking libtsan2:arm64 (14-20240303-1ubuntu1) ... 515s Selecting previously unselected package libubsan1:arm64. 515s Preparing to unpack .../021-libubsan1_14-20240303-1ubuntu1_arm64.deb ... 515s Unpacking libubsan1:arm64 (14-20240303-1ubuntu1) ... 515s Selecting previously unselected package libhwasan0:arm64. 515s Preparing to unpack .../022-libhwasan0_14-20240303-1ubuntu1_arm64.deb ... 515s Unpacking libhwasan0:arm64 (14-20240303-1ubuntu1) ... 515s Selecting previously unselected package libgcc-13-dev:arm64. 515s Preparing to unpack .../023-libgcc-13-dev_13.2.0-17ubuntu2_arm64.deb ... 515s Unpacking libgcc-13-dev:arm64 (13.2.0-17ubuntu2) ... 515s Selecting previously unselected package gcc-13-aarch64-linux-gnu. 515s Preparing to unpack .../024-gcc-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 515s Unpacking gcc-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 516s Selecting previously unselected package gcc-13. 516s Preparing to unpack .../025-gcc-13_13.2.0-17ubuntu2_arm64.deb ... 516s Unpacking gcc-13 (13.2.0-17ubuntu2) ... 516s Selecting previously unselected package gcc-aarch64-linux-gnu. 516s Preparing to unpack .../026-gcc-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 516s Unpacking gcc-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 516s Selecting previously unselected package gcc. 516s Preparing to unpack .../027-gcc_4%3a13.2.0-7ubuntu1_arm64.deb ... 516s Unpacking gcc (4:13.2.0-7ubuntu1) ... 516s Selecting previously unselected package libstdc++-13-dev:arm64. 516s Preparing to unpack .../028-libstdc++-13-dev_13.2.0-17ubuntu2_arm64.deb ... 516s Unpacking libstdc++-13-dev:arm64 (13.2.0-17ubuntu2) ... 516s Selecting previously unselected package g++-13-aarch64-linux-gnu. 516s Preparing to unpack .../029-g++-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 516s Unpacking g++-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 516s Selecting previously unselected package g++-13. 516s Preparing to unpack .../030-g++-13_13.2.0-17ubuntu2_arm64.deb ... 516s Unpacking g++-13 (13.2.0-17ubuntu2) ... 516s Selecting previously unselected package g++-aarch64-linux-gnu. 516s Preparing to unpack .../031-g++-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 516s Unpacking g++-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 516s Selecting previously unselected package g++. 516s Preparing to unpack .../032-g++_4%3a13.2.0-7ubuntu1_arm64.deb ... 516s Unpacking g++ (4:13.2.0-7ubuntu1) ... 516s Selecting previously unselected package build-essential. 516s Preparing to unpack .../033-build-essential_12.10ubuntu1_arm64.deb ... 516s Unpacking build-essential (12.10ubuntu1) ... 516s Selecting previously unselected package dctrl-tools. 516s Preparing to unpack .../034-dctrl-tools_2.24-3build2_arm64.deb ... 516s Unpacking dctrl-tools (2.24-3build2) ... 516s Selecting previously unselected package fonts-dejavu-mono. 516s Preparing to unpack .../035-fonts-dejavu-mono_2.37-8_all.deb ... 516s Unpacking fonts-dejavu-mono (2.37-8) ... 516s Selecting previously unselected package fonts-dejavu-core. 516s Preparing to unpack .../036-fonts-dejavu-core_2.37-8_all.deb ... 516s Unpacking fonts-dejavu-core (2.37-8) ... 516s Selecting previously unselected package fontconfig-config. 517s Preparing to unpack .../037-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 517s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 517s Selecting previously unselected package libfontconfig1:arm64. 517s Preparing to unpack .../038-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 517s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 517s Selecting previously unselected package fontconfig. 517s Preparing to unpack .../039-fontconfig_2.15.0-1ubuntu1_arm64.deb ... 517s Unpacking fontconfig (2.15.0-1ubuntu1) ... 517s Selecting previously unselected package libgfortran5:arm64. 517s Preparing to unpack .../040-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 517s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 517s Selecting previously unselected package libgfortran-13-dev:arm64. 517s Preparing to unpack .../041-libgfortran-13-dev_13.2.0-17ubuntu2_arm64.deb ... 517s Unpacking libgfortran-13-dev:arm64 (13.2.0-17ubuntu2) ... 517s Selecting previously unselected package gfortran-13-aarch64-linux-gnu. 517s Preparing to unpack .../042-gfortran-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 517s Unpacking gfortran-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 517s Selecting previously unselected package gfortran-13. 517s Preparing to unpack .../043-gfortran-13_13.2.0-17ubuntu2_arm64.deb ... 517s Unpacking gfortran-13 (13.2.0-17ubuntu2) ... 517s Selecting previously unselected package gfortran-aarch64-linux-gnu. 517s Preparing to unpack .../044-gfortran-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 517s Unpacking gfortran-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 517s Selecting previously unselected package gfortran. 517s Preparing to unpack .../045-gfortran_4%3a13.2.0-7ubuntu1_arm64.deb ... 517s Unpacking gfortran (4:13.2.0-7ubuntu1) ... 517s Selecting previously unselected package icu-devtools. 517s Preparing to unpack .../046-icu-devtools_74.2-1ubuntu1_arm64.deb ... 517s Unpacking icu-devtools (74.2-1ubuntu1) ... 517s Selecting previously unselected package libblas3:arm64. 517s Preparing to unpack .../047-libblas3_3.12.0-3_arm64.deb ... 517s Unpacking libblas3:arm64 (3.12.0-3) ... 517s Selecting previously unselected package libblas-dev:arm64. 517s Preparing to unpack .../048-libblas-dev_3.12.0-3_arm64.deb ... 517s Unpacking libblas-dev:arm64 (3.12.0-3) ... 517s Selecting previously unselected package libbz2-dev:arm64. 517s Preparing to unpack .../049-libbz2-dev_1.0.8-5ubuntu1_arm64.deb ... 517s Unpacking libbz2-dev:arm64 (1.0.8-5ubuntu1) ... 517s Selecting previously unselected package libpixman-1-0:arm64. 517s Preparing to unpack .../050-libpixman-1-0_0.42.2-1_arm64.deb ... 517s Unpacking libpixman-1-0:arm64 (0.42.2-1) ... 517s Selecting previously unselected package libxcb-render0:arm64. 517s Preparing to unpack .../051-libxcb-render0_1.15-1_arm64.deb ... 517s Unpacking libxcb-render0:arm64 (1.15-1) ... 517s Selecting previously unselected package libxcb-shm0:arm64. 517s Preparing to unpack .../052-libxcb-shm0_1.15-1_arm64.deb ... 517s Unpacking libxcb-shm0:arm64 (1.15-1) ... 517s Selecting previously unselected package libxrender1:arm64. 517s Preparing to unpack .../053-libxrender1_1%3a0.9.10-1.1_arm64.deb ... 517s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ... 517s Selecting previously unselected package libcairo2:arm64. 517s Preparing to unpack .../054-libcairo2_1.18.0-1_arm64.deb ... 517s Unpacking libcairo2:arm64 (1.18.0-1) ... 517s Selecting previously unselected package libdatrie1:arm64. 517s Preparing to unpack .../055-libdatrie1_0.2.13-3_arm64.deb ... 517s Unpacking libdatrie1:arm64 (0.2.13-3) ... 517s Selecting previously unselected package libdeflate0:arm64. 517s Preparing to unpack .../056-libdeflate0_1.19-1_arm64.deb ... 517s Unpacking libdeflate0:arm64 (1.19-1) ... 518s Selecting previously unselected package libgraphite2-3:arm64. 518s Preparing to unpack .../057-libgraphite2-3_1.3.14-2_arm64.deb ... 518s Unpacking libgraphite2-3:arm64 (1.3.14-2) ... 518s Selecting previously unselected package libharfbuzz0b:arm64. 518s Preparing to unpack .../058-libharfbuzz0b_8.3.0-2_arm64.deb ... 518s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ... 518s Selecting previously unselected package x11-common. 518s Preparing to unpack .../059-x11-common_1%3a7.7+23ubuntu2_all.deb ... 518s Unpacking x11-common (1:7.7+23ubuntu2) ... 518s Selecting previously unselected package libice6:arm64. 518s Preparing to unpack .../060-libice6_2%3a1.0.10-1build2_arm64.deb ... 518s Unpacking libice6:arm64 (2:1.0.10-1build2) ... 518s Selecting previously unselected package libicu-dev:arm64. 518s Preparing to unpack .../061-libicu-dev_74.2-1ubuntu1_arm64.deb ... 518s Unpacking libicu-dev:arm64 (74.2-1ubuntu1) ... 518s Selecting previously unselected package libjpeg-turbo8:arm64. 518s Preparing to unpack .../062-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ... 518s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 518s Selecting previously unselected package libjpeg-turbo8-dev:arm64. 518s Preparing to unpack .../063-libjpeg-turbo8-dev_2.1.5-2ubuntu1_arm64.deb ... 518s Unpacking libjpeg-turbo8-dev:arm64 (2.1.5-2ubuntu1) ... 518s Selecting previously unselected package libjpeg8:arm64. 518s Preparing to unpack .../064-libjpeg8_8c-2ubuntu11_arm64.deb ... 518s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 518s Selecting previously unselected package libjpeg8-dev:arm64. 518s Preparing to unpack .../065-libjpeg8-dev_8c-2ubuntu11_arm64.deb ... 518s Unpacking libjpeg8-dev:arm64 (8c-2ubuntu11) ... 518s Selecting previously unselected package libjpeg-dev:arm64. 518s Preparing to unpack .../066-libjpeg-dev_8c-2ubuntu11_arm64.deb ... 518s Unpacking libjpeg-dev:arm64 (8c-2ubuntu11) ... 518s Selecting previously unselected package liblapack3:arm64. 518s Preparing to unpack .../067-liblapack3_3.12.0-3_arm64.deb ... 518s Unpacking liblapack3:arm64 (3.12.0-3) ... 518s Selecting previously unselected package liblapack-dev:arm64. 518s Preparing to unpack .../068-liblapack-dev_3.12.0-3_arm64.deb ... 518s Unpacking liblapack-dev:arm64 (3.12.0-3) ... 518s Selecting previously unselected package liblerc4:arm64. 518s Preparing to unpack .../069-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ... 518s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 518s Selecting previously unselected package libncurses-dev:arm64. 518s Preparing to unpack .../070-libncurses-dev_6.4+20240113-1ubuntu1_arm64.deb ... 518s Unpacking libncurses-dev:arm64 (6.4+20240113-1ubuntu1) ... 519s Selecting previously unselected package libthai-data. 519s Preparing to unpack .../071-libthai-data_0.1.29-2_all.deb ... 519s Unpacking libthai-data (0.1.29-2) ... 519s Selecting previously unselected package libthai0:arm64. 519s Preparing to unpack .../072-libthai0_0.1.29-2_arm64.deb ... 519s Unpacking libthai0:arm64 (0.1.29-2) ... 519s Selecting previously unselected package libpango-1.0-0:arm64. 519s Preparing to unpack .../073-libpango-1.0-0_1.51.0+ds-4_arm64.deb ... 519s Unpacking libpango-1.0-0:arm64 (1.51.0+ds-4) ... 519s Selecting previously unselected package libpangoft2-1.0-0:arm64. 519s Preparing to unpack .../074-libpangoft2-1.0-0_1.51.0+ds-4_arm64.deb ... 519s Unpacking libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ... 519s Selecting previously unselected package libpangocairo-1.0-0:arm64. 519s Preparing to unpack .../075-libpangocairo-1.0-0_1.51.0+ds-4_arm64.deb ... 519s Unpacking libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ... 519s Selecting previously unselected package libpaper1:arm64. 519s Preparing to unpack .../076-libpaper1_1.1.29_arm64.deb ... 519s Unpacking libpaper1:arm64 (1.1.29) ... 519s Selecting previously unselected package libpaper-utils. 519s Preparing to unpack .../077-libpaper-utils_1.1.29_arm64.deb ... 519s Unpacking libpaper-utils (1.1.29) ... 519s Selecting previously unselected package libpcre2-16-0:arm64. 519s Preparing to unpack .../078-libpcre2-16-0_10.42-4ubuntu1_arm64.deb ... 519s Unpacking libpcre2-16-0:arm64 (10.42-4ubuntu1) ... 519s Selecting previously unselected package libpcre2-32-0:arm64. 519s Preparing to unpack .../079-libpcre2-32-0_10.42-4ubuntu1_arm64.deb ... 519s Unpacking libpcre2-32-0:arm64 (10.42-4ubuntu1) ... 519s Selecting previously unselected package libpcre2-posix3:arm64. 519s Preparing to unpack .../080-libpcre2-posix3_10.42-4ubuntu1_arm64.deb ... 519s Unpacking libpcre2-posix3:arm64 (10.42-4ubuntu1) ... 519s Selecting previously unselected package libpcre2-dev:arm64. 519s Preparing to unpack .../081-libpcre2-dev_10.42-4ubuntu1_arm64.deb ... 519s Unpacking libpcre2-dev:arm64 (10.42-4ubuntu1) ... 519s Selecting previously unselected package libpkgconf3:arm64. 519s Preparing to unpack .../082-libpkgconf3_1.8.1-2_arm64.deb ... 519s Unpacking libpkgconf3:arm64 (1.8.1-2) ... 519s Selecting previously unselected package zlib1g-dev:arm64. 519s Preparing to unpack .../083-zlib1g-dev_1%3a1.3.dfsg-3ubuntu1_arm64.deb ... 519s Unpacking zlib1g-dev:arm64 (1:1.3.dfsg-3ubuntu1) ... 519s Selecting previously unselected package libpng-dev:arm64. 519s Preparing to unpack .../084-libpng-dev_1.6.43-3_arm64.deb ... 519s Unpacking libpng-dev:arm64 (1.6.43-3) ... 519s Selecting previously unselected package libreadline-dev:arm64. 519s Preparing to unpack .../085-libreadline-dev_8.2-3.1_arm64.deb ... 519s Unpacking libreadline-dev:arm64 (8.2-3.1) ... 519s Selecting previously unselected package libsharpyuv0:arm64. 519s Preparing to unpack .../086-libsharpyuv0_1.3.2-0.4_arm64.deb ... 519s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ... 519s Selecting previously unselected package libsm6:arm64. 519s Preparing to unpack .../087-libsm6_2%3a1.2.3-1build2_arm64.deb ... 519s Unpacking libsm6:arm64 (2:1.2.3-1build2) ... 519s Selecting previously unselected package libtcl8.6:arm64. 519s Preparing to unpack .../088-libtcl8.6_8.6.13+dfsg-2_arm64.deb ... 519s Unpacking libtcl8.6:arm64 (8.6.13+dfsg-2) ... 519s Selecting previously unselected package libjbig0:arm64. 519s Preparing to unpack .../089-libjbig0_2.1-6.1ubuntu1_arm64.deb ... 519s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ... 519s Selecting previously unselected package libwebp7:arm64. 520s Preparing to unpack .../090-libwebp7_1.3.2-0.4_arm64.deb ... 520s Unpacking libwebp7:arm64 (1.3.2-0.4) ... 520s Selecting previously unselected package libtiff6:arm64. 520s Preparing to unpack .../091-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ... 520s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 520s Selecting previously unselected package libxft2:arm64. 520s Preparing to unpack .../092-libxft2_2.3.6-1_arm64.deb ... 520s Unpacking libxft2:arm64 (2.3.6-1) ... 520s Selecting previously unselected package libxss1:arm64. 520s Preparing to unpack .../093-libxss1_1%3a1.2.3-1build2_arm64.deb ... 520s Unpacking libxss1:arm64 (1:1.2.3-1build2) ... 520s Selecting previously unselected package libtk8.6:arm64. 520s Preparing to unpack .../094-libtk8.6_8.6.13-2_arm64.deb ... 520s Unpacking libtk8.6:arm64 (8.6.13-2) ... 520s Selecting previously unselected package libxt6t64:arm64. 520s Preparing to unpack .../095-libxt6t64_1%3a1.2.1-1.2_arm64.deb ... 520s Unpacking libxt6t64:arm64 (1:1.2.1-1.2) ... 520s Selecting previously unselected package zip. 520s Preparing to unpack .../096-zip_3.0-13_arm64.deb ... 520s Unpacking zip (3.0-13) ... 520s Selecting previously unselected package unzip. 520s Preparing to unpack .../097-unzip_6.0-28ubuntu3_arm64.deb ... 520s Unpacking unzip (6.0-28ubuntu3) ... 520s Selecting previously unselected package xdg-utils. 520s Preparing to unpack .../098-xdg-utils_1.1.3-4.1ubuntu3_all.deb ... 520s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ... 520s Selecting previously unselected package r-base-core. 520s Preparing to unpack .../099-r-base-core_4.3.3-2build1_arm64.deb ... 520s Unpacking r-base-core (4.3.3-2build1) ... 520s Selecting previously unselected package r-cran-littler. 520s Preparing to unpack .../100-r-cran-littler_0.3.19-1_arm64.deb ... 520s Unpacking r-cran-littler (0.3.19-1) ... 520s Selecting previously unselected package littler. 520s Preparing to unpack .../101-littler_0.3.19-1_all.deb ... 520s Unpacking littler (0.3.19-1) ... 520s Selecting previously unselected package pkgconf-bin. 520s Preparing to unpack .../102-pkgconf-bin_1.8.1-2_arm64.deb ... 520s Unpacking pkgconf-bin (1.8.1-2) ... 520s Selecting previously unselected package pkgconf:arm64. 520s Preparing to unpack .../103-pkgconf_1.8.1-2_arm64.deb ... 520s Unpacking pkgconf:arm64 (1.8.1-2) ... 520s Selecting previously unselected package pkg-config:arm64. 520s Preparing to unpack .../104-pkg-config_1.8.1-2_arm64.deb ... 520s Unpacking pkg-config:arm64 (1.8.1-2) ... 520s Selecting previously unselected package liblzma-dev:arm64. 520s Preparing to unpack .../105-liblzma-dev_5.4.5-0.3_arm64.deb ... 520s Unpacking liblzma-dev:arm64 (5.4.5-0.3) ... 520s Selecting previously unselected package r-base-dev. 520s Preparing to unpack .../106-r-base-dev_4.3.3-2build1_all.deb ... 520s Unpacking r-base-dev (4.3.3-2build1) ... 520s Selecting previously unselected package pkg-r-autopkgtest. 520s Preparing to unpack .../107-pkg-r-autopkgtest_20231212ubuntu1_all.deb ... 520s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ... 520s Selecting previously unselected package r-cran-boot. 520s Preparing to unpack .../108-r-cran-boot_1.3-30-1_all.deb ... 520s Unpacking r-cran-boot (1.3-30-1) ... 521s Selecting previously unselected package r-cran-brio. 521s Preparing to unpack .../109-r-cran-brio_1.1.4-1_arm64.deb ... 521s Unpacking r-cran-brio (1.1.4-1) ... 521s Selecting previously unselected package r-cran-ps. 521s Preparing to unpack .../110-r-cran-ps_1.7.6-1_arm64.deb ... 521s Unpacking r-cran-ps (1.7.6-1) ... 521s Selecting previously unselected package r-cran-r6. 521s Preparing to unpack .../111-r-cran-r6_2.5.1-1_all.deb ... 521s Unpacking r-cran-r6 (2.5.1-1) ... 521s Selecting previously unselected package r-cran-processx. 521s Preparing to unpack .../112-r-cran-processx_3.8.3-1_arm64.deb ... 521s Unpacking r-cran-processx (3.8.3-1) ... 521s Selecting previously unselected package r-cran-callr. 521s Preparing to unpack .../113-r-cran-callr_3.7.3-2_all.deb ... 521s Unpacking r-cran-callr (3.7.3-2) ... 521s Selecting previously unselected package r-cran-cli. 521s Preparing to unpack .../114-r-cran-cli_3.6.2-1_arm64.deb ... 521s Unpacking r-cran-cli (3.6.2-1) ... 521s Selecting previously unselected package r-cran-crayon. 521s Preparing to unpack .../115-r-cran-crayon_1.5.2-1_all.deb ... 521s Unpacking r-cran-crayon (1.5.2-1) ... 521s Selecting previously unselected package r-cran-desc. 521s Preparing to unpack .../116-r-cran-desc_1.4.3-1_all.deb ... 521s Unpacking r-cran-desc (1.4.3-1) ... 521s Selecting previously unselected package r-cran-diffobj. 521s Preparing to unpack .../117-r-cran-diffobj_0.3.5-1_arm64.deb ... 521s Unpacking r-cran-diffobj (0.3.5-1) ... 521s Selecting previously unselected package r-cran-digest. 521s Preparing to unpack .../118-r-cran-digest_0.6.34-1_arm64.deb ... 521s Unpacking r-cran-digest (0.6.34-1) ... 521s Selecting previously unselected package r-cran-evaluate. 521s Preparing to unpack .../119-r-cran-evaluate_0.23-1_all.deb ... 521s Unpacking r-cran-evaluate (0.23-1) ... 521s Selecting previously unselected package r-cran-fansi. 521s Preparing to unpack .../120-r-cran-fansi_1.0.5-1_arm64.deb ... 521s Unpacking r-cran-fansi (1.0.5-1) ... 521s Selecting previously unselected package r-cran-fs. 521s Preparing to unpack .../121-r-cran-fs_1.6.3+dfsg-1_arm64.deb ... 521s Unpacking r-cran-fs (1.6.3+dfsg-1) ... 521s Selecting previously unselected package r-cran-glue. 521s Preparing to unpack .../122-r-cran-glue_1.7.0-1_arm64.deb ... 521s Unpacking r-cran-glue (1.7.0-1) ... 521s Selecting previously unselected package r-cran-jsonlite. 521s Preparing to unpack .../123-r-cran-jsonlite_1.8.8+dfsg-1_arm64.deb ... 521s Unpacking r-cran-jsonlite (1.8.8+dfsg-1) ... 521s Selecting previously unselected package r-cran-lattice. 521s Preparing to unpack .../124-r-cran-lattice_0.22-5-1_arm64.deb ... 521s Unpacking r-cran-lattice (0.22-5-1) ... 521s Selecting previously unselected package r-cran-rlang. 521s Preparing to unpack .../125-r-cran-rlang_1.1.3-1_arm64.deb ... 521s Unpacking r-cran-rlang (1.1.3-1) ... 521s Selecting previously unselected package r-cran-lifecycle. 521s Preparing to unpack .../126-r-cran-lifecycle_1.0.4+dfsg-1_all.deb ... 521s Unpacking r-cran-lifecycle (1.0.4+dfsg-1) ... 521s Selecting previously unselected package r-cran-matrix. 521s Preparing to unpack .../127-r-cran-matrix_1.6-5-1_arm64.deb ... 521s Unpacking r-cran-matrix (1.6-5-1) ... 521s Selecting previously unselected package r-cran-mass. 521s Preparing to unpack .../128-r-cran-mass_7.3-60.0.1-1_arm64.deb ... 521s Unpacking r-cran-mass (7.3-60.0.1-1) ... 522s Selecting previously unselected package r-cran-nlme. 522s Preparing to unpack .../129-r-cran-nlme_3.1.164-1_arm64.deb ... 522s Unpacking r-cran-nlme (3.1.164-1) ... 522s Selecting previously unselected package r-cran-pkgkitten. 522s Preparing to unpack .../130-r-cran-pkgkitten_0.2.3-1_all.deb ... 522s Unpacking r-cran-pkgkitten (0.2.3-1) ... 522s Selecting previously unselected package r-cran-rcpp. 522s Preparing to unpack .../131-r-cran-rcpp_1.0.12-1_arm64.deb ... 522s Unpacking r-cran-rcpp (1.0.12-1) ... 522s Selecting previously unselected package r-cran-minqa. 522s Preparing to unpack .../132-r-cran-minqa_1.2.6-1_arm64.deb ... 522s Unpacking r-cran-minqa (1.2.6-1) ... 522s Selecting previously unselected package libnlopt0:arm64. 522s Preparing to unpack .../133-libnlopt0_2.7.1-5build2_arm64.deb ... 522s Unpacking libnlopt0:arm64 (2.7.1-5build2) ... 522s Selecting previously unselected package r-cran-magrittr. 522s Preparing to unpack .../134-r-cran-magrittr_2.0.3-1_arm64.deb ... 522s Unpacking r-cran-magrittr (2.0.3-1) ... 522s Selecting previously unselected package r-cran-pkgbuild. 522s Preparing to unpack .../135-r-cran-pkgbuild_1.4.3-1_all.deb ... 522s Unpacking r-cran-pkgbuild (1.4.3-1) ... 522s Selecting previously unselected package r-cran-rprojroot. 522s Preparing to unpack .../136-r-cran-rprojroot_2.0.4-1_all.deb ... 522s Unpacking r-cran-rprojroot (2.0.4-1) ... 522s Selecting previously unselected package r-cran-withr. 522s Preparing to unpack .../137-r-cran-withr_2.5.0-1_all.deb ... 522s Unpacking r-cran-withr (2.5.0-1) ... 522s Selecting previously unselected package r-cran-pkgload. 522s Preparing to unpack .../138-r-cran-pkgload_1.3.4-1_all.deb ... 522s Unpacking r-cran-pkgload (1.3.4-1) ... 522s Selecting previously unselected package r-cran-praise. 522s Preparing to unpack .../139-r-cran-praise_1.0.0-4build1_all.deb ... 522s Unpacking r-cran-praise (1.0.0-4build1) ... 522s Selecting previously unselected package r-cran-utf8. 522s Preparing to unpack .../140-r-cran-utf8_1.2.4-1_arm64.deb ... 522s Unpacking r-cran-utf8 (1.2.4-1) ... 522s Selecting previously unselected package r-cran-vctrs. 522s Preparing to unpack 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.../152-r-cran-nnet_7.3-19-2_arm64.deb ... 523s Unpacking r-cran-nnet (7.3-19-2) ... 523s Selecting previously unselected package r-cran-numderiv. 523s Preparing to unpack .../153-r-cran-numderiv_2016.8-1.1-3_all.deb ... 523s Unpacking r-cran-numderiv (2016.8-1.1-3) ... 523s Selecting previously unselected package r-cran-ucminf. 523s Preparing to unpack .../154-r-cran-ucminf_1.2.1-1_arm64.deb ... 523s Unpacking r-cran-ucminf (1.2.1-1) ... 523s Selecting previously unselected package r-cran-ordinal. 523s Preparing to unpack .../155-r-cran-ordinal_2023.12-4-1_arm64.deb ... 523s Unpacking r-cran-ordinal (2023.12-4-1) ... 523s Selecting previously unselected package r-cran-xtable. 523s Preparing to unpack .../156-r-cran-xtable_1%3a1.8-4-2_all.deb ... 523s Unpacking r-cran-xtable (1:1.8-4-2) ... 523s Selecting previously unselected package autopkgtest-satdep. 523s Preparing to unpack .../157-2-autopkgtest-satdep.deb ... 523s Unpacking autopkgtest-satdep (0) ... 523s Setting up libgraphite2-3:arm64 (1.3.14-2) ... 523s Setting up libpixman-1-0:arm64 (0.42.2-1) ... 523s Setting up libsharpyuv0:arm64 (1.3.2-0.4) ... 523s Setting up libpaper1:arm64 (1.1.29) ... 524s 524s Creating config file /etc/papersize with new version 524s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 524s Setting up libxrender1:arm64 (1:0.9.10-1.1) ... 524s Setting up libdatrie1:arm64 (0.2.13-3) ... 524s Setting up libtirpc3t64:arm64 (1.3.4+ds-1.1) ... 524s Setting up libxcb-render0:arm64 (1.15-1) ... 524s Setting up unzip (6.0-28ubuntu3) ... 524s Setting up x11-common (1:7.7+23ubuntu2) ... 524s Setting up libpsl5t64:arm64 (0.21.2-1.1) ... 524s Setting up libdeflate0:arm64 (1.19-1) ... 524s Setting up linux-libc-dev:arm64 (6.8.0-11.11) ... 524s Setting up libnlopt0:arm64 (2.7.1-5build2) ... 524s Setting up libxcb-shm0:arm64 (1.15-1) ... 524s Setting up libpaper-utils (1.1.29) ... 524s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 524s Setting up libjbig0:arm64 (2.1-6.1ubuntu1) ... 524s Setting up libpcre2-16-0:arm64 (10.42-4ubuntu1) ... 524s Setting up zip (3.0-13) ... 524s Setting up libpcre2-32-0:arm64 (10.42-4ubuntu1) ... 524s Setting up libblas3:arm64 (3.12.0-3) ... 524s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 524s Setting up libtirpc-dev:arm64 (1.3.4+ds-1.1) ... 524s Setting up libpkgconf3:arm64 (1.8.1-2) ... 524s Setting up rpcsvc-proto (1.4.2-0ubuntu6) ... 524s Setting up fonts-dejavu-mono (2.37-8) ... 524s Setting up libpng16-16t64:arm64 (1.6.43-3) ... 524s Setting up libmpc3:arm64 (1.3.1-1) ... 524s Setting up libatomic1:arm64 (14-20240303-1ubuntu1) ... 524s Setting up libtcl8.6:arm64 (8.6.13+dfsg-2) ... 524s Setting up icu-devtools (74.2-1ubuntu1) ... 524s Setting up fonts-dejavu-core (2.37-8) ... 524s Setting up pkgconf-bin (1.8.1-2) ... 524s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 524s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ... 524s Setting up libwebp7:arm64 (1.3.2-0.4) ... 524s Setting up libreadline8t64:arm64 (8.2-3.1) ... 524s Setting up liblzma-dev:arm64 (5.4.5-0.3) ... 524s Setting up libubsan1:arm64 (14-20240303-1ubuntu1) ... 524s Setting up libpcre2-posix3:arm64 (10.42-4ubuntu1) ... 524s Setting up libnsl-dev:arm64 (1.3.0-3) ... 524s Setting up libhwasan0:arm64 (14-20240303-1ubuntu1) ... 524s Setting up libcrypt-dev:arm64 (1:4.4.36-4) ... 524s Setting up libasan8:arm64 (14-20240303-1ubuntu1) ... 524s Setting up libharfbuzz0b:arm64 (8.3.0-2) ... 524s Setting up libthai-data (0.1.29-2) ... 524s Setting up libxss1:arm64 (1:1.2.3-1build2) ... 524s Setting up libtsan2:arm64 (14-20240303-1ubuntu1) ... 524s Setting up libisl23:arm64 (0.26-3) ... 524s Setting up libc-dev-bin (2.39-0ubuntu2) ... 524s Setting up xdg-utils (1.1.3-4.1ubuntu3) ... 524s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 524s Setting up libcc1-0:arm64 (14-20240303-1ubuntu1) ... 524s Setting up liblsan0:arm64 (14-20240303-1ubuntu1) ... 524s Setting up libblas-dev:arm64 (3.12.0-3) ... 524s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode 524s Setting up dctrl-tools (2.24-3build2) ... 524s Setting up libitm1:arm64 (14-20240303-1ubuntu1) ... 524s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 524s Setting up libice6:arm64 (2:1.0.10-1build2) ... 524s Setting up liblapack3:arm64 (3.12.0-3) ... 524s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 524s Setting up cpp-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 524s Setting up libcurl4t64:arm64 (8.5.0-2ubuntu7) ... 524s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 524s Setting up pkgconf:arm64 (1.8.1-2) ... 524s Setting up libthai0:arm64 (0.1.29-2) ... 524s Setting up cpp-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 524s Setting up liblapack-dev:arm64 (3.12.0-3) ... 524s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode 524s Setting up pkg-config:arm64 (1.8.1-2) ... 524s Setting up libgcc-13-dev:arm64 (13.2.0-17ubuntu2) ... 524s Setting up libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 524s Setting up libc6-dev:arm64 (2.39-0ubuntu2) ... 524s Setting up curl (8.5.0-2ubuntu7) ... 524s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 524s Setting up libgfortran-13-dev:arm64 (13.2.0-17ubuntu2) ... 524s Setting up libsm6:arm64 (2:1.2.3-1build2) ... 524s Setting up libicu-dev:arm64 (74.2-1ubuntu1) ... 524s Setting up libstdc++-13-dev:arm64 (13.2.0-17ubuntu2) ... 524s Setting up libbz2-dev:arm64 (1.0.8-5ubuntu1) ... 524s Setting up fontconfig (2.15.0-1ubuntu1) ... 526s Regenerating fonts cache... done. 526s Setting up libjpeg-turbo8-dev:arm64 (2.1.5-2ubuntu1) ... 526s Setting up libxft2:arm64 (2.3.6-1) ... 526s Setting up libncurses-dev:arm64 (6.4+20240113-1ubuntu1) ... 526s Setting up libpcre2-dev:arm64 (10.42-4ubuntu1) ... 526s Setting up cpp-13 (13.2.0-17ubuntu2) ... 526s Setting up libtk8.6:arm64 (8.6.13-2) ... 526s Setting up libpango-1.0-0:arm64 (1.51.0+ds-4) ... 526s Setting up gcc-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 526s Setting up libreadline-dev:arm64 (8.2-3.1) ... 526s Setting up libcairo2:arm64 (1.18.0-1) ... 526s Setting up libxt6t64:arm64 (1:1.2.1-1.2) ... 526s Setting up gcc-13 (13.2.0-17ubuntu2) ... 526s Setting up zlib1g-dev:arm64 (1:1.3.dfsg-3ubuntu1) ... 526s Setting up cpp (4:13.2.0-7ubuntu1) ... 526s Setting up libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ... 526s Setting up libjpeg8-dev:arm64 (8c-2ubuntu11) ... 526s Setting up libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ... 526s Setting up g++-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 526s Setting up gcc-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 526s Setting up g++-13 (13.2.0-17ubuntu2) ... 526s Setting up libpng-dev:arm64 (1.6.43-3) ... 526s Setting up libjpeg-dev:arm64 (8c-2ubuntu11) ... 526s Setting up gfortran-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 526s Setting up gcc (4:13.2.0-7ubuntu1) ... 526s Setting up gfortran-13 (13.2.0-17ubuntu2) ... 526s Setting up r-base-core (4.3.3-2build1) ... 527s 527s Creating config file /etc/R/Renviron with new version 527s Setting up r-cran-crayon (1.5.2-1) ... 527s Setting up r-cran-lattice (0.22-5-1) ... 527s Setting up r-cran-ps (1.7.6-1) ... 527s Setting up r-cran-nlme (3.1.164-1) ... 527s Setting up r-cran-statmod (1.5.0-1) ... 527s Setting up g++-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 527s Setting up r-cran-nnet (7.3-19-2) ... 527s Setting up gfortran-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 527s Setting up r-cran-r6 (2.5.1-1) ... 527s Setting up r-cran-pkgkitten (0.2.3-1) ... 527s Setting up r-cran-numderiv (2016.8-1.1-3) ... 527s Setting up r-cran-magrittr (2.0.3-1) ... 527s Setting up r-cran-littler (0.3.19-1) ... 527s Setting up r-cran-fs (1.6.3+dfsg-1) ... 527s Setting up r-cran-rcpp (1.0.12-1) ... 527s Setting up r-cran-brio (1.1.4-1) ... 527s Setting up r-cran-boot (1.3-30-1) ... 527s Setting up r-cran-diffobj (0.3.5-1) ... 527s Setting up r-cran-rlang (1.1.3-1) ... 527s Setting up littler (0.3.19-1) ... 527s Setting up r-cran-withr (2.5.0-1) ... 527s Setting up r-cran-processx (3.8.3-1) ... 527s Setting up r-cran-praise (1.0.0-4build1) ... 527s Setting up r-cran-digest (0.6.34-1) ... 527s Setting up r-cran-evaluate (0.23-1) ... 527s Setting up r-cran-fansi (1.0.5-1) ... 527s Setting up r-cran-mass (7.3-60.0.1-1) ... 527s Setting up r-cran-glue (1.7.0-1) ... 527s Setting up r-cran-xtable (1:1.8-4-2) ... 527s Setting up r-cran-cli (3.6.2-1) ... 527s Setting up gfortran (4:13.2.0-7ubuntu1) ... 527s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 527s update-alternatives: warning: skip creation of /usr/share/man/man1/f95.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f95) doesn't exist 527s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 527s update-alternatives: warning: skip creation of /usr/share/man/man1/f77.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f77) doesn't exist 527s Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... 527s Setting up r-cran-rprojroot (2.0.4-1) ... 527s Setting up r-cran-jsonlite (1.8.8+dfsg-1) ... 527s Setting up r-cran-pkgconfig (2.0.3-2build1) ... 527s Setting up r-cran-utf8 (1.2.4-1) ... 527s Setting up r-cran-ucminf (1.2.1-1) ... 527s Setting up r-cran-matrix (1.6-5-1) ... 527s Setting up g++ (4:13.2.0-7ubuntu1) ... 527s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 527s Setting up build-essential (12.10ubuntu1) ... 527s Setting up r-cran-vctrs (0.6.5-1) ... 527s Setting up r-cran-rcppeigen (0.3.3.9.4-1) ... 527s Setting up r-cran-pillar (1.9.0+dfsg-1) ... 527s Setting up r-cran-minqa (1.2.6-1) ... 527s Setting up r-base-dev (4.3.3-2build1) ... 527s Setting up r-cran-callr (3.7.3-2) ... 527s Setting up r-cran-ordinal (2023.12-4-1) ... 527s Setting up r-cran-desc (1.4.3-1) ... 527s Setting up r-cran-tibble (3.2.1+dfsg-2) ... 527s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 527s Setting up r-cran-pkgbuild (1.4.3-1) ... 527s Setting up r-cran-pkgload (1.3.4-1) ... 527s Setting up r-cran-rematch2 (2.1.2-2build1) ... 527s Setting up r-cran-waldo (0.5.2-1build1) ... 527s Setting up r-cran-testthat (3.2.1-1) ... 527s Setting up r-cran-nloptr (2.0.3-1) ... 527s Setting up r-cran-lme4 (1.1-35.1-4) ... 527s Setting up autopkgtest-satdep (0) ... 527s Processing triggers for man-db (2.12.0-3) ... 528s Processing triggers for install-info (7.1-3) ... 528s Processing triggers for libc-bin (2.39-0ubuntu2) ... 536s (Reading database ... 86110 files and directories currently installed.) 536s Removing autopkgtest-satdep (0) ... 538s autopkgtest [19:32:23]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 538s autopkgtest [19:32:23]: test pkg-r-autopkgtest: [----------------------- 538s Test: Try to load the R library ordinal 538s 538s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 538s Copyright (C) 2024 The R Foundation for Statistical Computing 538s Platform: aarch64-unknown-linux-gnu (64-bit) 538s 538s R is free software and comes with ABSOLUTELY NO WARRANTY. 538s You are welcome to redistribute it under certain conditions. 538s Type 'license()' or 'licence()' for distribution details. 538s 538s R is a collaborative project with many contributors. 538s Type 'contributors()' for more information and 538s 'citation()' on how to cite R or R packages in publications. 538s 538s Type 'demo()' for some demos, 'help()' for on-line help, or 538s 'help.start()' for an HTML browser interface to help. 538s Type 'q()' to quit R. 538s 539s > library('ordinal') 540s > 540s > 540s Other tests are currently unsupported! 540s They will be progressively added. 540s autopkgtest [19:32:25]: test pkg-r-autopkgtest: -----------------------] 540s pkg-r-autopkgtest PASS 540s autopkgtest [19:32:25]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 541s autopkgtest [19:32:26]: @@@@@@@@@@@@@@@@@@@@ summary 541s run-unit-test PASS 541s pkg-r-autopkgtest PASS 552s Creating nova instance adt-noble-arm64-r-cran-ordinal-20240316-192325-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240314.img (UUID 7faf5f09-d335-4346-a441-4eab2f9c04fe)... 552s Creating nova instance adt-noble-arm64-r-cran-ordinal-20240316-192325-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240314.img (UUID 7faf5f09-d335-4346-a441-4eab2f9c04fe)...