0s autopkgtest [23:51:44]: starting date and time: 2026-02-09 23:51:44+0000 0s autopkgtest [23:51:44]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [23:51:44]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.y5yrpgal/out --timeout-copy=6000 --needs-internet=try --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:r-cran-ggplot2 --apt-upgrade r-cran-lmertest --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=r-cran-ggplot2/4.0.2+dfsg-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-arm64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@sto01-arm64-14.secgroup --name adt-resolute-arm64-r-cran-lmertest-20260209-235144-juju-7f2275-prod-proposed-migration-environment-15-6b77ceeb-fcee-48ca-83ac-c129a712a281 --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-autopkgtest-workers-arm64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-arm64-r-cran-lmertest-20260209-235144-juju-7f2275-prod-proposed-migration-environment-15-6b77ceeb-fcee-48ca-83ac-c129a712a281 from image adt/ubuntu-resolute-arm64-server-20260209.img (UUID 793037ca-75af-461b-82de-f8081300b2e3)... 136s autopkgtest [23:54:00]: testbed dpkg architecture: arm64 137s autopkgtest [23:54:01]: testbed apt version: 3.1.15 137s autopkgtest [23:54:01]: @@@@@@@@@@@@@@@@@@@@ test bed setup 137s autopkgtest [23:54:01]: testbed release detected to be: None 138s autopkgtest [23:54:02]: updating testbed package index (apt update) 138s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 138s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 138s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 138s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 139s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [176 kB] 139s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [29.4 kB] 139s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1645 kB] 142s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [246 kB] 142s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 c-n-f Metadata [6216 B] 142s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 c-n-f Metadata [304 B] 142s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [1580 kB] 144s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 c-n-f Metadata [32.0 kB] 144s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [21.7 kB] 144s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 c-n-f Metadata [688 B] 146s Fetched 3862 kB in 6s (625 kB/s) 147s Reading package lists... 148s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 148s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 148s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 148s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 149s Reading package lists... 149s Reading package lists... 149s Building dependency tree... 149s Reading state information... 150s Calculating upgrade... 150s The following packages will be upgraded: 150s cryptsetup-bin dracut-install iproute2 iptables libcryptsetup12 libip4tc2 150s libip6tc2 libxtables12 wget 150s 9 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 150s Need to get 2534 kB of archives. 150s After this operation, 18.4 kB of additional disk space will be used. 150s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 iptables arm64 1.8.11-2ubuntu3 [386 kB] 151s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libip4tc2 arm64 1.8.11-2ubuntu3 [24.3 kB] 151s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libip6tc2 arm64 1.8.11-2ubuntu3 [24.7 kB] 151s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 libxtables12 arm64 1.8.11-2ubuntu3 [36.7 kB] 151s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 iproute2 arm64 6.18.0-1ubuntu1 [1171 kB] 153s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libcryptsetup12 arm64 2:2.8.0-1ubuntu3 [274 kB] 153s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 wget arm64 1.25.0-2ubuntu4 [344 kB] 153s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 cryptsetup-bin arm64 2:2.8.0-1ubuntu3 [227 kB] 153s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 dracut-install arm64 109-11ubuntu1 [45.3 kB] 153s dpkg-preconfigure: unable to re-open stdin: No such file or directory 153s Fetched 2534 kB in 3s (911 kB/s) 153s (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 ... 136597 files and directories currently installed.) 153s Preparing to unpack .../0-iptables_1.8.11-2ubuntu3_arm64.deb ... 153s Unpacking iptables (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 154s Preparing to unpack .../1-libip4tc2_1.8.11-2ubuntu3_arm64.deb ... 154s Unpacking libip4tc2:arm64 (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 154s Preparing to unpack .../2-libip6tc2_1.8.11-2ubuntu3_arm64.deb ... 154s Unpacking libip6tc2:arm64 (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 154s Preparing to unpack .../3-libxtables12_1.8.11-2ubuntu3_arm64.deb ... 154s Unpacking libxtables12:arm64 (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 154s Preparing to unpack .../4-iproute2_6.18.0-1ubuntu1_arm64.deb ... 154s Unpacking iproute2 (6.18.0-1ubuntu1) over (6.16.0-1ubuntu3) ... 154s Preparing to unpack .../5-libcryptsetup12_2%3a2.8.0-1ubuntu3_arm64.deb ... 154s Unpacking libcryptsetup12:arm64 (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ... 154s Preparing to unpack .../6-wget_1.25.0-2ubuntu4_arm64.deb ... 154s Unpacking wget (1.25.0-2ubuntu4) over (1.25.0-2ubuntu3) ... 155s Preparing to unpack .../7-cryptsetup-bin_2%3a2.8.0-1ubuntu3_arm64.deb ... 155s Unpacking cryptsetup-bin (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ... 155s Preparing to unpack .../8-dracut-install_109-11ubuntu1_arm64.deb ... 155s Unpacking dracut-install (109-11ubuntu1) over (109-9ubuntu1) ... 155s Setting up libip4tc2:arm64 (1.8.11-2ubuntu3) ... 155s Setting up wget (1.25.0-2ubuntu4) ... 155s Setting up libip6tc2:arm64 (1.8.11-2ubuntu3) ... 155s Setting up libxtables12:arm64 (1.8.11-2ubuntu3) ... 155s Setting up dracut-install (109-11ubuntu1) ... 155s Setting up libcryptsetup12:arm64 (2:2.8.0-1ubuntu3) ... 155s Setting up cryptsetup-bin (2:2.8.0-1ubuntu3) ... 155s Setting up iptables (1.8.11-2ubuntu3) ... 155s Setting up iproute2 (6.18.0-1ubuntu1) ... 155s Processing triggers for man-db (2.13.1-1build1) ... 157s Processing triggers for install-info (7.2-5) ... 157s Processing triggers for libc-bin (2.42-2ubuntu4) ... 157s autopkgtest [23:54:21]: upgrading testbed (apt dist-upgrade and autopurge) 157s Reading package lists... 157s Building dependency tree... 157s Reading state information... 157s Calculating upgrade... 158s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 158s Reading package lists... 158s Building dependency tree... 158s Reading state information... 158s Solving dependencies... 159s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 161s autopkgtest [23:54:25]: testbed running kernel: Linux 6.19.0-3-generic #3-Ubuntu SMP PREEMPT_DYNAMIC Fri Jan 23 19:46:27 UTC 2026 162s autopkgtest [23:54:26]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-lmertest 163s Get:1 http://ftpmaster.internal/ubuntu resolute/universe r-cran-lmertest 3.2-0-1 (dsc) [2247 B] 163s Get:2 http://ftpmaster.internal/ubuntu resolute/universe r-cran-lmertest 3.2-0-1 (tar) [198 kB] 163s Get:3 http://ftpmaster.internal/ubuntu resolute/universe r-cran-lmertest 3.2-0-1 (diff) [3788 B] 163s gpgv: Signature made Thu Jan 22 00:11:29 2026 UTC 163s gpgv: using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502 163s gpgv: issuer "plessy@debian.org" 163s gpgv: Can't check signature: No public key 163s dpkg-source: warning: cannot verify inline signature for ./r-cran-lmertest_3.2-0-1.dsc: no acceptable signature found 163s autopkgtest [23:54:27]: testing package r-cran-lmertest version 3.2-0-1 163s autopkgtest [23:54:27]: build not needed 165s autopkgtest [23:54:29]: test run-unit-test: preparing testbed 165s Reading package lists... 165s Building dependency tree... 165s Reading state information... 165s Solving dependencies... 166s The following NEW packages will be installed: 166s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 166s fonts-glyphicons-halflings fonts-mathjax libblas3 libcairo2 libdatrie1 166s libdeflate0 libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 166s libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 libjs-bootstrap 166s libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-mathjax 166s liblapack3 liblerc4 libnlopt0 libpango-1.0-0 libpangocairo-1.0-0 166s libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 166s libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 166s libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 node-normalize.css 166s r-base-core r-cran-backports r-cran-boot r-cran-broom r-cran-cli 166s r-cran-colorspace r-cran-cowplot r-cran-cpp11 r-cran-curl r-cran-deriv 166s r-cran-doby r-cran-dplyr r-cran-evaluate r-cran-fansi r-cran-farver 166s r-cran-forecast r-cran-fracdiff r-cran-generics r-cran-ggplot2 r-cran-glue 166s r-cran-gtable r-cran-highr r-cran-isoband r-cran-jsonlite r-cran-knitr 166s r-cran-labeling r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-lme4 166s r-cran-lmertest r-cran-lmtest r-cran-magrittr r-cran-mass r-cran-matrix 166s r-cran-microbenchmark r-cran-minqa r-cran-modelr r-cran-nlme r-cran-nloptr 166s r-cran-nnet r-cran-numderiv r-cran-pbkrtest r-cran-pillar r-cran-pkgconfig 166s r-cran-pkgkitten r-cran-purrr r-cran-quadprog r-cran-quantmod r-cran-r6 166s r-cran-rbibutils r-cran-rcolorbrewer r-cran-rcpp r-cran-rcpparmadillo 166s r-cran-rcppeigen r-cran-rdpack r-cran-reformulas r-cran-rlang r-cran-s7 166s r-cran-scales r-cran-statmod r-cran-stringi r-cran-stringr r-cran-tibble 166s r-cran-tidyr r-cran-tidyselect r-cran-timedate r-cran-tseries r-cran-ttr 166s r-cran-urca r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr 166s r-cran-xfun r-cran-xts r-cran-yaml r-cran-zoo unzip x11-common xdg-utils zip 167s 0 upgraded, 130 newly installed, 0 to remove and 0 not upgraded. 167s Need to get 112 MB of archives. 167s After this operation, 254 MB of additional disk space will be used. 167s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-mono all 2.37-8build1 [502 kB] 167s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-core all 2.37-8build1 [834 kB] 169s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 fontconfig-config arm64 2.17.1-3ubuntu1 [38.5 kB] 169s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 libfontconfig1 arm64 2.17.1-3ubuntu1 [144 kB] 169s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 fontconfig arm64 2.17.1-3ubuntu1 [181 kB] 169s Get:6 http://ftpmaster.internal/ubuntu resolute/universe arm64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-6 [119 kB] 169s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-mathjax all 2.7.9+dfsg-1build1 [2283 kB] 173s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas3 arm64 3.12.1-7ubuntu1 [181 kB] 173s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 libpixman-1-0 arm64 0.46.4-1 [204 kB] 173s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-render0 arm64 1.17.0-2ubuntu1 [16.4 kB] 173s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-shm0 arm64 1.17.0-2ubuntu1 [5938 B] 173s Get:12 http://ftpmaster.internal/ubuntu resolute/main arm64 libxrender1 arm64 1:0.9.12-1 [19.5 kB] 173s Get:13 http://ftpmaster.internal/ubuntu resolute/main arm64 libcairo2 arm64 1.18.4-3 [556 kB] 174s Get:14 http://ftpmaster.internal/ubuntu resolute/main arm64 libdatrie1 arm64 0.2.14-1 [19.6 kB] 174s Get:15 http://ftpmaster.internal/ubuntu resolute/main arm64 libdeflate0 arm64 1.23-2build1 [46.8 kB] 174s Get:16 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran5 arm64 15.2.0-12ubuntu1 [451 kB] 174s Get:17 http://ftpmaster.internal/ubuntu resolute/main arm64 libgomp1 arm64 15.2.0-12ubuntu1 [147 kB] 174s Get:18 http://ftpmaster.internal/ubuntu resolute/main arm64 libgraphite2-3 arm64 1.3.14-11ubuntu1 [72.1 kB] 174s Get:19 http://ftpmaster.internal/ubuntu resolute/main arm64 libharfbuzz0b arm64 12.3.2-1 [510 kB] 174s Get:20 http://ftpmaster.internal/ubuntu resolute/main arm64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 174s Get:21 http://ftpmaster.internal/ubuntu resolute/main arm64 libice6 arm64 2:1.1.1-1build1 [43.0 kB] 174s Get:22 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg-turbo8 arm64 2.1.5-4ubuntu3 [161 kB] 174s Get:23 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 174s Get:24 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-bootstrap all 3.4.1+dfsg-6 [129 kB] 174s Get:25 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-highlight.js all 10.7.3+dfsg-2 [144 kB] 174s Get:26 http://ftpmaster.internal/ubuntu resolute/main arm64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 174s Get:27 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-jquery-datatables all 1.11.5+dfsg-2build1 [145 kB] 174s Get:28 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack3 arm64 3.12.1-7ubuntu1 [2299 kB] 177s Get:29 http://ftpmaster.internal/ubuntu resolute/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu2 [174 kB] 177s Get:30 http://ftpmaster.internal/ubuntu resolute/main arm64 libthai-data all 0.1.30-1 [155 kB] 178s Get:31 http://ftpmaster.internal/ubuntu resolute/main arm64 libthai0 arm64 0.1.30-1 [18.3 kB] 178s Get:32 http://ftpmaster.internal/ubuntu resolute/main arm64 libpango-1.0-0 arm64 1.57.0-1 [238 kB] 178s Get:33 http://ftpmaster.internal/ubuntu resolute/main arm64 libpangoft2-1.0-0 arm64 1.57.0-1 [51.5 kB] 178s Get:34 http://ftpmaster.internal/ubuntu resolute/main arm64 libpangocairo-1.0-0 arm64 1.57.0-1 [27.9 kB] 178s Get:35 http://ftpmaster.internal/ubuntu resolute/main arm64 libpaper2 arm64 2.2.5-0.3build1 [17.3 kB] 178s Get:36 http://ftpmaster.internal/ubuntu resolute/main arm64 libpaper-utils arm64 2.2.5-0.3build1 [15.4 kB] 178s Get:37 http://ftpmaster.internal/ubuntu resolute/main arm64 libsharpyuv0 arm64 1.5.0-0.1build1 [16.7 kB] 178s Get:38 http://ftpmaster.internal/ubuntu resolute/main arm64 libsm6 arm64 2:1.2.6-1build1 [16.8 kB] 178s Get:39 http://ftpmaster.internal/ubuntu resolute/main arm64 libtcl8.6 arm64 8.6.17+dfsg-1build1 [983 kB] 180s Get:40 http://ftpmaster.internal/ubuntu resolute/main arm64 libjbig0 arm64 2.1-6.1ubuntu3 [29.2 kB] 180s Get:41 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebp7 arm64 1.5.0-0.1build1 [205 kB] 180s Get:42 http://ftpmaster.internal/ubuntu resolute/main arm64 libtiff6 arm64 4.7.0-3ubuntu3 [196 kB] 180s Get:43 http://ftpmaster.internal/ubuntu resolute/main arm64 libxft2 arm64 2.3.6-1build2 [43.2 kB] 180s Get:44 http://ftpmaster.internal/ubuntu resolute/main arm64 libxss1 arm64 1:1.2.3-1build4 [7102 B] 180s Get:45 http://ftpmaster.internal/ubuntu resolute/main arm64 libtk8.6 arm64 8.6.17-1 [811 kB] 181s Get:46 http://ftpmaster.internal/ubuntu resolute/main arm64 libxt6t64 arm64 1:1.2.1-1.3 [168 kB] 181s Get:47 http://ftpmaster.internal/ubuntu resolute/universe arm64 node-normalize.css all 8.0.1-5.1 [10.4 kB] 181s Get:48 http://ftpmaster.internal/ubuntu resolute/main arm64 zip arm64 3.0-15ubuntu3 [170 kB] 181s Get:49 http://ftpmaster.internal/ubuntu resolute/main arm64 unzip arm64 6.0-29ubuntu1 [176 kB] 181s Get:50 http://ftpmaster.internal/ubuntu resolute/main arm64 xdg-utils all 1.2.1-2ubuntu2 [66.1 kB] 181s Get:51 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-base-core arm64 4.5.2-1ubuntu2 [28.6 MB] 235s Get:52 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-backports arm64 1.5.0-2 [121 kB] 236s Get:53 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-boot all 1.3-32-1 [636 kB] 237s Get:54 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-cli arm64 3.6.4-1 [1374 kB] 240s Get:55 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-generics all 0.1.4-1 [84.0 kB] 240s Get:56 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-glue arm64 1.8.0-1 [163 kB] 240s Get:57 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rlang arm64 1.1.5-3 [1706 kB] 244s Get:58 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-lifecycle all 1.0.5+dfsg-1 [120 kB] 244s Get:59 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-magrittr arm64 2.0.3-1 [154 kB] 244s Get:60 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-utf8 arm64 1.2.4-1 [140 kB] 244s Get:61 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-vctrs arm64 0.6.5-1 [1327 kB] 247s Get:62 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-pillar all 1.11.1+dfsg-1 [456 kB] 247s Get:63 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-r6 all 2.6.1-1 [101 kB] 247s Get:64 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-fansi arm64 1.0.6-2 [627 kB] 248s Get:65 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-pkgconfig all 2.0.3-2build2 [20.4 kB] 248s Get:66 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-tibble arm64 3.2.1+dfsg-3 [420 kB] 248s Get:67 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-withr all 3.0.2+dfsg-1 [214 kB] 248s Get:68 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-tidyselect arm64 1.2.1+dfsg-1 [222 kB] 249s Get:69 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-dplyr arm64 1.1.4-4 [1534 kB] 252s Get:70 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-purrr arm64 1.0.4-1 [552 kB] 253s Get:71 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-stringi arm64 1.8.4-1build2 [901 kB] 255s Get:72 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-stringr all 1.5.1-1 [290 kB] 255s Get:73 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-cpp11 all 0.5.3-1 [242 kB] 255s Get:74 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-tidyr arm64 1.3.1-1 [1154 kB] 257s Get:75 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-broom all 1.0.12+dfsg-1 [1708 kB] 260s Get:76 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-colorspace arm64 2.1-1+dfsg-1 [1563 kB] 264s Get:77 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-gtable all 0.3.6+dfsg-1 [199 kB] 264s Get:78 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-isoband arm64 0.2.7-1 [1481 kB] 267s Get:79 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-s7 arm64 0.2.0-1 [329 kB] 267s Get:80 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-farver arm64 2.1.2-1 [1344 kB] 270s Get:81 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-labeling all 0.4.3-1 [62.1 kB] 270s Get:82 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rcolorbrewer all 1.1-3-1build2 [54.0 kB] 270s Get:83 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-viridislite all 0.4.3-1 [1088 kB] 272s Get:84 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-scales all 1.4.0-1 [725 kB] 273s Get:85 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 r-cran-ggplot2 all 4.0.2+dfsg-1 [4941 kB] 282s Get:86 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-cowplot all 1.1.3+dfsg-1 [614 kB] 284s Get:87 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-curl arm64 7.0.0+dfsg-1 [202 kB] 284s Get:88 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-deriv all 4.2.0-1 [154 kB] 284s Get:89 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-fracdiff arm64 1.5-3-1 [108 kB] 284s Get:90 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-lattice arm64 0.22-7-1 [1365 kB] 286s Get:91 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-zoo arm64 1.8-15-1 [1025 kB] 288s Get:92 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-lmtest arm64 0.9.40-1build1 [400 kB] 288s Get:93 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-nnet arm64 7.3-20-1 [113 kB] 288s Get:94 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-littler arm64 0.3.22-1 [85.1 kB] 288s Get:95 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 288s Get:96 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rcpp arm64 1.1.0-1 [2011 kB] 292s Get:97 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-timedate arm64 4052.112-1 [1298 kB] 295s Get:98 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-quadprog arm64 1.5-8-1build2 [31.9 kB] 295s Get:99 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-xts arm64 0.14.1-1 [1189 kB] 297s Get:100 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-ttr arm64 0.24.4-1 [509 kB] 297s Get:101 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-jsonlite arm64 1.9.1+dfsg-1 [445 kB] 297s Get:102 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-quantmod all 0.4.28-1 [1037 kB] 299s Get:103 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-tseries arm64 0.10-59-3 [381 kB] 299s Get:104 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-nlme arm64 3.1.168-1 [2310 kB] 303s Get:105 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-urca arm64 1.3-4-1build1 [1050 kB] 305s Get:106 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rcpparmadillo arm64 15.2.3-1-1 [916 kB] 307s Get:107 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-forecast arm64 8.23.0-1 [1564 kB] 310s Get:108 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-mass arm64 7.3-65-1 [1109 kB] 312s Get:109 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-matrix arm64 1.7-4-1 [4146 kB] 319s Get:110 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-modelr all 0.1.11-1 [195 kB] 319s Get:111 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-microbenchmark arm64 1.5.0-1 [67.5 kB] 319s Get:112 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-doby all 4.7.1-3 [4741 kB] 328s Get:113 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-evaluate all 1.0.5-1 [117 kB] 328s Get:114 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-xfun arm64 0.55+dfsg-1 [587 kB] 329s Get:115 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-highr all 0.11+dfsg-1 [38.5 kB] 329s Get:116 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-yaml arm64 2.3.10-1 [108 kB] 329s Get:117 http://ftpmaster.internal/ubuntu resolute/main arm64 libjs-mathjax all 2.7.9+dfsg-1build1 [6017 kB] 341s Get:118 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-knitr all 1.51+dfsg-1 [847 kB] 342s Get:119 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-minqa arm64 1.2.8-1 [112 kB] 342s Get:120 http://ftpmaster.internal/ubuntu resolute/universe arm64 libnlopt0 arm64 2.7.1-7ubuntu1 [177 kB] 342s Get:121 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-nloptr arm64 2.2.1-2 [250 kB] 343s Get:122 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rbibutils arm64 2.3-1 [1016 kB] 344s Get:123 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rdpack all 2.6.3-1 [636 kB] 345s Get:124 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-reformulas all 0.4.4-1 [151 kB] 345s Get:125 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rcppeigen arm64 0.3.4.0.2-1 [1422 kB] 348s Get:126 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-statmod arm64 1.5.0-1 [294 kB] 348s Get:127 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-lme4 arm64 1.1-38-1 [4177 kB] 355s Get:128 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-numderiv all 2016.8-1.1-3build1 [116 kB] 355s Get:129 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-lmertest all 3.2-0-1 [535 kB] 356s Get:130 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-pbkrtest all 0.5.5-1 [217 kB] 356s Preconfiguring packages ... 356s Fetched 112 MB in 3min 10s (588 kB/s) 356s Selecting previously unselected package fonts-dejavu-mono. 356s (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 ... 136600 files and directories currently installed.) 356s Preparing to unpack .../000-fonts-dejavu-mono_2.37-8build1_all.deb ... 356s Unpacking fonts-dejavu-mono (2.37-8build1) ... 356s Selecting previously unselected package fonts-dejavu-core. 356s Preparing to unpack .../001-fonts-dejavu-core_2.37-8build1_all.deb ... 356s Unpacking fonts-dejavu-core (2.37-8build1) ... 356s Selecting previously unselected package fontconfig-config. 356s Preparing to unpack .../002-fontconfig-config_2.17.1-3ubuntu1_arm64.deb ... 357s Unpacking fontconfig-config (2.17.1-3ubuntu1) ... 357s Selecting previously unselected package libfontconfig1:arm64. 357s Preparing to unpack .../003-libfontconfig1_2.17.1-3ubuntu1_arm64.deb ... 357s Unpacking libfontconfig1:arm64 (2.17.1-3ubuntu1) ... 357s Selecting previously unselected package fontconfig. 357s Preparing to unpack .../004-fontconfig_2.17.1-3ubuntu1_arm64.deb ... 357s Unpacking fontconfig (2.17.1-3ubuntu1) ... 357s Selecting previously unselected package fonts-glyphicons-halflings. 357s Preparing to unpack .../005-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-6_all.deb ... 357s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-6) ... 357s Selecting previously unselected package fonts-mathjax. 357s Preparing to unpack .../006-fonts-mathjax_2.7.9+dfsg-1build1_all.deb ... 357s Unpacking fonts-mathjax (2.7.9+dfsg-1build1) ... 357s Selecting previously unselected package libblas3:arm64. 357s Preparing to unpack .../007-libblas3_3.12.1-7ubuntu1_arm64.deb ... 357s Unpacking libblas3:arm64 (3.12.1-7ubuntu1) ... 357s Selecting previously unselected package libpixman-1-0:arm64. 357s Preparing to unpack .../008-libpixman-1-0_0.46.4-1_arm64.deb ... 357s Unpacking libpixman-1-0:arm64 (0.46.4-1) ... 357s Selecting previously unselected package libxcb-render0:arm64. 357s Preparing to unpack .../009-libxcb-render0_1.17.0-2ubuntu1_arm64.deb ... 357s Unpacking libxcb-render0:arm64 (1.17.0-2ubuntu1) ... 357s Selecting previously unselected package libxcb-shm0:arm64. 357s Preparing to unpack .../010-libxcb-shm0_1.17.0-2ubuntu1_arm64.deb ... 357s Unpacking libxcb-shm0:arm64 (1.17.0-2ubuntu1) ... 357s Selecting previously unselected package libxrender1:arm64. 357s Preparing to unpack .../011-libxrender1_1%3a0.9.12-1_arm64.deb ... 357s Unpacking libxrender1:arm64 (1:0.9.12-1) ... 357s Selecting previously unselected package libcairo2:arm64. 357s Preparing to unpack .../012-libcairo2_1.18.4-3_arm64.deb ... 357s Unpacking libcairo2:arm64 (1.18.4-3) ... 357s Selecting previously unselected package libdatrie1:arm64. 357s Preparing to unpack .../013-libdatrie1_0.2.14-1_arm64.deb ... 357s Unpacking libdatrie1:arm64 (0.2.14-1) ... 357s Selecting previously unselected package libdeflate0:arm64. 357s Preparing to unpack .../014-libdeflate0_1.23-2build1_arm64.deb ... 357s Unpacking libdeflate0:arm64 (1.23-2build1) ... 357s Selecting previously unselected package libgfortran5:arm64. 357s Preparing to unpack .../015-libgfortran5_15.2.0-12ubuntu1_arm64.deb ... 357s Unpacking libgfortran5:arm64 (15.2.0-12ubuntu1) ... 357s Selecting previously unselected package libgomp1:arm64. 357s Preparing to unpack .../016-libgomp1_15.2.0-12ubuntu1_arm64.deb ... 357s Unpacking libgomp1:arm64 (15.2.0-12ubuntu1) ... 357s Selecting previously unselected package libgraphite2-3:arm64. 357s Preparing to unpack .../017-libgraphite2-3_1.3.14-11ubuntu1_arm64.deb ... 357s Unpacking libgraphite2-3:arm64 (1.3.14-11ubuntu1) ... 357s Selecting previously unselected package libharfbuzz0b:arm64. 357s Preparing to unpack .../018-libharfbuzz0b_12.3.2-1_arm64.deb ... 357s Unpacking libharfbuzz0b:arm64 (12.3.2-1) ... 357s Selecting previously unselected package x11-common. 357s Preparing to unpack .../019-x11-common_1%3a7.7+24ubuntu1_all.deb ... 357s Unpacking x11-common (1:7.7+24ubuntu1) ... 357s Selecting previously unselected package libice6:arm64. 358s Preparing to unpack .../020-libice6_2%3a1.1.1-1build1_arm64.deb ... 358s Unpacking libice6:arm64 (2:1.1.1-1build1) ... 358s Selecting previously unselected package libjpeg-turbo8:arm64. 358s Preparing to unpack .../021-libjpeg-turbo8_2.1.5-4ubuntu3_arm64.deb ... 358s Unpacking libjpeg-turbo8:arm64 (2.1.5-4ubuntu3) ... 358s Selecting previously unselected package libjpeg8:arm64. 358s Preparing to unpack .../022-libjpeg8_8c-2ubuntu11_arm64.deb ... 358s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 358s Selecting previously unselected package libjs-bootstrap. 358s Preparing to unpack .../023-libjs-bootstrap_3.4.1+dfsg-6_all.deb ... 358s Unpacking libjs-bootstrap (3.4.1+dfsg-6) ... 358s Selecting previously unselected package libjs-highlight.js. 358s Preparing to unpack .../024-libjs-highlight.js_10.7.3+dfsg-2_all.deb ... 358s Unpacking libjs-highlight.js (10.7.3+dfsg-2) ... 358s Selecting previously unselected package libjs-jquery. 358s Preparing to unpack .../025-libjs-jquery_3.7.1+dfsg+~3.5.33-1build1_all.deb ... 358s Unpacking libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 358s Selecting previously unselected package libjs-jquery-datatables. 358s Preparing to unpack .../026-libjs-jquery-datatables_1.11.5+dfsg-2build1_all.deb ... 358s Unpacking libjs-jquery-datatables (1.11.5+dfsg-2build1) ... 358s Selecting previously unselected package liblapack3:arm64. 358s Preparing to unpack .../027-liblapack3_3.12.1-7ubuntu1_arm64.deb ... 358s Unpacking liblapack3:arm64 (3.12.1-7ubuntu1) ... 358s Selecting previously unselected package liblerc4:arm64. 358s Preparing to unpack .../028-liblerc4_4.0.0+ds-5ubuntu2_arm64.deb ... 358s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu2) ... 358s Selecting previously unselected package libthai-data. 358s Preparing to unpack .../029-libthai-data_0.1.30-1_all.deb ... 358s Unpacking libthai-data (0.1.30-1) ... 358s Selecting previously unselected package libthai0:arm64. 358s Preparing to unpack .../030-libthai0_0.1.30-1_arm64.deb ... 358s Unpacking libthai0:arm64 (0.1.30-1) ... 358s Selecting previously unselected package libpango-1.0-0:arm64. 358s Preparing to unpack .../031-libpango-1.0-0_1.57.0-1_arm64.deb ... 358s Unpacking libpango-1.0-0:arm64 (1.57.0-1) ... 358s Selecting previously unselected package libpangoft2-1.0-0:arm64. 358s Preparing to unpack .../032-libpangoft2-1.0-0_1.57.0-1_arm64.deb ... 358s Unpacking libpangoft2-1.0-0:arm64 (1.57.0-1) ... 358s Selecting previously unselected package libpangocairo-1.0-0:arm64. 358s Preparing to unpack .../033-libpangocairo-1.0-0_1.57.0-1_arm64.deb ... 358s Unpacking libpangocairo-1.0-0:arm64 (1.57.0-1) ... 358s Selecting previously unselected package libpaper2:arm64. 358s Preparing to unpack .../034-libpaper2_2.2.5-0.3build1_arm64.deb ... 358s Unpacking libpaper2:arm64 (2.2.5-0.3build1) ... 358s Selecting previously unselected package libpaper-utils. 358s Preparing to unpack .../035-libpaper-utils_2.2.5-0.3build1_arm64.deb ... 358s Unpacking libpaper-utils (2.2.5-0.3build1) ... 358s Selecting previously unselected package libsharpyuv0:arm64. 358s Preparing to unpack .../036-libsharpyuv0_1.5.0-0.1build1_arm64.deb ... 358s Unpacking libsharpyuv0:arm64 (1.5.0-0.1build1) ... 358s Selecting previously unselected package libsm6:arm64. 358s Preparing to unpack .../037-libsm6_2%3a1.2.6-1build1_arm64.deb ... 358s Unpacking libsm6:arm64 (2:1.2.6-1build1) ... 358s Selecting previously unselected package libtcl8.6:arm64. 358s Preparing to unpack .../038-libtcl8.6_8.6.17+dfsg-1build1_arm64.deb ... 358s Unpacking libtcl8.6:arm64 (8.6.17+dfsg-1build1) ... 358s Selecting previously unselected package libjbig0:arm64. 358s Preparing to unpack .../039-libjbig0_2.1-6.1ubuntu3_arm64.deb ... 358s Unpacking libjbig0:arm64 (2.1-6.1ubuntu3) ... 358s Selecting previously unselected package libwebp7:arm64. 358s Preparing to unpack .../040-libwebp7_1.5.0-0.1build1_arm64.deb ... 358s Unpacking libwebp7:arm64 (1.5.0-0.1build1) ... 358s Selecting previously unselected package libtiff6:arm64. 358s Preparing to unpack .../041-libtiff6_4.7.0-3ubuntu3_arm64.deb ... 358s Unpacking libtiff6:arm64 (4.7.0-3ubuntu3) ... 359s Selecting previously unselected package libxft2:arm64. 359s Preparing to unpack .../042-libxft2_2.3.6-1build2_arm64.deb ... 359s Unpacking libxft2:arm64 (2.3.6-1build2) ... 359s Selecting previously unselected package libxss1:arm64. 359s Preparing to unpack .../043-libxss1_1%3a1.2.3-1build4_arm64.deb ... 359s Unpacking libxss1:arm64 (1:1.2.3-1build4) ... 359s Selecting previously unselected package libtk8.6:arm64. 359s Preparing to unpack .../044-libtk8.6_8.6.17-1_arm64.deb ... 359s Unpacking libtk8.6:arm64 (8.6.17-1) ... 359s Selecting previously unselected package libxt6t64:arm64. 359s Preparing to unpack .../045-libxt6t64_1%3a1.2.1-1.3_arm64.deb ... 359s Unpacking libxt6t64:arm64 (1:1.2.1-1.3) ... 359s Selecting previously unselected package node-normalize.css. 359s Preparing to unpack .../046-node-normalize.css_8.0.1-5.1_all.deb ... 359s Unpacking node-normalize.css (8.0.1-5.1) ... 359s Selecting previously unselected package zip. 359s Preparing to unpack .../047-zip_3.0-15ubuntu3_arm64.deb ... 359s Unpacking zip (3.0-15ubuntu3) ... 359s Selecting previously unselected package unzip. 359s Preparing to unpack .../048-unzip_6.0-29ubuntu1_arm64.deb ... 359s Unpacking unzip (6.0-29ubuntu1) ... 359s Selecting previously unselected package xdg-utils. 359s Preparing to unpack .../049-xdg-utils_1.2.1-2ubuntu2_all.deb ... 359s Unpacking xdg-utils (1.2.1-2ubuntu2) ... 359s Selecting previously unselected package r-base-core. 359s Preparing to unpack .../050-r-base-core_4.5.2-1ubuntu2_arm64.deb ... 359s Unpacking r-base-core (4.5.2-1ubuntu2) ... 359s Selecting previously unselected package r-cran-backports. 359s Preparing to unpack .../051-r-cran-backports_1.5.0-2_arm64.deb ... 359s Unpacking r-cran-backports (1.5.0-2) ... 359s Selecting previously unselected package r-cran-boot. 359s Preparing to unpack .../052-r-cran-boot_1.3-32-1_all.deb ... 359s Unpacking r-cran-boot (1.3-32-1) ... 359s Selecting previously unselected package r-cran-cli. 359s Preparing to unpack .../053-r-cran-cli_3.6.4-1_arm64.deb ... 359s Unpacking r-cran-cli (3.6.4-1) ... 359s Selecting previously unselected package r-cran-generics. 359s Preparing to unpack .../054-r-cran-generics_0.1.4-1_all.deb ... 359s Unpacking r-cran-generics (0.1.4-1) ... 359s Selecting previously unselected package r-cran-glue. 359s Preparing to unpack .../055-r-cran-glue_1.8.0-1_arm64.deb ... 359s Unpacking r-cran-glue (1.8.0-1) ... 359s Selecting previously unselected package r-cran-rlang. 359s Preparing to unpack .../056-r-cran-rlang_1.1.5-3_arm64.deb ... 359s Unpacking r-cran-rlang (1.1.5-3) ... 359s Selecting previously unselected package r-cran-lifecycle. 359s Preparing to unpack .../057-r-cran-lifecycle_1.0.5+dfsg-1_all.deb ... 359s Unpacking r-cran-lifecycle (1.0.5+dfsg-1) ... 360s Selecting previously unselected package r-cran-magrittr. 360s Preparing to unpack .../058-r-cran-magrittr_2.0.3-1_arm64.deb ... 360s Unpacking r-cran-magrittr (2.0.3-1) ... 360s Selecting previously unselected package r-cran-utf8. 360s Preparing to unpack .../059-r-cran-utf8_1.2.4-1_arm64.deb ... 360s Unpacking r-cran-utf8 (1.2.4-1) ... 360s Selecting previously unselected package r-cran-vctrs. 360s Preparing to unpack .../060-r-cran-vctrs_0.6.5-1_arm64.deb ... 360s Unpacking r-cran-vctrs (0.6.5-1) ... 360s Selecting previously unselected package r-cran-pillar. 360s Preparing to unpack .../061-r-cran-pillar_1.11.1+dfsg-1_all.deb ... 360s Unpacking r-cran-pillar (1.11.1+dfsg-1) ... 360s Selecting previously unselected package r-cran-r6. 360s Preparing to unpack .../062-r-cran-r6_2.6.1-1_all.deb ... 360s Unpacking r-cran-r6 (2.6.1-1) ... 360s Selecting previously unselected package r-cran-fansi. 360s Preparing to unpack .../063-r-cran-fansi_1.0.6-2_arm64.deb ... 360s Unpacking r-cran-fansi (1.0.6-2) ... 360s Selecting previously unselected package r-cran-pkgconfig. 360s Preparing to unpack .../064-r-cran-pkgconfig_2.0.3-2build2_all.deb ... 360s Unpacking r-cran-pkgconfig (2.0.3-2build2) ... 360s Selecting previously unselected package r-cran-tibble. 360s Preparing to unpack .../065-r-cran-tibble_3.2.1+dfsg-3_arm64.deb ... 360s Unpacking r-cran-tibble (3.2.1+dfsg-3) ... 360s Selecting previously unselected package r-cran-withr. 360s Preparing to unpack .../066-r-cran-withr_3.0.2+dfsg-1_all.deb ... 360s Unpacking r-cran-withr (3.0.2+dfsg-1) ... 360s Selecting previously unselected package r-cran-tidyselect. 360s Preparing to unpack .../067-r-cran-tidyselect_1.2.1+dfsg-1_arm64.deb ... 360s Unpacking r-cran-tidyselect (1.2.1+dfsg-1) ... 360s Selecting previously unselected package r-cran-dplyr. 360s Preparing to unpack .../068-r-cran-dplyr_1.1.4-4_arm64.deb ... 360s Unpacking r-cran-dplyr (1.1.4-4) ... 360s Selecting previously unselected package r-cran-purrr. 360s Preparing to unpack .../069-r-cran-purrr_1.0.4-1_arm64.deb ... 360s Unpacking r-cran-purrr (1.0.4-1) ... 360s Selecting previously unselected package r-cran-stringi. 360s Preparing to unpack .../070-r-cran-stringi_1.8.4-1build2_arm64.deb ... 360s Unpacking r-cran-stringi (1.8.4-1build2) ... 360s Selecting previously unselected package r-cran-stringr. 360s Preparing to unpack .../071-r-cran-stringr_1.5.1-1_all.deb ... 360s Unpacking r-cran-stringr (1.5.1-1) ... 360s Selecting previously unselected package r-cran-cpp11. 360s Preparing to unpack .../072-r-cran-cpp11_0.5.3-1_all.deb ... 360s Unpacking r-cran-cpp11 (0.5.3-1) ... 360s Selecting previously unselected package r-cran-tidyr. 360s Preparing to unpack .../073-r-cran-tidyr_1.3.1-1_arm64.deb ... 360s Unpacking r-cran-tidyr (1.3.1-1) ... 360s Selecting previously unselected package r-cran-broom. 360s Preparing to unpack .../074-r-cran-broom_1.0.12+dfsg-1_all.deb ... 360s Unpacking r-cran-broom (1.0.12+dfsg-1) ... 360s Selecting previously unselected package r-cran-colorspace. 360s Preparing to unpack .../075-r-cran-colorspace_2.1-1+dfsg-1_arm64.deb ... 360s Unpacking r-cran-colorspace (2.1-1+dfsg-1) ... 360s Selecting previously unselected package r-cran-gtable. 360s Preparing to unpack .../076-r-cran-gtable_0.3.6+dfsg-1_all.deb ... 360s Unpacking r-cran-gtable (0.3.6+dfsg-1) ... 360s Selecting previously unselected package r-cran-isoband. 361s Preparing to unpack .../077-r-cran-isoband_0.2.7-1_arm64.deb ... 361s Unpacking r-cran-isoband (0.2.7-1) ... 361s Selecting previously unselected package r-cran-s7. 361s 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... 361s Selecting previously unselected package r-cran-ggplot2. 361s Preparing to unpack .../084-r-cran-ggplot2_4.0.2+dfsg-1_all.deb ... 361s Unpacking r-cran-ggplot2 (4.0.2+dfsg-1) ... 361s Selecting previously unselected package r-cran-cowplot. 361s Preparing to unpack .../085-r-cran-cowplot_1.1.3+dfsg-1_all.deb ... 361s Unpacking r-cran-cowplot (1.1.3+dfsg-1) ... 361s Selecting previously unselected package r-cran-curl. 361s Preparing to unpack .../086-r-cran-curl_7.0.0+dfsg-1_arm64.deb ... 361s Unpacking r-cran-curl (7.0.0+dfsg-1) ... 361s Selecting previously unselected package r-cran-deriv. 361s Preparing to unpack .../087-r-cran-deriv_4.2.0-1_all.deb ... 361s Unpacking r-cran-deriv (4.2.0-1) ... 361s Selecting previously unselected package r-cran-fracdiff. 361s Preparing to unpack .../088-r-cran-fracdiff_1.5-3-1_arm64.deb ... 361s Unpacking r-cran-fracdiff (1.5-3-1) ... 361s Selecting previously unselected package r-cran-lattice. 361s Preparing to unpack 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unselected package r-cran-rcpp. 362s Preparing to unpack .../095-r-cran-rcpp_1.1.0-1_arm64.deb ... 362s Unpacking r-cran-rcpp (1.1.0-1) ... 362s Selecting previously unselected package r-cran-timedate. 362s Preparing to unpack .../096-r-cran-timedate_4052.112-1_arm64.deb ... 362s Unpacking r-cran-timedate (4052.112-1) ... 362s Selecting previously unselected package r-cran-quadprog. 362s Preparing to unpack .../097-r-cran-quadprog_1.5-8-1build2_arm64.deb ... 362s Unpacking r-cran-quadprog (1.5-8-1build2) ... 362s Selecting previously unselected package r-cran-xts. 362s Preparing to unpack .../098-r-cran-xts_0.14.1-1_arm64.deb ... 362s Unpacking r-cran-xts (0.14.1-1) ... 362s Selecting previously unselected package r-cran-ttr. 362s Preparing to unpack .../099-r-cran-ttr_0.24.4-1_arm64.deb ... 362s Unpacking r-cran-ttr (0.24.4-1) ... 362s Selecting previously unselected package r-cran-jsonlite. 362s Preparing to unpack .../100-r-cran-jsonlite_1.9.1+dfsg-1_arm64.deb ... 362s Unpacking r-cran-jsonlite (1.9.1+dfsg-1) ... 362s Selecting previously unselected package r-cran-quantmod. 362s Preparing to unpack .../101-r-cran-quantmod_0.4.28-1_all.deb ... 362s Unpacking r-cran-quantmod (0.4.28-1) ... 362s Selecting previously unselected package r-cran-tseries. 362s Preparing to unpack .../102-r-cran-tseries_0.10-59-3_arm64.deb ... 362s Unpacking r-cran-tseries (0.10-59-3) ... 362s Selecting previously unselected package r-cran-nlme. 362s Preparing to unpack .../103-r-cran-nlme_3.1.168-1_arm64.deb ... 362s Unpacking r-cran-nlme (3.1.168-1) ... 362s Selecting previously unselected package r-cran-urca. 362s Preparing to unpack .../104-r-cran-urca_1.3-4-1build1_arm64.deb ... 362s Unpacking r-cran-urca (1.3-4-1build1) ... 362s Selecting previously unselected package r-cran-rcpparmadillo. 362s Preparing to unpack .../105-r-cran-rcpparmadillo_15.2.3-1-1_arm64.deb ... 362s Unpacking r-cran-rcpparmadillo (15.2.3-1-1) ... 362s Selecting previously unselected package r-cran-forecast. 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(1.0.12+dfsg-1) ... 367s Setting up r-cran-forecast (8.23.0-1) ... 367s Setting up r-cran-modelr (0.1.11-1) ... 367s Setting up r-cran-doby (4.7.1-3) ... 367s Setting up r-cran-pbkrtest (0.5.5-1) ... 367s Processing triggers for libc-bin (2.42-2ubuntu4) ... 367s Processing triggers for man-db (2.13.1-1build1) ... 368s Processing triggers for install-info (7.2-5) ... 369s autopkgtest [23:57:53]: test run-unit-test: [----------------------- 369s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 369s BEGIN TEST test_a_utils.R 369s 369s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 369s Copyright (C) 2025 The R Foundation for Statistical Computing 369s Platform: aarch64-unknown-linux-gnu 369s 369s R is free software and comes with ABSOLUTELY NO WARRANTY. 369s You are welcome to redistribute it under certain conditions. 369s Type 'license()' or 'licence()' for distribution details. 369s 369s R is a collaborative project with many contributors. 369s Type 'contributors()' for more information and 369s 'citation()' on how to cite R or R packages in publications. 369s 369s Type 'demo()' for some demos, 'help()' for on-line help, or 369s 'help.start()' for an HTML browser interface to help. 369s Type 'q()' to quit R. 369s 369s > # test_a_utils.R 369s > 369s > library(lmerTest) 369s Loading required package: lme4 369s Loading required package: Matrix 371s 371s Attaching package: 'lmerTest' 371s 371s The following object is masked from 'package:lme4': 371s 371s lmer 371s 371s The following object is masked from 'package:stats': 371s 371s step 371s 371s > 371s > # test safeDeparse() - equivalence and differences to deparse(): 371s > deparse_args <- formals(deparse) 371s > safeDeparse_args <- formals(lmerTest:::safeDeparse) 371s > stopifnot( 371s + all.equal(names(deparse_args), names(safeDeparse_args)), 371s + all.equal(deparse_args[!names(deparse_args) %in% c("control", "width.cutoff")], 371s + safeDeparse_args[!names(safeDeparse_args) %in% c("control", "width.cutoff")]), 371s + all.equal(deparse_args[["width.cutoff"]], 60L), 371s + all(eval(safeDeparse_args[["control"]]) %in% eval(deparse_args[["control"]])), 371s + all.equal(safeDeparse_args[["width.cutoff"]], 500L) 371s + ) 371s > 371s > 371s BEGIN TEST test_anova.R 371s 371s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 371s Copyright (C) 2025 The R Foundation for Statistical Computing 371s Platform: aarch64-unknown-linux-gnu 371s 371s R is free software and comes with ABSOLUTELY NO WARRANTY. 371s You are welcome to redistribute it under certain conditions. 371s Type 'license()' or 'licence()' for distribution details. 371s 371s R is a collaborative project with many contributors. 371s Type 'contributors()' for more information and 371s 'citation()' on how to cite R or R packages in publications. 371s 371s Type 'demo()' for some demos, 'help()' for on-line help, or 371s 'help.start()' for an HTML browser interface to help. 371s Type 'q()' to quit R. 371s 371s > # test_anova.R 371s > library(lmerTest) 371s Loading required package: lme4 371s Loading required package: Matrix 373s 373s Attaching package: 'lmerTest' 373s 373s The following object is masked from 'package:lme4': 373s 373s lmer 373s 373s The following object is masked from 'package:stats': 373s 373s step 373s 373s > 373s > # WRE says "using if(requireNamespace("pkgname")) is preferred, if possible." 373s > # even in tests: 373s > assertError <- function(expr, ...) 373s + if(requireNamespace("tools")) tools::assertError(expr, ...) else invisible() 373s > assertWarning <- function(expr, ...) 373s + if(requireNamespace("tools")) tools::assertWarning(expr, ...) else invisible() 373s > 373s > # Kenward-Roger only available with pbkrtest and only then validated in R >= 3.3.3 373s > # (faulty results for R < 3.3.3 may be due to unstated dependencies in pbkrtest) 373s > has_pbkrtest <- requireNamespace("pbkrtest", quietly = TRUE) && getRversion() >= "3.3.3" 373s > 373s > data("sleepstudy", package="lme4") 373s > TOL <- 1e-4 373s > 373s > #################################### 373s > ## Basic anova tests 373s > #################################### 373s > 373s > m <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy) 373s > 373s > ####### ddf argument: 373s > (an1 <- anova(m)) # Also testing print method. 373s Type III Analysis of Variance Table with Satterthwaite's method 373s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 373s Days 30031 30031 1 17 45.853 3.264e-06 *** 373s --- 373s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 373s > (an2 <- anova(m, ddf="Satterthwaite")) 373s Type III Analysis of Variance Table with Satterthwaite's method 373s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 373s Days 30031 30031 1 17 45.853 3.264e-06 *** 373s --- 373s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 373s > (an2b <- anova(m, ddf="Satterthwaite", type=3)) 373s Type III Analysis of Variance Table with Satterthwaite's method 373s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 373s Days 30031 30031 1 17 45.853 3.264e-06 *** 373s --- 373s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 373s > (an2c <- anova(m, ddf="Satterthwaite", type=2)) 373s Type II Analysis of Variance Table with Satterthwaite's method 373s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 373s Days 30031 30031 1 17 45.853 3.264e-06 *** 373s --- 373s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 373s > stopifnot(isTRUE( 373s + all.equal(an1, an2, tolerance=TOL) 373s + )) 373s > (an3 <- anova(m, ddf="Sat")) ## Abbreviated argument 373s Type III Analysis of Variance Table with Satterthwaite's method 373s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 373s Days 30031 30031 1 17 45.853 3.264e-06 *** 373s --- 373s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 373s > stopifnot(isTRUE( 373s + all.equal(an1, an3, tolerance=TOL) 373s + )) 373s > if(has_pbkrtest) { 373s + (anova(m, ddf="Kenward-Roger")) 373s + (anova(m, ddf="Kenward-Roger", type=3)) 373s + } 374s Type III Analysis of Variance Table with Kenward-Roger's method 374s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 374s Days 30031 30031 1 17 45.853 3.264e-06 *** 374s --- 374s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 374s > (an1 <- anova(m, ddf="lme4")) 374s Analysis of Variance Table 374s npar Sum Sq Mean Sq F value 374s Days 1 30031 30031 45.853 374s > (an2 <- anova(m, ddf="lme4", type=3)) # 'type' is ignored with ddf="lme4" 374s Analysis of Variance Table 374s npar Sum Sq Mean Sq F value 374s Days 1 30031 30031 45.853 374s > stopifnot(isTRUE( 374s + all.equal(an1, an2, tolerance=TOL) 374s + )) 374s > res <- assertError(anova(m, ddf="KR")) ## Error on incorrect arg. 374s > stopifnot( 374s + grepl("'arg' should be one of ", unlist(res[[1]])$message) 374s + ) 374s > 374s > ## lme4 method: 374s > an1 <- anova(m, ddf="lme4") 374s > an2 <- anova(as(m, "lmerMod")) 374s > stopifnot(isTRUE( 374s + all.equal(an1, an2, tolerance=TOL) 374s + )) 374s > 374s > ###### type argument: 374s > (an1 <- anova(m, type="1")) # valid type arg. 374s Type I Analysis of Variance Table with Satterthwaite's method 374s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 374s Days 30031 30031 1 17 45.853 3.264e-06 *** 374s --- 374s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 374s > (an2 <- anova(m, type="I")) # same 374s Type I Analysis of Variance Table with Satterthwaite's method 374s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 374s Days 30031 30031 1 17 45.853 3.264e-06 *** 374s --- 374s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 374s > stopifnot(isTRUE( 374s + all.equal(an1, an2, tolerance=TOL) 374s + )) 374s > (an3 <- anova(m, type=1)) # Not strictly valid, but accepted 374s Type I Analysis of Variance Table with Satterthwaite's method 374s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 374s Days 30031 30031 1 17 45.853 3.264e-06 *** 374s --- 374s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 374s > stopifnot(isTRUE( 374s + all.equal(an1, an3, tolerance=TOL) 374s + )) 374s > 374s > (an1 <- anova(m, type="2")) # valid type arg. 374s Type II Analysis of Variance Table with Satterthwaite's method 374s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 374s Days 30031 30031 1 17 45.853 3.264e-06 *** 374s --- 374s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 374s > (an2 <- anova(m, type="II")) # same 374s Type II Analysis of Variance Table with Satterthwaite's method 374s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 374s Days 30031 30031 1 17 45.853 3.264e-06 *** 374s --- 374s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 374s > stopifnot(isTRUE( 374s + all.equal(an1, an2, tolerance=TOL) 374s + )) 374s > (an3 <- anova(m, type=3)) # Not strictly valid, but accepted 374s Type III Analysis of Variance Table with Satterthwaite's method 374s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 374s Days 30031 30031 1 17 45.853 3.264e-06 *** 374s --- 374s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 374s > stopifnot(isTRUE( 374s + all.equal(an1, an3, check.attributes=FALSE, tolerance=TOL) 374s + )) 374s > 374s > (an1 <- anova(m, type="3")) # valid type arg. 374s Type III Analysis of Variance Table with Satterthwaite's method 374s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 374s Days 30031 30031 1 17 45.853 3.264e-06 *** 374s --- 374s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 374s > (an2 <- anova(m, type="III")) # same 374s Type III Analysis of Variance Table with Satterthwaite's method 374s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 374s Days 30031 30031 1 17 45.853 3.264e-06 *** 374s --- 374s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 374s > stopifnot(isTRUE( 374s + all.equal(an1, an2, tolerance=TOL) 374s + )) 374s > (an3 <- anova(m, type=3)) # Not strictly valid, but accepted 374s Type III Analysis of Variance Table with Satterthwaite's method 374s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 374s Days 30031 30031 1 17 45.853 3.264e-06 *** 374s --- 374s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 374s > stopifnot(isTRUE( 374s + all.equal(an1, an3, tolerance=TOL) 374s + )) 374s > assertError(anova(m, type=0)) # Not valid arg. 374s > assertError(anova(m, type="i")) # Not valid arg. 374s > 374s > ####### Model comparison: 374s > fm <- lm(Reaction ~ Days, sleepstudy) 374s > (an <- anova(m, fm)) 374s refitting model(s) with ML (instead of REML) 374s Data: sleepstudy 374s Models: 374s fm: Reaction ~ Days 374s m: Reaction ~ Days + (Days | Subject) 374s npar AIC BIC logLik -2*log(L) Chisq Df Pr(>Chisq) 374s fm 3 1906.3 1915.9 -950.15 1900.3 374s m 6 1763.9 1783.1 -875.97 1751.9 148.35 3 < 2.2e-16 *** 374s --- 374s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 374s > stopifnot( 374s + nrow(an) == 2L, 374s + rownames(an)[2] == "m" 374s + ) 374s > 374s > m2 <- lmer(Reaction ~ Days + I(Days^2) + (Days | Subject), sleepstudy) 374s > (an <- anova(m, m2, refit=FALSE)) 374s Data: sleepstudy 374s Models: 374s m: Reaction ~ Days + (Days | Subject) 374s m2: Reaction ~ Days + I(Days^2) + (Days | Subject) 374s npar AIC BIC logLik -2*log(L) Chisq Df Pr(>Chisq) 374s m 6 1755.6 1774.8 -871.81 1743.6 374s m2 7 1756.8 1779.2 -871.41 1742.8 0.8127 1 0.3673 374s > stopifnot( 374s + nrow(an) == 2L, 374s + rownames(an)[1] == "m" 374s + ) 374s > 374s > 374s > #################################### 374s > ## Example with factor fixef: 374s > #################################### 374s > 374s > ## 'temp' is continuous, 'temperature' an ordered factor with 6 levels 374s > data("cake", package="lme4") 374s > m <- lmer(angle ~ recipe * temp + (1|recipe:replicate), cake) 374s > (an <- anova(m)) 374s Type III Analysis of Variance Table with Satterthwaite's method 374s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 374s recipe 4.00 2.00 2 254.02 0.0957 0.9088 374s temp 1966.71 1966.71 1 222.00 94.1632 <2e-16 *** 374s recipe:temp 1.74 0.87 2 222.00 0.0417 0.9592 374s --- 374s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 374s > (an_lme4 <- anova(m, ddf="lme4")) 374s Analysis of Variance Table 374s npar Sum Sq Mean Sq F value 374s recipe 2 10.39 5.20 0.2488 374s temp 1 1966.71 1966.71 94.1632 374s recipe:temp 2 1.74 0.87 0.0417 374s > 374s > if(has_pbkrtest) { 374s + (an_KR <- anova(m, ddf="Kenward-Roger")) 374s + # res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")], 374s + # an_lme4[, c("Sum Sq", "Mean Sq", "F value")]) 374s + # stopifnot(isTRUE(res)) 374s + res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")], 374s + an_KR[, c("Sum Sq", "Mean Sq", "F value")], tolerance=TOL) 374s + stopifnot(isTRUE(res)) 374s + } 374s > stopifnot(all.equal(c(2, 1, 2), an$NumDF, tol=1e-6), 374s + all.equal(c(254.0157612, 222, 222), an$DenDF, tol=TOL)) 374s > 374s > an3 <- anova(m, type=3) 374s > an2 <- anova(m, type=2) 374s > an1 <- anova(m, type=1) 374s > 374s > ## Data is balanced, so Type II and III should be identical: 374s > ## One variable is continuous, so Type I and II/III are different: 374s > stopifnot( 374s + isTRUE(all.equal(an3, an2, check.attributes=FALSE, tolerance=TOL)), 374s + !isTRUE(all.equal(an1, an2, check.attributes=FALSE, tolerance=1e-8)) 374s + ) 374s > 374s > # Using an ordered factor: 374s > m <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake) 374s > (an1 <- anova(m, type=1)) 374s Type I Analysis of Variance Table with Satterthwaite's method 374s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 374s recipe 10.19 5.09 2 42 0.2488 0.7809 374s temperature 2100.30 420.06 5 210 20.5199 <2e-16 *** 374s recipe:temperature 205.98 20.60 10 210 1.0062 0.4393 374s --- 374s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 374s > (an2 <- anova(m, type=2)) 374s Type II Analysis of Variance Table with Satterthwaite's method 374s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 374s recipe 10.19 5.09 2 42 0.2488 0.7809 374s temperature 2100.30 420.06 5 210 20.5199 <2e-16 *** 374s recipe:temperature 205.98 20.60 10 210 1.0062 0.4393 374s --- 374s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 374s > # Type 3 is also available with ordered factors: 374s > (an3 <- anova(m, type=3)) 374s Type III Analysis of Variance Table with Satterthwaite's method 374s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 374s recipe 10.19 5.09 2 42 0.2488 0.7809 374s temperature 2100.30 420.06 5 210 20.5199 <2e-16 *** 374s recipe:temperature 205.98 20.60 10 210 1.0062 0.4393 374s --- 374s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 374s > ## Balanced data and only factors: Type I, II and III should be the same: 374s > stopifnot( 374s + isTRUE(all.equal(an1, an2, check.attributes=FALSE, tolerance=TOL)), 374s + isTRUE(all.equal(an1, an3, check.attributes=FALSE, tolerance=TOL)) 374s + ) 374s > 374s > (an <- anova(m, type=1)) 374s Type I Analysis of Variance Table with Satterthwaite's method 374s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 374s recipe 10.19 5.09 2 42 0.2488 0.7809 374s temperature 2100.30 420.06 5 210 20.5199 <2e-16 *** 374s recipe:temperature 205.98 20.60 10 210 1.0062 0.4393 374s --- 374s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 374s > (an_lme4 <- anova(m, type=1, ddf="lme4")) 374s Analysis of Variance Table 374s npar Sum Sq Mean Sq F value 374s recipe 2 10.19 5.09 0.2488 374s temperature 5 2100.30 420.06 20.5199 374s recipe:temperature 10 205.98 20.60 1.0062 374s > res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")], 374s + an_lme4[, c("Sum Sq", "Mean Sq", "F value")], tolerance=TOL) 374s > stopifnot(isTRUE(res)) 374s > if(has_pbkrtest) { 374s + (an_KR <- anova(m, type=1, ddf="Kenward-Roger")) 374s + res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")], 374s + an_KR[, c("Sum Sq", "Mean Sq", "F value")], tolerance=TOL) 374s + stopifnot(isTRUE(res)) 374s + } 374s > stopifnot(all.equal(c(2, 5, 10), an$NumDF, tolerance=TOL), 374s + all.equal(c(42, 210, 210), an$DenDF, tolerance=TOL)) 374s > 374s > ######## 374s > ## Make case with balanced unordered factors: 374s > cake2 <- cake 374s > cake2$temperature <- factor(cake2$temperature, ordered = FALSE) 374s > # str(cake2) 374s > stopifnot( 374s + !is.ordered(cake2$temperature) 374s + ) 374s > m <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake2) 374s > (an1 <- anova(m, type=1)) 374s Type I Analysis of Variance Table with Satterthwaite's method 374s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 374s recipe 10.19 5.09 2 42 0.2488 0.7809 374s temperature 2100.30 420.06 5 210 20.5199 <2e-16 *** 374s recipe:temperature 205.98 20.60 10 210 1.0062 0.4393 374s --- 374s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 374s > (an2 <- anova(m, type=2)) 374s Type II Analysis of Variance Table with Satterthwaite's method 374s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 374s recipe 10.19 5.09 2 42 0.2488 0.7809 374s temperature 2100.30 420.06 5 210 20.5199 <2e-16 *** 374s recipe:temperature 205.98 20.60 10 210 1.0062 0.4393 374s --- 374s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 374s > (an3 <- anova(m, type=3)) 374s Type III Analysis of Variance Table with Satterthwaite's method 374s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 374s recipe 10.19 5.09 2 42 0.2488 0.7809 374s temperature 2100.30 420.06 5 210 20.5199 <2e-16 *** 374s recipe:temperature 205.98 20.60 10 210 1.0062 0.4393 374s --- 374s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 374s > ## Balanced data and only factors: Type I, II, and III should be the same: 374s > stopifnot( 374s + isTRUE(all.equal(an1, an2, check.attributes=FALSE, tolerance=TOL)), 374s + isTRUE(all.equal(an3, an2, check.attributes=FALSE, tolerance=TOL)) 374s + ) 374s > ######## 374s > 374s > # No intercept: 374s > m <- lmer(angle ~ 0 + recipe * temp + (1|recipe:replicate), cake) 375s > (an <- anova(m, type=1)) 375s Type I Analysis of Variance Table with Satterthwaite's method 375s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 375s recipe 21442.9 7147.6 3 42 342.2200 <2e-16 *** 375s temp 1966.7 1966.7 1 222 94.1632 <2e-16 *** 375s recipe:temp 1.7 0.9 2 222 0.0417 0.9592 375s --- 375s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 375s > (an2 <- anova(m, type=2)) 375s Type II Analysis of Variance Table with Satterthwaite's method 375s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 375s recipe 4.48 1.49 3 254.02 0.0714 0.9752 375s temp 1966.71 1966.71 1 222.00 94.1632 <2e-16 *** 375s recipe:temp 1.74 0.87 2 222.00 0.0417 0.9592 375s --- 375s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 375s > (an2 <- anova(m, type=3)) 375s Type III Analysis of Variance Table with Satterthwaite's method 375s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 375s recipe 4.48 1.49 3 254.02 0.0714 0.9752 375s temp 1966.71 1966.71 1 222.00 94.1632 <2e-16 *** 375s recipe:temp 1.74 0.87 2 222.00 0.0417 0.9592 375s --- 375s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 375s > if(has_pbkrtest) 375s + (an_KR <- anova(m, ddf="Kenward-Roger")) 375s Type III Analysis of Variance Table with Kenward-Roger's method 375s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 375s recipe 4.48 1.49 3 254.02 0.0714 0.9752 375s temp 1966.71 1966.71 1 222.00 94.1632 <2e-16 *** 375s recipe:temp 1.74 0.87 2 222.00 0.0417 0.9592 375s --- 375s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 375s > (an_lme4 <- anova(m, ddf="lme4")) 375s Analysis of Variance Table 375s npar Sum Sq Mean Sq F value 375s recipe 3 21442.9 7147.6 342.2200 375s temp 1 1966.7 1966.7 94.1632 375s recipe:temp 2 1.7 0.9 0.0417 375s > res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")], 375s + an_lme4[, c("Sum Sq", "Mean Sq", "F value")], tolerance=TOL) 375s > stopifnot(isTRUE(res)) 375s > 375s > # ML-fit: 375s > m <- lmer(angle ~ recipe * temp + (1|recipe:replicate), cake, REML=FALSE) 375s > (an <- anova(m, type=1)) 375s Type I Analysis of Variance Table with Satterthwaite's method 375s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 375s recipe 10.99 5.49 2 45 0.2666 0.7672 375s temp 1966.71 1966.71 1 225 95.4357 <2e-16 *** 375s recipe:temp 1.74 0.87 2 225 0.0423 0.9586 375s --- 375s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 375s > if(has_pbkrtest) 375s + assertError(an <- anova(m, ddf="Kenward-Roger")) # KR fits should be REML 375s > (an_lme4 <- anova(m, ddf="lme4")) 375s Analysis of Variance Table 375s npar Sum Sq Mean Sq F value 375s recipe 2 10.99 5.49 0.2666 375s temp 1 1966.71 1966.71 95.4357 375s recipe:temp 2 1.74 0.87 0.0423 375s > res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")], 375s + an_lme4[, c("Sum Sq", "Mean Sq", "F value")], tolerance=TOL) 375s > stopifnot(isTRUE(res)) 375s > 375s > #################################### 375s > ## Using contr.sum: 375s > #################################### 375s > 375s > m <- lmer(angle ~ recipe * temp + (1|recipe:replicate), cake, 375s + contrasts = list('recipe' = "contr.sum")) 375s > (an <- anova(m, type=1)) 375s Type I Analysis of Variance Table with Satterthwaite's method 375s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 375s recipe 10.39 5.20 2 42 0.2488 0.7809 375s temp 1966.71 1966.71 1 222 94.1632 <2e-16 *** 375s recipe:temp 1.74 0.87 2 222 0.0417 0.9592 375s --- 375s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 375s > (an2 <- anova(m, type=2)) 375s Type II Analysis of Variance Table with Satterthwaite's method 375s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 375s recipe 4.00 2.00 2 254.02 0.0957 0.9088 375s temp 1966.71 1966.71 1 222.00 94.1632 <2e-16 *** 375s recipe:temp 1.74 0.87 2 222.00 0.0417 0.9592 375s --- 375s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 375s > (an3 <- anova(m, type=3)) 375s Type III Analysis of Variance Table with Satterthwaite's method 375s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 375s recipe 4.00 2.00 2 254.02 0.0957 0.9088 375s temp 1966.71 1966.71 1 222.00 94.1632 <2e-16 *** 375s recipe:temp 1.74 0.87 2 222.00 0.0417 0.9592 375s --- 375s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 375s > stopifnot( 375s + isTRUE(all.equal(an2, an3, check.attributes=FALSE, tolerance=TOL)) 375s + ) 375s > if(has_pbkrtest) 375s + (an_KR <- anova(m, type=1, ddf="Kenward-Roger")) 375s Type I Analysis of Variance Table with Kenward-Roger's method 375s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 375s recipe 10.39 5.20 2 42 0.2488 0.7809 375s temp 1966.71 1966.71 1 222 94.1632 <2e-16 *** 375s recipe:temp 1.74 0.87 2 222 0.0417 0.9592 375s --- 375s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 375s > (an_lme4 <- anova(m, ddf="lme4")) 375s Analysis of Variance Table 375s npar Sum Sq Mean Sq F value 375s recipe 2 10.39 5.20 0.2488 375s temp 1 1966.71 1966.71 94.1632 375s recipe:temp 2 1.74 0.87 0.0417 375s > res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")], 375s + an_lme4[, c("Sum Sq", "Mean Sq", "F value")], tolerance=TOL) 375s > stopifnot(isTRUE(res)) 375s > 375s > 375s > #################################### 375s > ## Example with continuous fixef: 375s > #################################### 375s > 375s > # Example with no fixef: 375s > m <- lmer(Reaction ~ -1 + (Days | Subject), sleepstudy) 375s > # m <- lmer(Reaction ~ 0 + (Days | Subject), sleepstudy) # alternative 375s > stopifnot(length(fixef(m)) == 0L) 375s > (an <- anova(m, type=1)) 375s Type I Analysis of Variance Table with Satterthwaite's method 375s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 375s > (an_2 <- anova(m, type=2)) 375s Type II Analysis of Variance Table with Satterthwaite's method 375s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 375s > (an_3 <- anova(m, type=3)) 375s Type III Analysis of Variance Table with Satterthwaite's method 375s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 375s > stopifnot(nrow(an) == 0L, 375s + nrow(an_2) == 0L, 375s + nrow(an_3) == 0L) 375s > # anova(m, ddf="lme4") # Bug in lme4 it seems 375s > if(has_pbkrtest) { 375s + (an_KR <- anova(m, ddf="Kenward-Roger")) 375s + stopifnot( 375s + nrow(an_KR) == 0L 375s + ) 375s + } 375s > 375s > # Example with intercept only: 375s > m <- lmer(Reaction ~ (Days | Subject), sleepstudy) 375s > # m <- lmer(Reaction ~ 1 + (Days | Subject), sleepstudy) # alternative 375s > stopifnot(length(fixef(m)) == 1L, 375s + names(fixef(m)) == "(Intercept)") 375s > (an <- anova(m)) 375s Type III Analysis of Variance Table with Satterthwaite's method 375s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 375s > (an_2 <- anova(m, type=2)) 375s Type II Analysis of Variance Table with Satterthwaite's method 375s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 375s > (an_3 <- anova(m, type=3)) 375s Type III Analysis of Variance Table with Satterthwaite's method 375s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 375s > (an_lme4 <- anova(m, ddf="lme4")) 375s Analysis of Variance Table 375s npar Sum Sq Mean Sq F value 375s > stopifnot(nrow(an) == 0L, 375s + nrow(an_2) == 0L, 375s + nrow(an_3) == 0L, 375s + nrow(an_lme4) == 0L) 375s > if(has_pbkrtest) { 375s + (an_KR <- anova(m, ddf="Kenward-Roger")) 375s + stopifnot( 375s + nrow(an_KR) == 0L 375s + ) 375s + } 375s > 375s > # Example with 1 fixef without intercept: 375s > # for packageVersion("lme4") < 1.1.20 375s > # mOld <- lmer(Reaction ~ Days - 1 + (Days | Subject), sleepstudy) 375s > # for packageVersion("lme4") >= 1.1.20 we need to specify the old default 375s > # optimizer to get the model to converge well enough. 375s > m <- lmer(Reaction ~ Days - 1 + (Days | Subject), sleepstudy, 375s + control=lmerControl(optimizer="bobyqa")) 375s > # m <- lmer(Reaction ~ 0 + Days + (Days | Subject), sleepstudy) # alternative 375s > stopifnot(length(fixef(m)) == 1L, 375s + names(fixef(m)) == "Days") 375s > (an <- anova(m)) 375s Type III Analysis of Variance Table with Satterthwaite's method 375s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 375s Days 93564 93564 1 17 142.86 1.069e-09 *** 375s --- 375s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 375s > (an_2 <- anova(m, type=2)) 375s Type II Analysis of Variance Table with Satterthwaite's method 375s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 375s Days 93564 93564 1 17 142.86 1.069e-09 *** 375s --- 375s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 375s > (an_3 <- anova(m, type=3)) 375s Type III Analysis of Variance Table with Satterthwaite's method 375s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 375s Days 93564 93564 1 17 142.86 1.069e-09 *** 375s --- 375s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 375s > (an_lme4 <- anova(m, ddf="lme4")) 375s Analysis of Variance Table 375s npar Sum Sq Mean Sq F value 375s Days 1 93564 93564 142.86 375s > stopifnot(nrow(an) == 1L, 375s + nrow(an_2) == 1L, 375s + nrow(an_3) == 1L, 375s + nrow(an_lme4) == 1L) 375s > if(has_pbkrtest) { 375s + (an_KR <- anova(m, ddf="Kenward-Roger")) 375s + stopifnot( 375s + nrow(an_KR) == 1L 375s + ) 375s + } 375s > 375s > res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")], 375s + an_lme4[, c("Sum Sq", "Mean Sq", "F value")], tolerance=TOL) 375s > stopifnot(isTRUE(res)) 375s > stopifnot(isTRUE(all.equal( 375s + c(1, 17), unname(unlist(an[, c("NumDF", "DenDF")])), tolerance=TOL 375s + ))) 375s > 375s > # Example with >1 fixef without intercept: 375s > m <- lmer(Reaction ~ Days - 1 + I(Days^2) + (Days | Subject), sleepstudy) 375s > stopifnot(length(fixef(m)) == 2L, 375s + names(fixef(m)) == c("Days", "I(Days^2)")) 375s > (an <- anova(m)) 375s Type III Analysis of Variance Table with Satterthwaite's method 375s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 375s Days 22140.3 22140.3 1 69.049 33.9480 1.638e-07 *** 375s I(Days^2) 744.7 744.7 1 143.679 1.1419 0.287 375s --- 375s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 375s > (an_2 <- anova(m, type=2)) 375s Type II Analysis of Variance Table with Satterthwaite's method 375s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 375s Days 22140.3 22140.3 1 69.049 33.9480 1.638e-07 *** 375s I(Days^2) 744.7 744.7 1 143.679 1.1419 0.287 375s --- 375s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 375s > (an_3 <- anova(m, type=3)) 375s Type III Analysis of Variance Table with Satterthwaite's method 375s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 375s Days 22140.3 22140.3 1 69.049 33.9480 1.638e-07 *** 375s I(Days^2) 744.7 744.7 1 143.679 1.1419 0.287 375s --- 375s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 375s > (an_lme4 <- anova(m, ddf="lme4")) 375s Analysis of Variance Table 375s npar Sum Sq Mean Sq F value 375s Days 1 93171 93171 142.8612 375s I(Days^2) 1 745 745 1.1419 375s > stopifnot(nrow(an) == 2L, 375s + nrow(an_3) == 2L, 375s + nrow(an_lme4) == 2L) 375s > if(has_pbkrtest) { 375s + (an_KR <- anova(m, ddf="Kenward-Roger")) 375s + stopifnot( 375s + nrow(an_KR) == 2L 375s + ) 375s + } 375s > # Here is a diff in SSQ which doesn't seem well-defined anyway... 375s > # SSQ for I(Days^2) agree though. 375s > # t-statistics also agree: 375s > coef(summary(m)) 375s Estimate Std. Error df t value Pr(>|t|) 375s Days 15.8889259 2.7270141 69.04948 5.826492 1.638111e-07 375s I(Days^2) 0.2795489 0.2616038 143.67907 1.068597 2.870436e-01 375s > Lmat <- diag(length(fixef(m))) 375s > lmerTest:::rbindall(lapply(1:nrow(Lmat), function(i) contest1D(m, Lmat[i, ]))) 375s Estimate Std. Error df t value Pr(>|t|) 375s 1 15.8889259 2.7270141 69.04948 5.826492 1.638111e-07 375s 2 0.2795489 0.2616038 143.67907 1.068597 2.870436e-01 375s > 375s > # Example with >1 fixef and intercept: 375s > m <- lmer(Reaction ~ Days + I(Days^2) + (Days | Subject), sleepstudy) 376s > stopifnot(length(fixef(m)) == 3L) 376s > (an <- anova(m, type=1)) 376s Type I Analysis of Variance Table with Satterthwaite's method 376s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 376s Days 29894.8 29894.8 1 17 45.8530 3.264e-06 *** 376s I(Days^2) 1079.5 1079.5 1 143 1.6558 0.2003 376s --- 376s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 376s > (an_2 <- anova(m, type=2)) 376s Type II Analysis of Variance Table with Satterthwaite's method 376s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 376s Days 4534.5 4534.5 1 114.43 6.9551 0.00952 ** 376s I(Days^2) 1079.5 1079.5 1 143.00 1.6558 0.20026 376s --- 376s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 376s > (an_3 <- anova(m, type=3)) 376s Type III Analysis of Variance Table with Satterthwaite's method 376s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 376s Days 4534.5 4534.5 1 114.43 6.9551 0.00952 ** 376s I(Days^2) 1079.5 1079.5 1 143.00 1.6558 0.20026 376s --- 376s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 376s > (an_lme4 <- anova(m, ddf="lme4")) 376s Analysis of Variance Table 376s npar Sum Sq Mean Sq F value 376s Days 1 29894.8 29894.8 45.8530 376s I(Days^2) 1 1079.5 1079.5 1.6558 376s > res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")], 376s + an_lme4[, c("Sum Sq", "Mean Sq", "F value")], tolerance=TOL) 376s > stopifnot(isTRUE(res)) 376s > 376s > if(has_pbkrtest) { 376s + (an_KR <- anova(m, ddf="Kenward-Roger")) 376s + res <- all.equal(an_3[, c("Sum Sq", "Mean Sq", "DenDF", "F value")], 376s + an_KR[, c("Sum Sq", "Mean Sq", "DenDF", "F value")], tolerance=TOL) 376s + stopifnot(isTRUE(res)) 376s + } 376s > 376s > ## FIXME: Test the use of refit arg to lme4:::anova.merMod 376s > 376s > ############################## 376s > # Test that type III anova is the same regardless of contrast coding: 376s > # 3 x 3 factorial with missing diagonal 376s > data("cake", package="lme4") 376s > cake4 <- cake 376s > cake4$temperature <- factor(cake4$temperature, ordered=FALSE) 376s > cake4 <- droplevels(subset(cake4, temperature %in% levels(cake4$temperature)[1:3])) 376s > cake4 <- droplevels(subset(cake4, !((recipe == "A" & temperature == "175") | 376s + (recipe == "B" & temperature == "185") | 376s + (recipe == "C" & temperature == "195") ))) 376s > str(cake4) 376s 'data.frame': 90 obs. of 5 variables: 376s $ replicate : Factor w/ 15 levels "1","2","3","4",..: 1 1 1 1 1 1 2 2 2 2 ... 376s $ recipe : Factor w/ 3 levels "A","B","C": 1 1 2 2 3 3 1 1 2 2 ... 376s $ temperature: Factor w/ 3 levels "175","185","195": 2 3 1 3 1 2 2 3 1 3 ... 376s $ angle : int 46 47 39 51 46 44 29 35 35 47 ... 376s $ temp : num 185 195 175 195 175 185 185 195 175 195 ... 376s > with(cake4, table(recipe, temperature)) 376s temperature 376s recipe 175 185 195 376s A 0 15 15 376s B 15 0 15 376s C 15 15 0 376s > # load_all(r2path) 376s > 376s > fm1 <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake4) 376s fixed-effect model matrix is rank deficient so dropping 3 columns / coefficients 376s > fm2 <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake4, 376s + contrasts=list(recipe="contr.sum", temperature="contr.SAS")) 376s fixed-effect model matrix is rank deficient so dropping 3 columns / coefficients 376s > fm3 <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake4, 376s + contrasts=list(recipe="contr.sum", temperature="contr.poly")) 376s fixed-effect model matrix is rank deficient so dropping 3 columns / coefficients 376s > fm4 <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake4, 376s + contrasts=list(recipe=contr.helmert, temperature="contr.poly")) 376s fixed-effect model matrix is rank deficient so dropping 3 columns / coefficients 376s > (an1 <- anova(fm1)) 376s Missing cells for: recipeA:temperature175, recipeB:temperature185, recipeC:temperature195. 376s Interpret type III hypotheses with care. 376s Type III Analysis of Variance Table with Satterthwaite's method 376s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 376s recipe 2.282 1.141 2 45.888 0.0871 0.916766 376s temperature 136.267 68.133 2 42.000 5.1998 0.009602 ** 376s recipe:temperature 52.900 52.900 1 42.000 4.0372 0.050963 . 376s --- 376s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 376s > (an2 <- anova(fm2)) 376s Missing cells for: recipeA:temperature175, recipeB:temperature185, recipeC:temperature195. 376s Interpret type III hypotheses with care. 376s Type III Analysis of Variance Table with Satterthwaite's method 376s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 376s recipe 2.282 1.141 2 45.888 0.0871 0.916766 376s temperature 136.267 68.133 2 42.000 5.1998 0.009602 ** 376s recipe:temperature 52.900 52.900 1 42.000 4.0372 0.050963 . 376s --- 376s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 376s > (an3 <- anova(fm3)) 376s Missing cells for: recipeA:temperature175, recipeB:temperature185, recipeC:temperature195. 376s Interpret type III hypotheses with care. 376s Type III Analysis of Variance Table with Satterthwaite's method 376s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 376s recipe 2.282 1.141 2 45.888 0.0871 0.916766 376s temperature 136.267 68.133 2 42.000 5.1998 0.009602 ** 376s recipe:temperature 52.900 52.900 1 42.000 4.0372 0.050963 . 376s --- 376s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 376s > (an4 <- anova(fm4)) 376s Missing cells for: recipeA:temperature175, recipeB:temperature185, recipeC:temperature195. 376s Interpret type III hypotheses with care. 376s Type III Analysis of Variance Table with Satterthwaite's method 376s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 376s recipe 2.282 1.141 2 45.888 0.0871 0.916766 376s temperature 136.267 68.133 2 42.000 5.1998 0.009602 ** 376s recipe:temperature 52.900 52.900 1 42.000 4.0372 0.050963 . 376s --- 376s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 376s > options("contrasts") 376s $contrasts 376s unordered ordered 376s "contr.treatment" "contr.poly" 376s 376s > options(contrasts = c("contr.sum", "contr.poly")) 376s > fm5 <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake4) 376s fixed-effect model matrix is rank deficient so dropping 3 columns / coefficients 376s > (an5 <- anova(fm5)) 376s Missing cells for: recipeA:temperature175, recipeB:temperature185, recipeC:temperature195. 376s Interpret type III hypotheses with care. 376s Type III Analysis of Variance Table with Satterthwaite's method 376s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 376s recipe 2.282 1.141 2 45.888 0.0871 0.916766 376s temperature 136.267 68.133 2 42.000 5.1998 0.009602 ** 376s recipe:temperature 52.900 52.900 1 42.000 4.0372 0.050963 . 376s --- 376s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 376s > options(contrasts = c("contr.treatment", "contr.poly")) 376s > options("contrasts") 376s $contrasts 376s [1] "contr.treatment" "contr.poly" 376s 376s > stopifnot( 376s + isTRUE(all.equal(an1, an2, check.attributes=FALSE, tolerance=TOL)), 376s + isTRUE(all.equal(an1, an3, check.attributes=FALSE, tolerance=TOL)), 376s + isTRUE(all.equal(an1, an4, check.attributes=FALSE, tolerance=TOL)), 376s + isTRUE(all.equal(an1, an5, check.attributes=FALSE, tolerance=TOL)) 376s + ) 376s > 376s > 376s BEGIN TEST test_compare_sas.R 376s 376s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 376s Copyright (C) 2025 The R Foundation for Statistical Computing 376s Platform: aarch64-unknown-linux-gnu 376s 376s R is free software and comes with ABSOLUTELY NO WARRANTY. 376s You are welcome to redistribute it under certain conditions. 376s Type 'license()' or 'licence()' for distribution details. 376s 376s R is a collaborative project with many contributors. 376s Type 'contributors()' for more information and 376s 'citation()' on how to cite R or R packages in publications. 376s 376s Type 'demo()' for some demos, 'help()' for on-line help, or 376s 'help.start()' for an HTML browser interface to help. 376s Type 'q()' to quit R. 376s 376s > # test_compare_sas.R 376s > library(lmerTest) 376s Loading required package: lme4 376s Loading required package: Matrix 378s > 378s > # WRE says "using if(requireNamespace("pkgname")) is preferred, if possible." 378s > # even in tests: 378s > assertError <- function(expr, ...) 378s + if(requireNamespace("tools")) tools::assertError(expr, ...) else invisible() 378s > assertWarning <- function(expr, ...) 378s + if(requireNamespace("tools")) tools::assertWarning(expr, ...) else invisible() 378s > 378s > ##################################################################### 378s > 378s > 378s > # Use contrasts to get particular estimates for the summary table: 378s > l <- list(Frequency="contr.SAS", Income="contr.SAS") 378s > m.carrots <- lmer(Preference ~ sens2*Frequency*Income 378s + +(1+sens2|Consumer), data=carrots, contrasts=l) 378s 378s Attaching package: 'lmerTest' 378s 378s The following object is masked from 'package:lme4': 378s 378s lmer 378s 378s The following object is masked from 'package:stats': 378s 378s step 378s 378s fixed-effect model matrix is rank deficient so dropping 12 columns / coefficients 378s > an.m <- anova(m.carrots) 378s Missing cells for: Frequency3:Income1, Frequency5:Income1, Frequency4:Income2, Frequency3:Income4, Frequency4:Income4, Frequency5:Income4, sens2:Frequency3:Income1, sens2:Frequency5:Income1, sens2:Frequency4:Income2, sens2:Frequency3:Income4, sens2:Frequency4:Income4, sens2:Frequency5:Income4. 378s Interpret type III hypotheses with care. 378s > 378s > TOL <- 1e-4 378s > TOL2 <- 1e-5 378s > # with 4 decimals should agree with SAS output 378s > # numbers before decimals should agree with SAS output 378s > stopifnot( 378s + all.equal(an.m[,"Pr(>F)"], 378s + c(2e-5, 0.15512, 0.06939, 0.08223, 0.52459, 0.03119, 0.48344), 378s + tolerance = TOL), 378s + all.equal(round(an.m$DenDF), c(83, 83, 83, 83, 83, 83, 83)) 378s + ) 378s > 378s > sm <- summary(m.carrots) 378s > stopifnot( 378s + isTRUE(all.equal(sm$coefficients[,"Pr(>|t|)"], 378s + c(1e-10, 0.005061, 0.6865554, 0.342613, 0.129157, 378s + 0.088231, 0.846000, 0.354472, 0.526318, 0.020646, 0.010188, 378s + 0.031242, 0.055356, 0.694689, 0.099382, 0.28547, 378s + 0.977774, 0.855653, 0.427737, 0.321086, 0.417465 , 0.204385, 0.784437, 378s + 0.681434, 0.106180, 0.149122, 0.390870, 0.273686), tolerance=TOL, 378s + check.attributes = FALSE)) 378s + ) 378s > 378s > # Takes too long to run: 378s > # if(requireNamespace("pbkrtest", quietly = TRUE)) { 378s > # sm.kr <- summary(m.carrots, ddf = "Kenward-Roger") 378s > # 378s > # ## coefficients for Sat and KR agree in this example 378s > # # cbind(sm$coefficients[,"Pr(>|t|)"], sm.kr$coefficients[,"Pr(>|t|)"]) 378s > # all.equal(sm$coefficients[,"Pr(>|t|)"], sm.kr$coefficients[,"Pr(>|t|)"], 378s > # tol=TOL) 378s > # } 378s > 378s > ################################################################################ 378s > ## checking lsmeans and difflsmeans 378s > ## compare with SAS output 378s > m <- lmer(Informed.liking ~ Product*Information*Gender 378s + + (1|Product:Consumer) + (1|Consumer) , data=ham) 379s > 379s > 379s > lsm <- lsmeansLT(m, which = "Product") 379s > # head(lsm) 379s > 379s > stopifnot( 379s + isTRUE(all.equal(lsm[, "Estimate"], c(5.8084, 5.1012, 6.0909, 5.9256), 379s + tol=TOL, check.attributes = FALSE)), 379s + isTRUE(all.equal(round(lsm[, "t value"], 2), c(24.93, 21.89, 26.14, 25.43), tolerance=TOL, 379s + check.attributes = FALSE)), 379s + isTRUE(all.equal(lsm[, "lower"], c(5.3499, 4.6428, 5.6324, 5.4672), tolerance=TOL, 379s + check.attributes = FALSE)), 379s + isTRUE(all.equal(lsm[, "upper"], c(6.2668, 5.5597, 6.5493, 6.3840), tolerance=TOL, 379s + check.attributes = FALSE)) 379s + ) 379s > 379s > ################################################################################ 379s > # Not actually 'hard-coded' tests versus SAS results... 379s > 379s > m.carrots <- lmer(Preference ~ 0 + sens2 + Homesize + 379s + (1+sens2 | Consumer), data=carrots, 379s + control=lmerControl(optimizer="bobyqa")) 379s > summary(m.carrots) 379s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 379s lmerModLmerTest] 379s Formula: Preference ~ 0 + sens2 + Homesize + (1 + sens2 | Consumer) 379s Data: carrots 379s Control: lmerControl(optimizer = "bobyqa") 379s 379s REML criterion at convergence: 3748.9 379s 379s Scaled residuals: 379s Min 1Q Median 3Q Max 379s -3.5322 -0.5571 0.0308 0.6297 2.8552 379s 379s Random effects: 379s Groups Name Variance Std.Dev. Corr 379s Consumer (Intercept) 0.195168 0.44178 379s sens2 0.002779 0.05271 0.18 379s Residual 1.070441 1.03462 379s Number of obs: 1233, groups: Consumer, 103 379s 379s Fixed effects: 379s Estimate Std. Error df t value Pr(>|t|) 379s sens2 7.068e-02 9.545e-03 1.020e+02 7.404 3.89e-11 *** 379s Homesize1 4.910e+00 7.056e-02 1.013e+02 69.586 < 2e-16 *** 379s Homesize3 4.661e+00 7.850e-02 1.013e+02 59.374 < 2e-16 *** 379s --- 379s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 379s 379s Correlation of Fixed Effects: 379s sens2 Homsz1 379s Homesize1 0.061 379s Homesize3 0.055 0.003 379s > 379s > (an.1 <- anova(m.carrots, type=1)) 379s Type I Analysis of Variance Table with Satterthwaite's method 379s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 379s sens2 60.5 60.5 1 102.01 56.539 2.211e-11 *** 379s Homesize 8927.2 4463.6 2 101.31 4169.863 < 2.2e-16 *** 379s --- 379s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 379s > (an.3 <- anova(m.carrots)) 379s Type III Analysis of Variance Table with Satterthwaite's method 379s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 379s sens2 58.7 58.7 1 102.01 54.821 3.892e-11 *** 379s Homesize 8927.2 4463.6 2 101.31 4169.863 < 2.2e-16 *** 379s --- 379s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 379s > (an.lme4 <- anova(m.carrots, ddf = "lme4")) # difference in SSQ MS and F-values 379s Analysis of Variance Table 379s npar Sum Sq Mean Sq F value 379s sens2 1 0.0 0.0 0.0122 379s Homesize 2 8927.2 4463.6 4169.8634 379s > # Is this a problem with lme4? 379s > # fm <- lm(Preference ~ 0 + sens2 + Homesize, data=carrots) 379s > # anova(fm) 379s > # coef(summary(fm)) 379s > # Here the F value is a little greater than the squared t-value (as expected) 379s > 379s > stopifnot(all.equal(an.1[, "F value"], c(56.5394, 4169.87), tolerance = TOL2), 379s + all.equal(an.3[, "F value"], c(54.8206, 4169.87), tolerance = TOL2)) 379s > 379s > 379s > ################################################################################ 379s > # Check exmaple from GLM SAS report 379s > 379s > ### example from the paper GLM SAS 101 report 379s > a <- factor(c(1,1,1,2,2,2,2,2,1,2)) 379s > b <- factor(c(1,1,2,1,2,2,2,2,2,1)) 379s > f=factor(c(1,2,1,2,1,2,1,2,1,2)) 379s > y <- c(12,14,11,20,17,23,35,46,15,16) 379s > dd <- data.frame(a=a, b=b, y=y, f=f) 379s > 379s > ## check type 2 is order independent 379s > model <- lmer(y ~ a*b + (1|f), data=dd) 379s boundary (singular) fit: see help('isSingular') 379s > model2 <- lmer(y ~ b*a + (1|f), data=dd) 379s boundary (singular) fit: see help('isSingular') 379s > (an <- anova(model, type=2)) 379s Type II Analysis of Variance Table with Satterthwaite's method 379s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 379s a 336.00 336.00 1 6 3.9013 0.09566 . 379s b 114.33 114.33 1 6 1.3275 0.29308 379s a:b 85.75 85.75 1 6 0.9956 0.35689 379s --- 379s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 379s > (an2 <- anova(model2, type=2)) 379s Type II Analysis of Variance Table with Satterthwaite's method 379s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 379s b 114.33 114.33 1 6 1.3275 0.29308 379s a 336.00 336.00 1 6 3.9013 0.09566 . 379s b:a 85.75 85.75 1 6 0.9956 0.35689 379s --- 379s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 379s > stopifnot( 379s + isTRUE(all.equal(an,an2[c(2,1,3),], check.attributes = FALSE, tolerance=TOL2)) 379s + ) 379s > 379s > ## check the results are the same as from SAS proc mixed 379s > stopifnot( 379s + isTRUE(all.equal(an[,"F value"], c(3.90131, 1.32753, 0.99565), tolerance=TOL2)) 379s + ) 379s > ################################################################################ 379s > ## Check type II and III anova tables versus SAS 379s > 379s > m.carrots <- lmer(Preference ~ sens2*Homesize 379s + +(1+sens2|Consumer), data=carrots) 379s > (ancar <- anova(m.carrots, type=2)) 379s Type II Analysis of Variance Table with Satterthwaite's method 379s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 379s sens2 58.697 58.697 1 101.02 54.8339 4.042e-11 *** 379s Homesize 5.526 5.526 1 100.99 5.1621 0.02521 * 379s sens2:Homesize 1.103 1.103 1 101.02 1.0303 0.31251 379s --- 379s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 379s > 379s > stopifnot( 379s + isTRUE(all.equal(ancar[,"F value"], c(54.8361, 5.16138, 1.03035), tolerance = TOL)) 379s + ) 379s > 379s > m <- lmer(Informed.liking ~ Product*Age 379s + + (1|Consumer) , data=ham) 379s > (an <- anova(m, type=2)) 379s Type II Analysis of Variance Table with Satterthwaite's method 379s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 379s Product 32.498 10.8327 3 561 2.4814 0.06014 . 379s Age 0.024 0.0235 1 79 0.0054 0.94168 379s Product:Age 19.442 6.4808 3 561 1.4845 0.21772 379s --- 379s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 379s > 379s > stopifnot( 379s + isTRUE(all.equal(an[,"F value"], c(2.48135, .005387, 1.48451), tolerance = TOL2)) 379s + ) 379s > 379s > 379s > fm <- lmer(Preference ~ sens2*Homesize*sens1 + (1|Product), 379s + data=carrots) 379s > (ant2 <- anova(fm, type=2)) 379s Type II Analysis of Variance Table with Satterthwaite's method 379s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 379s sens2 21.0228 21.0228 1 7.97 16.4832 0.0036583 ** 379s Homesize 17.8570 17.8570 1 1217.01 14.0010 0.0001912 *** 379s sens1 0.6709 0.6709 1 7.98 0.5260 0.4889911 379s sens2:Homesize 1.5068 1.5068 1 1216.99 1.1814 0.2772780 379s sens2:sens1 0.1372 0.1372 1 7.98 0.1076 0.7513796 379s Homesize:sens1 0.4275 0.4275 1 1217.00 0.3352 0.5627339 379s sens2:Homesize:sens1 1.3512 1.3512 1 1216.99 1.0595 0.3035426 379s --- 379s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 379s > (ant3 <- anova(fm, type=3)) 379s Type III Analysis of Variance Table with Satterthwaite's method 379s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 379s sens2 21.5710 21.5710 1 8.02 16.9130 0.0033602 ** 379s Homesize 17.8570 17.8570 1 1217.01 14.0010 0.0001912 *** 379s sens1 0.6136 0.6136 1 8.03 0.4811 0.5074890 379s sens2:Homesize 1.5068 1.5068 1 1216.99 1.1814 0.2772780 379s sens2:sens1 0.0946 0.0946 1 8.02 0.0742 0.7922017 379s Homesize:sens1 0.4275 0.4275 1 1217.00 0.3352 0.5627339 379s sens2:Homesize:sens1 1.3512 1.3512 1 1216.99 1.0595 0.3035426 379s --- 379s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 379s > 379s > stopifnot( 379s + isTRUE(all.equal(ant2[,"F value"], 379s + c(16.4842, 14.0010, .526076, 1.18144, 379s + .107570, .335177, 1.05946), tolerance = TOL)), 379s + isTRUE(all.equal(ant3[,"F value"], 379s + c(16.9140, 14.0010,.481148, 1.18144, 379s + .074201, .335177, 1.05946), tolerance = TOL)) 379s + ) 379s > 379s > ################################################################################ 379s > 379s > 379s > 379s BEGIN TEST test_contest1D.R 379s 379s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 379s Copyright (C) 2025 The R Foundation for Statistical Computing 379s Platform: aarch64-unknown-linux-gnu 379s 379s R is free software and comes with ABSOLUTELY NO WARRANTY. 379s You are welcome to redistribute it under certain conditions. 379s Type 'license()' or 'licence()' for distribution details. 379s 379s R is a collaborative project with many contributors. 379s Type 'contributors()' for more information and 379s 'citation()' on how to cite R or R packages in publications. 379s 379s Type 'demo()' for some demos, 'help()' for on-line help, or 379s 'help.start()' for an HTML browser interface to help. 379s Type 'q()' to quit R. 379s 380s > # test_contest1D.R 380s > library(lmerTest) 380s Loading required package: lme4 380s Loading required package: Matrix 381s 381s Attaching package: 'lmerTest' 381s 381s The following object is masked from 'package:lme4': 381s 381s lmer 381s 381s The following object is masked from 'package:stats': 381s 381s step 381s 381s > 381s > # WRE says "using if(requireNamespace("pkgname")) is preferred, if possible." 381s > # even in tests: 381s > assertError <- function(expr, ...) 381s + if(requireNamespace("tools")) tools::assertError(expr, ...) else invisible() 381s > assertWarning <- function(expr, ...) 381s + if(requireNamespace("tools")) tools::assertWarning(expr, ...) else invisible() 381s > 381s > TOL <- 1e-4 381s > # Kenward-Roger only available with pbkrtest and only then validated in R >= 3.3.3 381s > # (faulty results for R < 3.3.3 may be due to unstated dependencies in pbkrtest) 381s > has_pbkrtest <- requireNamespace("pbkrtest", quietly = TRUE) && getRversion() >= "3.3.3" 382s > 382s > data("sleepstudy", package="lme4") 382s > 382s > #################################### 382s > ## Tests of contest1D 382s > #################################### 382s > 382s > fm <- lmer(Reaction ~ Days + I(Days^2) + (1|Subject) + (0+Days|Subject), 382s + sleepstudy) 382s > # Basic tests: 382s > L <- c(0, 1, 0) 382s > contest1D(fm, L) 382s Estimate Std. Error df t value Pr(>|t|) 382s 1 7.434085 2.824283 114.9943 2.632203 0.00964808 382s > contest1D(fm, L, confint = TRUE) 382s Estimate Std. Error df t value lower upper Pr(>|t|) 382s 1 7.434085 2.824283 114.9943 2.632203 1.839722 13.02845 0.00964808 382s > contest1D(fm, L, confint = TRUE, level=0.99) 382s Estimate Std. Error df t value lower upper Pr(>|t|) 382s 1 7.434085 2.824283 114.9943 2.632203 0.03655396 14.83162 0.00964808 382s > if(has_pbkrtest) 382s + contest1D(fm, L, ddf="Kenward-Roger") 382s Estimate Std. Error df t value Pr(>|t|) 382s 1 7.434085 2.824283 115.5148 2.632203 0.009642692 382s > 382s > # Test too long L 382s > assertError(contest1D(fm, c(0, 1, 1, 1))) 382s > 382s > # Test too short L 382s > assertError(contest1D(fm, c(0, 1))) 382s > 382s > # Test matrix L 382s > contest1D(fm, matrix(L, nrow=1)) 382s Estimate Std. Error df t value Pr(>|t|) 382s 1 7.434085 2.824283 114.9943 2.632203 0.00964808 382s > contest1D(fm, matrix(L, ncol=1)) 382s Estimate Std. Error df t value Pr(>|t|) 382s 1 7.434085 2.824283 114.9943 2.632203 0.00964808 382s > assertError(contest1D(fm, matrix(c(0, 1), ncol=1))) 382s > assertError(contest1D(fm, matrix(c(0, 1, 0, 0), nrow=1))) 382s > L <- matrix(numeric(0L), ncol=3) 382s > assertError(contest1D(fm, L)) # "empty" matrix 382s > assertError(contest1D(fm, matrix(1, ncol=3, nrow=2))) 382s > 382s > # Test list L 382s > assertError(contest1D(fm, list(c(0, 1, 0)))) 382s > 382s > # Test equivalence to coef(summary(fm)): 382s > Lmat <- diag(length(fixef(fm))) 382s > (coef_mat <- lmerTest:::rbindall(lapply(1:ncol(Lmat), function(i) 382s + contest1D(fm, Lmat[i, ])))) 382s Estimate Std. Error df t value Pr(>|t|) 382s 1 255.4493728 7.5663677 26.22939 33.761163 3.810057e-23 382s 2 7.4340850 2.8242827 114.99433 2.632203 9.648080e-03 382s 3 0.3370223 0.2616475 144.63110 1.288078 1.997759e-01 382s > (coef_mat_lme4 <- coef(summary(fm, ddf="lme4"))) 382s Estimate Std. Error t value 382s (Intercept) 255.4493728 7.5663677 33.761163 382s Days 7.4340850 2.8242827 2.632203 382s I(Days^2) 0.3370223 0.2616475 1.288078 382s > rownames(coef_mat) <- rownames(coef_mat_lme4) 382s > stopifnot(isTRUE( 382s + all.equal(as.data.frame(coef_mat_lme4), 382s + coef_mat[, c("Estimate", "Std. Error", "t value")], tolerance=TOL) 382s + )) 382s > 382s > if(has_pbkrtest) { 382s + (coef_mat_KR <- lmerTest:::rbindall(lapply(1:ncol(Lmat), function(i) 382s + contest1D(fm, Lmat[i, ], ddf="Kenward-Roger")))) 382s + rownames(coef_mat_KR) <- rownames(coef_mat_lme4) 382s + stopifnot(isTRUE( 382s + all.equal(as.data.frame(coef_mat_lme4), 382s + coef_mat_KR[, c("Estimate", "Std. Error", "t value")], tolerance=TOL) 382s + )) 382s + } 382s > # Test of 0-length beta 382s > fm1 <- lmer(Reaction ~ 0 + (1|Subject) + (0+Days|Subject), 382s + sleepstudy) 382s > stopifnot(length(fixef(fm1)) == 0L) 382s > if(has_pbkrtest) { 382s + (ans <- contest1D(fm1, numeric(0L), ddf="Kenward-Roger")) 382s + stopifnot(nrow(ans) == 0L) 382s + } 382s > 382s > ## Test rhs argument: 382s > fm <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy) 382s > contest1D(fm, L=cbind(0, 1)) 382s Estimate Std. Error df t value Pr(>|t|) 382s 1 10.46729 1.54579 16.99998 6.771481 3.263824e-06 382s > contest1D(fm, L=cbind(0, 1), rhs=10) 382s Estimate Std. Error df t value Pr(>|t|) 382s 1 10.46729 1.54579 16.99998 0.302296 0.7660937 382s > if(has_pbkrtest) { 382s + contest1D(fm, L=cbind(0, 1), ddf="Kenward-Roger") 382s + contest1D(fm, L=cbind(0, 1), ddf="Kenward-Roger", rhs=10) 382s + } 382s Estimate Std. Error df t value Pr(>|t|) 382s 1 10.46729 1.54579 17 0.302296 0.7660937 382s > 382s > contest1D(fm, L=c(0, 1), rhs = 10.467) 382s Estimate Std. Error df t value Pr(>|t|) 382s 1 10.46729 1.54579 16.99998 0.0001849926 0.9998546 382s > 382s > (ct1 <- contest1D(fm, L=cbind(c(0, 1)), rhs = 10)) 382s Estimate Std. Error df t value Pr(>|t|) 382s 1 10.46729 1.54579 16.99998 0.302296 0.7660937 382s > (ct2 <- contestMD(fm, L=rbind(c(0, 1)), rhs = 10)) 382s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 382s 1 59.85028 59.85028 1 16.99998 0.09138285 0.7660937 382s > stopifnot( 382s + isTRUE(all.equal(ct1[, "t value"]^2, ct2[, "F value"], tolerance=1e-6)) 382s + ) 382s > 382s > ## Test 'lmerMod' method: 382s > fm <- lme4::lmer(Reaction ~ Days + I(Days^2) + (1|Subject) + (0+Days|Subject), 382s + sleepstudy) 383s > # Basic tests: 383s > L <- c(0, 1, 0) 383s > contest1D(fm, L) 383s Estimate Std. Error df t value Pr(>|t|) 383s 1 7.434085 2.824283 114.9943 2.632203 0.00964808 383s > contest1D(fm, L, confint = TRUE) 383s Estimate Std. Error df t value lower upper Pr(>|t|) 383s 1 7.434085 2.824283 114.9943 2.632203 1.839722 13.02845 0.00964808 383s > contest1D(fm, L, confint = TRUE, level=0.99) 383s Estimate Std. Error df t value lower upper Pr(>|t|) 383s 1 7.434085 2.824283 114.9943 2.632203 0.03655396 14.83162 0.00964808 383s > if(has_pbkrtest) 383s + contest1D(fm, L, ddf="Kenward-Roger") 383s Estimate Std. Error df t value Pr(>|t|) 383s 1 7.434085 2.824283 115.5148 2.632203 0.009642692 383s > 383s > 383s BEGIN TEST test_contestMD.R 383s 383s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 383s Copyright (C) 2025 The R Foundation for Statistical Computing 383s Platform: aarch64-unknown-linux-gnu 383s 383s R is free software and comes with ABSOLUTELY NO WARRANTY. 383s You are welcome to redistribute it under certain conditions. 383s Type 'license()' or 'licence()' for distribution details. 383s 383s R is a collaborative project with many contributors. 383s Type 'contributors()' for more information and 383s 'citation()' on how to cite R or R packages in publications. 383s 383s Type 'demo()' for some demos, 'help()' for on-line help, or 383s 'help.start()' for an HTML browser interface to help. 383s Type 'q()' to quit R. 383s 383s > # test_contestMD.R 383s > library(lmerTest) 383s Loading required package: lme4 383s Loading required package: Matrix 385s 385s Attaching package: 'lmerTest' 385s 385s The following object is masked from 'package:lme4': 385s 385s lmer 385s 385s The following object is masked from 'package:stats': 385s 385s step 385s 385s > 385s > # WRE says "using if(requireNamespace("pkgname")) is preferred, if possible." 385s > # even in tests: 385s > assertError <- function(expr, ...) 385s + if(requireNamespace("tools")) tools::assertError(expr, ...) else invisible() 385s > assertWarning <- function(expr, ...) 385s + if(requireNamespace("tools")) tools::assertWarning(expr, ...) else invisible() 385s > 385s > # Kenward-Roger only available with pbkrtest and only then validated in R >= 3.3.3 385s > # (faulty results for R < 3.3.3 may be due to unstated dependencies in pbkrtest) 385s > has_pbkrtest <- requireNamespace("pbkrtest", quietly = TRUE) && getRversion() >= "3.3.3" 385s > 385s > data("sleepstudy", package="lme4") 385s > 385s > #################################### 385s > ## Tests of contestMD 385s > #################################### 385s > 385s > fm <- lmer(Reaction ~ Days + I(Days^2) + (1|Subject) + (0+Days|Subject), 385s + sleepstudy) 385s > # Basic tests: 385s > L <- diag(3L) 385s > contestMD(fm, L) 385s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 385s 1 990089.3 330029.8 3 42.15441 507.24 4.351211e-33 385s > 385s > # Tests of ddf arg: 385s > contestMD(fm, L, ddf="Sat") 385s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 385s 1 990089.3 330029.8 3 42.15441 507.24 4.351211e-33 385s > if(has_pbkrtest) 385s + contestMD(fm, L, ddf="Kenward-Roger") 385s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 385s 1 990089.3 330029.8 3 38.84733 490.1937 6.706733e-31 385s > assertError(contestMD(fm, L, ddf="sat")) # Invalid ddf arg. 385s > 385s > # Tests of simple 2-df test: 385s > (ans <- contestMD(fm, L[2:3, ], ddf="Sat")) 385s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 385s 1 30399.15 15199.57 2 54.40752 23.36102 4.744897e-08 385s > stopifnot(nrow(ans) == 1L, 385s + ans$NumDF == 2L) 385s > if(has_pbkrtest) { 385s + (ans <- contestMD(fm, L[2:3, ], ddf="Kenward-Roger")) 385s + stopifnot(nrow(ans) == 1L, 385s + ans$NumDF == 2L) 385s + } 385s > 385s > # Tests of simple 1-df test: 385s > (ans <- contestMD(fm, L[3, , drop=FALSE], ddf="Sat")) 385s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 385s 1 1079.503 1079.503 1 144.6311 1.659144 0.1997759 385s > stopifnot(nrow(ans) == 1L, 385s + ans$NumDF == 1L) 385s > if(has_pbkrtest) { 385s + (ans <- contestMD(fm, L[3, , drop=FALSE], ddf="Kenward-Roger")) 385s + stopifnot(nrow(ans) == 1L, 385s + ans$NumDF == 1L) 385s + } 386s > 386s > # Test of vector input: 386s > (ans <- contestMD(fm, L[3, ], ddf="Sat")) # OK since length(L[3, ]) == length(fixef(fm)) 386s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 386s 1 1079.503 1079.503 1 144.6311 1.659144 0.1997759 386s > stopifnot(nrow(ans) == 1L, 386s + ans$NumDF == 1L) 386s > assertError(contestMD(fm, c(1, 0))) # L is too short 386s > assertError(contestMD(fm, c(1, 0, 1, 1))) # L is too long 386s > 386s > # Test of list input: 386s > assertError(contestMD(fm, list(L[3, , drop=FALSE]), ddf="Sat")) # Need L to be a matrix 386s > 386s > # zero-row L's are allowed (if ncol(L) is correct): 386s > ans1 <- contestMD(fm, L[0, , drop=FALSE], ddf="Sat") 386s > stopifnot(nrow(ans1) == 0L) 386s > if(has_pbkrtest) { 386s + ans2 <- contestMD(fm, L[0, , drop=FALSE], ddf="Kenward-Roger") 386s + stopifnot(nrow(ans2) == 0L) 386s + } 386s > 386s > # Test wrong ncol(L): 386s > assertError(contestMD(fm, L[2:3, 2:3])) # need ncol(L) == length(fixef(fm)) 386s > 386s > # row-rank deficient L are allowed: 386s > L <- rbind(c(1, 0, 1), 386s + c(0, 1, 0), 386s + c(1, -1, 1)) 386s > ans <- contestMD(fm, L) 386s > stopifnot(nrow(L) == 3L, 386s + qr(L)$rank == 2, 386s + ans$NumDF == 2) 386s > if(has_pbkrtest) { 386s + ans_KR <- contestMD(fm, L, ddf="Kenward-Roger") 386s + stopifnot(ans_KR$NumDF == 2) 386s + } 386s > 386s > # Test of 0-length beta 386s > fm1 <- lmer(Reaction ~ 0 + (1|Subject) + (0+Days|Subject), 386s + sleepstudy) 386s > stopifnot(length(fixef(fm1)) == 0L) 386s > L <- numeric(0L) 386s > (ans <- contestMD(fm1, L)) 386s [1] Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 386s <0 rows> (or 0-length row.names) 386s > stopifnot(nrow(ans) == 0L) 386s > L <- matrix(numeric(0L), ncol=0L) 386s > (ans <- contestMD(fm1, L)) 386s [1] Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 386s <0 rows> (or 0-length row.names) 386s > stopifnot(nrow(ans) == 0L) 386s > 386s > 386s > ## rhs argument: 386s > data("cake", package="lme4") 386s > model <- lmer(angle ~ recipe * temp + (1|recipe:replicate), cake) 386s > (L <- diag(length(fixef(model)))[2:3, ]) 386s [,1] [,2] [,3] [,4] [,5] [,6] 386s [1,] 0 1 0 0 0 0 386s [2,] 0 0 1 0 0 0 386s > (an <- anova(model, type="marginal")) 386s Marginal Analysis of Variance Table with Satterthwaite's method 386s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 386s recipe 4.00 2.00 2 254.02 0.0957 0.9088 386s temp 620.24 620.24 1 222.00 29.6961 1.339e-07 *** 386s recipe:temp 1.74 0.87 2 222.00 0.0417 0.9592 386s --- 386s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 386s > 386s > ct <- contestMD(model, L, rhs = 0) 386s > ct2 <- contestMD(model, L, rhs = c(2, 2)) 386s > stopifnot( 386s + isTRUE(all.equal(ct[1, ], an[1, ], check.attributes=FALSE, tolerance=1e-6)), 386s + ct[, "F value"] < ct2[, "F value"] 386s + ) 386s > 386s > L2 <- rbind(L, L[1, ] + L[2, ]) # rank deficient! 386s > contestMD(model, L2, rhs = c(0, 0, 0)) # no warning 386s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 386s 1 3.996684 1.998342 2 254.0158 0.09567796 0.9087894 386s > assertWarning(contestMD(model, L2, rhs = c(2, 2, 2))) # warning since L2 is rank def. 386s > if(has_pbkrtest) 386s + assertWarning(contestMD(model, L2, rhs = c(2, 2, 2), ddf="Kenward-Roger")) 386s > 386s > fm <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy) 386s > contestMD(fm, L=cbind(0, 1)) 386s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 386s 1 30030.94 30030.94 1 16.99998 45.85296 3.263824e-06 386s > contestMD(fm, L=cbind(0, 1), rhs=10) 386s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 386s 1 59.85028 59.85028 1 16.99998 0.09138285 0.7660937 386s > if(has_pbkrtest) { 386s + contestMD(fm, L=cbind(0, 1), ddf="Kenward-Roger") 386s + contestMD(fm, L=cbind(0, 1), ddf="Kenward-Roger", rhs=10) 386s + } 386s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 386s 1 59.85028 59.85028 1 17 0.09138285 0.7660937 386s > 386s > 386s > ## Test 'lmerMod' method: 386s > fm <- lme4::lmer(Reaction ~ Days + (Days|Subject), sleepstudy) 386s > contestMD(fm, L=cbind(0, 1)) 386s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 386s 1 30030.94 30030.94 1 16.99998 45.85296 3.263824e-06 386s > contestMD(fm, L=cbind(0, 1), rhs=10) 386s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 386s 1 59.85028 59.85028 1 16.99998 0.09138285 0.7660937 386s > if(has_pbkrtest) { 386s + contestMD(fm, L=cbind(0, 1), ddf="Kenward-Roger") 386s + contestMD(fm, L=cbind(0, 1), ddf="Kenward-Roger", rhs=10) 386s + } 386s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 386s 1 59.85028 59.85028 1 17 0.09138285 0.7660937 386s > 386s BEGIN TEST test_contrast_utils.R 386s 386s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 386s Copyright (C) 2025 The R Foundation for Statistical Computing 386s Platform: aarch64-unknown-linux-gnu 386s 386s R is free software and comes with ABSOLUTELY NO WARRANTY. 386s You are welcome to redistribute it under certain conditions. 386s Type 'license()' or 'licence()' for distribution details. 386s 386s R is a collaborative project with many contributors. 386s Type 'contributors()' for more information and 386s 'citation()' on how to cite R or R packages in publications. 386s 386s Type 'demo()' for some demos, 'help()' for on-line help, or 386s 'help.start()' for an HTML browser interface to help. 386s Type 'q()' to quit R. 386s 386s > # test_contrast_utils.R 386s > 386s > library(lmerTest) 386s Loading required package: lme4 386s Loading required package: Matrix 388s 388s Attaching package: 'lmerTest' 388s 388s The following object is masked from 'package:lme4': 388s 388s lmer 388s 388s The following object is masked from 'package:stats': 388s 388s step 388s 388s > 388s > ########## 388s > # Test that a message is printed if some cells have zero data: 388s > # Missing a single cell: 388s > data("cake", package="lme4") 388s > cake4 <- cake 388s > cake4$temperature <- factor(cake4$temperature, ordered=FALSE) 388s > cake4 <- droplevels(subset(cake4, !(recipe == "A" & temperature == "175") )) 388s > with(cake4, table(recipe, temperature)) 388s temperature 388s recipe 175 185 195 205 215 225 388s A 0 15 15 15 15 15 388s B 15 15 15 15 15 15 388s C 15 15 15 15 15 15 388s > 388s > fm1 <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake4) 388s fixed-effect model matrix is rank deficient so dropping 1 column / coefficient 389s > an <- anova(fm1) 389s Missing cells for: recipeA:temperature175. 389s Interpret type III hypotheses with care. 389s > txt <- capture.output(an <- anova(fm1), type = "message") 389s > stopifnot(length(grep("Missing cells for:", txt)) > 0, 389s + length(grep("Interpret type III hypotheses with care.", txt)) > 0) 389s > 389s > ########## 389s > # Test that a message is printed if some cells have zero data: 389s > # Missing diagonal: 389s > cake4 <- cake 389s > cake4$temperature <- factor(cake4$temperature, ordered=FALSE) 389s > cake4 <- droplevels(subset(cake4, temperature %in% levels(cake4$temperature)[1:3])) 389s > cake4 <- droplevels(subset(cake4, !((recipe == "A" & temperature == "175") | 389s + (recipe == "B" & temperature == "185") | 389s + (recipe == "C" & temperature == "195") ))) 389s > cake4$temp0 <- cake4$temp - mean(cake4$temp) 389s > with(cake4, table(recipe, temperature)) 389s temperature 389s recipe 175 185 195 389s A 0 15 15 389s B 15 0 15 389s C 15 15 0 389s > 389s > fm1 <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake4) 389s fixed-effect model matrix is rank deficient so dropping 3 columns / coefficients 389s > an <- anova(fm1) 389s Missing cells for: recipeA:temperature175, recipeB:temperature185, recipeC:temperature195. 389s Interpret type III hypotheses with care. 389s > txt <- capture.output(an <- anova(fm1), type = "message") 389s > stopifnot(length(grep("Missing cells for:", txt)) > 0, 389s + length(grep("Interpret type III hypotheses with care.", txt)) > 0) 389s > 389s > ########## 389s > # Test that a message is NOT printed with centered covariates: 389s > fm1 <- lmer(angle ~ recipe * temp0 + (1|recipe:replicate), cake4) 389s > an <- anova(fm1) 389s > txt <- capture.output(an <- anova(fm1), type = "message") 389s > stopifnot(length(grep("Missing cells for:", txt)) == 0, 389s + length(grep("Interpret type III hypotheses with care.", txt)) == 0) 389s > # Note: in many cases a message would not be printed anyway because the 389s > # columns sums in the rdX design matrix would not be exactly zero but just a 389s > # small number very close to zero. 389s > 389s > 389s > 389s > 389s BEGIN TEST test_devfun_vp.R 389s 389s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 389s Copyright (C) 2025 The R Foundation for Statistical Computing 389s Platform: aarch64-unknown-linux-gnu 389s 389s R is free software and comes with ABSOLUTELY NO WARRANTY. 389s You are welcome to redistribute it under certain conditions. 389s Type 'license()' or 'licence()' for distribution details. 389s 389s R is a collaborative project with many contributors. 389s Type 'contributors()' for more information and 389s 'citation()' on how to cite R or R packages in publications. 389s 389s Type 'demo()' for some demos, 'help()' for on-line help, or 389s 'help.start()' for an HTML browser interface to help. 389s Type 'q()' to quit R. 389s 389s > # test_devfun_vp.R 389s > 389s > # library(devtools) 389s > # # has_devel() 389s > # r2path <- "~/GitHub/lmerTestR/lmerTest" 389s > # # document(pkg=r2path) 389s > # load_all(r2path) 389s > # 389s > # # ?`Covariance-class` 389s > 389s > library(lmerTest) 389s Loading required package: lme4 389s Loading required package: Matrix 391s 391s Attaching package: 'lmerTest' 391s 391s The following object is masked from 'package:lme4': 391s 391s lmer 391s 391s The following object is masked from 'package:stats': 391s 391s step 391s 391s > 391s > has_pkgs <- requireNamespace("utils", quietly = TRUE) && 391s + requireNamespace("numDeriv", quietly = TRUE) && 391s + requireNamespace("lme4", quietly = TRUE) 391s > is_lme4_2_0_0 <- utils::packageVersion("lme4") >= "2.0.0" 391s > 391s > if(has_pkgs && is_lme4_2_0_0) { 391s + ## Functions: 391s + devfun_vp <- lmerTest:::devfun_vp 391s + getOptPar <- lmerTest:::getOptPar 391s + getVarPar <- lmerTest:::getVarPar 391s + 391s + ## Unstructured 391s + fm1.us <- lme4::lmer(Reaction ~ Days + us(Days | Subject), sleepstudy) 391s + ## Diagional 391s + fm1.diag <- lme4::lmer(Reaction ~ Days + diag(Days | Subject), sleepstudy) 391s + fm1.diag.hom <- lme4::lmer(Reaction ~ Days + diag(Days | Subject, hom = TRUE), 391s + sleepstudy) 391s + ## Compound symmetry 391s + fm1.cs <- lme4::lmer(Reaction ~ Days + cs(Days | Subject), sleepstudy) 391s + fm1.cs.hom <- lme4::lmer(Reaction ~ Days + cs(Days | Subject, hom = TRUE), 391s + sleepstudy) 391s + ## Auto-regressive order 1 391s + sleepstudy$Daysf <- factor(sleepstudy$Days, ordered = TRUE) 391s + fm1.ar1 <- lme4::lmer(Reaction ~ Daysf + ar1(0 + Daysf | Subject, hom = TRUE), 391s + sleepstudy, REML = TRUE) 391s + 391s + lme4models <- namedList(fm1.us, 391s + fm1.diag, 391s + fm1.diag.hom, 391s + fm1.cs, 391s + fm1.cs.hom, 391s + fm1.ar1) 391s + 391s + for(model in lme4models) { # model <- lme4models[[1]] 391s + ## Native devfun: 391s + devfun <- update(model, devFunOnly=TRUE) 391s + ## Evaluate native devfun at optimum: 391s + devfun(getOptPar(model)) 391s + ## Check that devfun returns the same value as that saved in the model object: 391s + stopifnot( 391s + all.equal(unname(getME(model, "devcomp")$cmp["REML"]), 391s + devfun(getOptPar(model)), tolerance=1e-6) # TRUE 391s + ) 391s + ## Get varpar (including residual SD): 391s + (varpar <- getVarPar(model)) 391s + ## Evaluate devfun_vp at the optimum: 391s + devfun_vp(varpar, devfun, reml=TRUE) 391s + ## Check that devfun_vp returns the same value as native devfun: 391s + stopifnot( 391s + all.equal(unname(getME(model, "devcomp")$cmp["REML"]), 391s + devfun(getOptPar(model))) # TRUE 391s + ) 391s + } 391s + 391s + ## Here we also want to check that devfun and and devfun_vp returns the same 391s + ## value at non-optimum values of varpar. 391s + ## Because sigma is profiled out of devfun this cannot be done right away. 391s + ## We need to optimize over all parameters to get equivalence. 391s + ## We should be able to set one of the parameters in common to a 391s + ## particular value and optimize the rest. This will build confidence that 391s + ## the likelihood in devfun_vp is the same as that returned by 391s + ## lme4::lmer(., devFunOnly=TRUE). 391s + 391s + do_trace <- 0 391s + for(i in seq_along(lme4models)) { # i <- 4 391s + if(do_trace) print(i) 391s + model <- lme4models[[i]] 391s + devfun <- update(model, devFunOnly=TRUE) 391s + (optpar <- getOptPar(model)) 391s + (varpar <- getVarPar(model)) 391s + (optpar2 <- optpar * 1.1) 391s + (varpar2 <- c(optpar2, varpar[length(varpar)])) 391s + 391s + ## Evaluate gradients to ensure that devfun and devfun_vp are both 391s + ## functions with optima at optpar and varpar respectively: 391s + (g_devfun <- numDeriv::grad(devfun, optpar)) 391s + (g_devfun_vp <- numDeriv::grad(devfun_vp, varpar, devfun=devfun, reml=TRUE)) 391s + stopifnot( 391s + if(i != 4) all(abs(g_devfun) < 1e-3) else all(abs(g_devfun) < 1e-2), 391s + if(i != 4) all(abs(g_devfun_vp) < 1e-3) else all(abs(g_devfun_vp) < 1e-2) 391s + ) 391s + ## These are not zero as expected: 391s + (g_devfun <- numDeriv::grad(devfun, optpar2)) 391s + (g_devfun_vp <- numDeriv::grad(devfun_vp, varpar2, devfun=devfun, reml=TRUE)) 391s + ## Try optimizing devfun_vp: 391s + x <- nlminb(start=varpar2, objective = devfun_vp, devfun=devfun, reml=TRUE, 391s + control=list(trace=do_trace)) 391s + ## Check that the optimum is re-achieved: 391s + stopifnot( 391s + all(abs(varpar - x$par) < 1e-4), 391s + abs(devfun_vp(varpar, devfun=devfun, reml=TRUE) - 391s + devfun_vp(x$par, devfun=devfun, reml=TRUE)) < 1e-6 391s + ) 391s + 391s + ## Optimize devfun and devfun_vp over all but one of the parameters in turn to 391s + ## check that devfun and devfun_vp gives the same deviance and parameter values 391s + ## for settings away from the REML optimum. This is to build confidence that 391s + ## devfun_vp is a valid implementation of the deviance function from LLMs. 391s + if(length(optpar) > 1) for(j in seq_along(optpar)) { # j <- 1 391s + ## Check that all parameters are within bounds: 391s + stopifnot( 391s + model@lower < optpar, 391s + optpar < attr(model, "upper"), 391s + model@lower < optpar2, 391s + optpar2 < attr(model, "upper") 391s + ) 391s + ## Evaluate deviance function at optimum (for safety): 391s + devfun(optpar) 391s + ## Optimize devfun over all but the j'th parameter: 391s + (startpar <- optpar[-j]) 391s + res <- nlminb(start=startpar, objective = function(p) { 391s + (Par <- optpar2) 391s + (Par[-j] <- p) 391s + devfun(Par) 391s + }, control = list(trace=do_trace), 391s + lower = model@lower[-j], 391s + upper = attr(model, "upper")[-j]) 391s + ## Evaluate devfun_vp: 391s + devfun_vp(varpar, devfun=devfun, reml=TRUE) 391s + ## Optimize devfun_vp over all but the j'th parameter: 391s + (startpar_vp <- varpar[-j]) 391s + (np <- length(startpar_vp)) 391s + res_vp <- nlminb(start=startpar_vp, objective = function(p) { 391s + (Par <- optpar2) 391s + (Par[-j] <- p[-np]) 391s + Par <- c(Par, p[np]) 391s + devfun_vp(Par, devfun=devfun, reml=TRUE) 391s + }, control = list(trace=do_trace), 391s + lower = c(model@lower[-j], 0), 391s + upper = c(attr(model, "upper")[-j], Inf)) 391s + ## Compare parameter estimates (except for sigma): 391s + res$objective - res_vp$objective 391s + res$par - res_vp$par[seq_along(res$par)] 391s + ## Check that parameter estimates and deviance values agree: 391s + stopifnot( 391s + abs(res$objective - res_vp$objective) < 1e-8, 391s + all(abs(res$par - res_vp$par[seq_along(res$par)]) < 1e-4) 391s + ) 391s + } 391s + } 391s + 391s + } 391s > 391s > 391s > 391s BEGIN TEST test_drop1.R 391s 391s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 391s Copyright (C) 2025 The R Foundation for Statistical Computing 391s Platform: aarch64-unknown-linux-gnu 391s 391s R is free software and comes with ABSOLUTELY NO WARRANTY. 391s You are welcome to redistribute it under certain conditions. 391s Type 'license()' or 'licence()' for distribution details. 391s 391s R is a collaborative project with many contributors. 391s Type 'contributors()' for more information and 391s 'citation()' on how to cite R or R packages in publications. 391s 391s Type 'demo()' for some demos, 'help()' for on-line help, or 391s 'help.start()' for an HTML browser interface to help. 391s Type 'q()' to quit R. 391s 391s > # test_drop1.R 391s > 391s > library(lmerTest) 391s Loading required package: lme4 391s Loading required package: Matrix 393s 393s Attaching package: 'lmerTest' 393s 393s The following object is masked from 'package:lme4': 393s 393s lmer 393s 393s The following object is masked from 'package:stats': 393s 393s step 393s 393s > 393s > # WRE says "using if(requireNamespace("pkgname")) is preferred, if possible." 393s > # even in tests: 393s > assertError <- function(expr, ...) 393s + if(requireNamespace("tools")) tools::assertError(expr, ...) else invisible() 393s > assertWarning <- function(expr, ...) 393s + if(requireNamespace("tools")) tools::assertWarning(expr, ...) else invisible() 393s > 393s > TOL <- 1e-4 393s > # Kenward-Roger only available with pbkrtest and only then validated in R >= 3.3.3 393s > # (faulty results for R < 3.3.3 may be due to unstated dependencies in pbkrtest) 393s > has_pbkrtest <- requireNamespace("pbkrtest", quietly = TRUE) && getRversion() >= "3.3.3" 393s > 393s > data("sleepstudy", package="lme4") 393s > 393s > ######### Basic usage 393s > 393s > data("cake", package="lme4") 393s > cake2 <- cake 393s > cake2$temperature <- factor(cake2$temperature, ordered = FALSE) 393s > fm <- lmer(angle ~ recipe + temperature + (1|recipe:replicate), cake2) 393s > (an1 <- drop1(fm)) 393s Single term deletions using Satterthwaite's method: 393s 393s Model: 393s angle ~ recipe + temperature + (1 | recipe:replicate) 393s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 393s recipe 10.19 5.09 2 42 0.2488 0.7809 393s temperature 2100.30 420.06 5 220 20.5141 <2e-16 *** 393s --- 393s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 393s > (an2 <- drop1(fm, force_get_contrasts = TRUE)) 393s Single term deletions using Satterthwaite's method: 393s 393s Model: 393s angle ~ recipe + temperature + (1 | recipe:replicate) 393s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 393s recipe 10.19 5.09 2 42 0.2488 0.7809 393s temperature 2100.30 420.06 5 220 20.5141 <2e-16 *** 393s --- 393s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 393s > drop1(fm, ddf="lme4", test="Chi") 394s Single term deletions 394s 394s Model: 394s angle ~ recipe + temperature + (1 | recipe:replicate) 394s npar AIC LRT Pr(Chi) 394s 1709.6 394s recipe 2 1706.1 0.530 0.7672 394s temperature 5 1785.7 86.106 <2e-16 *** 394s --- 394s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 394s > if(has_pbkrtest) 394s + drop1(fm, ddf="Kenward-Roger") 394s Single term deletions using Kenward-Roger's method: 394s 394s Model: 394s angle ~ recipe + temperature + (1 | recipe:replicate) 394s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 394s recipe 10.19 5.09 2 42 0.2488 0.7809 394s temperature 2100.30 420.06 5 220 20.5141 <2e-16 *** 394s --- 394s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 394s > 394s > tests1 <- show_tests(an1) 394s > tests2 <- show_tests(an2) 394s > 394s > stopifnot( 394s + # Tests are the same: 394s + isTRUE(all.equal(an1, an2, check.attributes = FALSE, tolerance=TOL)), 394s + # But contrast matrices are not: 394s + all(!mapply(function(x, y) isTRUE(all.equal(x, y)), tests1, tests2)) 394s + ) 394s > 394s > fm <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake2) 394s > drop1(fm) 394s Single term deletions using Satterthwaite's method: 394s 394s Model: 394s angle ~ recipe * temperature + (1 | recipe:replicate) 394s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 394s recipe:temperature 205.98 20.598 10 210 1.0062 0.4393 394s > drop1(fm, ddf="lme4") 394s Single term deletions 394s 394s Model: 394s angle ~ recipe * temperature + (1 | recipe:replicate) 394s npar AIC 394s 1719.0 394s recipe:temperature 10 1709.6 394s > if(has_pbkrtest) 394s + drop1(fm, ddf="Kenward-Roger") 394s Single term deletions using Kenward-Roger's method: 394s 394s Model: 394s angle ~ recipe * temperature + (1 | recipe:replicate) 394s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 394s recipe:temperature 205.98 20.598 10 210 1.0062 0.4393 394s > 394s > # Incorrect arguments: 394s > assertError(drop1(fm, scope="recipe")) # Correct Error 394s > assertError(drop1(fm, scope=3)) # Correct Error 394s > assertError(drop1(fm, scope=list("recipe"))) # Correct Error 394s > 394s > # Polynomial terms: 394s > 394s > fm <- lmer(Reaction ~ 0 + (Days|Subject), sleepstudy) 394s > (an0 <- drop1(fm)) # No fixef! 394s Single term deletions using Satterthwaite's method: 394s 394s Model: 394s Reaction ~ 0 + (Days | Subject) 394s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 394s > fm <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy) 394s > (an1 <- drop1(fm)) 394s Single term deletions using Satterthwaite's method: 394s 394s Model: 394s Reaction ~ Days + (Days | Subject) 394s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 394s Days 30031 30031 1 17 45.853 3.264e-06 *** 394s --- 394s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 394s > fm <- lmer(Reaction ~ Days + I(Days^2) + (Days|Subject), sleepstudy) 394s > (an2 <- (drop1(fm))) 394s Single term deletions using Satterthwaite's method: 394s 394s Model: 394s Reaction ~ Days + I(Days^2) + (Days | Subject) 394s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 394s Days 4534.5 4534.5 1 114.43 6.9551 0.00952 ** 394s I(Days^2) 1079.5 1079.5 1 143.00 1.6558 0.20026 394s --- 394s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 394s > fm <- lmer(Reaction ~ poly(Days, 2) + (Days|Subject), sleepstudy) 394s > (an3 <- drop1(fm)) 394s Single term deletions using Satterthwaite's method: 394s 394s Model: 394s Reaction ~ poly(Days, 2) + (Days | Subject) 394s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 394s poly(Days, 2) 30974 15487 2 29.115 23.754 7.625e-07 *** 394s --- 394s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 394s > stopifnot( 394s + nrow(an0) == 0L, 394s + nrow(an1) == 1L, 394s + nrow(an2) == 2L, 394s + nrow(an3) == 1L 394s + ) 394s > 394s > # Consider a rank-deficient design matrix: 394s > fm <- lmer(angle ~ recipe + temp + temperature + (1|recipe:replicate), cake) 394s fixed-effect model matrix is rank deficient so dropping 1 column / coefficient 394s > # Here temp accounts for the linear effect of temperature, and 394s > # temperature is an (ordered) factor that accounts for the remaining 394s > # variation between temperatures (4 df). 394s > (an4 <- drop1(fm)) 394s Single term deletions using Satterthwaite's method: 394s 394s Model: 394s angle ~ recipe + temp + temperature + (1 | recipe:replicate) 394s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 394s recipe 10.189 5.094 2 42 0.2488 0.7809 394s temp 394s temperature 133.595 33.399 4 220 1.6311 0.1674 394s > # While temperature is in the model, we cannot test the effect of dropping 394s > # temp. After removing temperature we can test the effect of dropping temp: 394s > (an5 <- drop1(update(fm, ~.-temperature))) 394s Single term deletions using Satterthwaite's method: 394s 394s Model: 394s angle ~ recipe + temp + (1 | recipe:replicate) 394s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 394s recipe 10.3 5.15 2 42 0.2488 0.7809 394s temp 1966.7 1966.71 1 224 94.9759 <2e-16 *** 394s --- 394s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 394s > 394s > stopifnot( 394s + nrow(an4) == 3, 394s + rownames(an4)[2] == "temp", 394s + all(is.na(an4[2, ])), 394s + all(!is.na(an4[-2, ])), 394s + all(rownames(an5) == c("recipe", "temp")) 394s + ) 394s > 394s > 394s > 394s > 394s BEGIN TEST test_legacy.R 395s 395s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 395s Copyright (C) 2025 The R Foundation for Statistical Computing 395s Platform: aarch64-unknown-linux-gnu 395s 395s R is free software and comes with ABSOLUTELY NO WARRANTY. 395s You are welcome to redistribute it under certain conditions. 395s Type 'license()' or 'licence()' for distribution details. 395s 395s R is a collaborative project with many contributors. 395s Type 'contributors()' for more information and 395s 'citation()' on how to cite R or R packages in publications. 395s 395s Type 'demo()' for some demos, 'help()' for on-line help, or 395s 'help.start()' for an HTML browser interface to help. 395s Type 'q()' to quit R. 395s 395s > # test_legacy.R 395s > library(lmerTest) 395s Loading required package: lme4 395s Loading required package: Matrix 397s 397s Attaching package: 'lmerTest' 397s 397s The following object is masked from 'package:lme4': 397s 397s lmer 397s 397s The following object is masked from 'package:stats': 397s 397s step 397s 397s > TOL <- 1e-4 397s > ##################################################################### 397s > 397s > # Read in data set 397s > load(system.file("testdata", "legacy_fits.RData", package="lmerTest")) 397s > # Generated with the following code using lmerTest version 2.0-37.9002 397s > # 397s > # library("lmerTest") 397s > # packageVersion("lmerTest") 397s > # fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy) 397s > # (an1 <- anova(fm1)) 397s > # (sfm1 <- summary(fm1)) 397s > # 397s > # fm2 <- lmer(Informed.liking ~ Product + Information + Gender + 397s > # (1|Product:Consumer) , data=ham) 397s > # (an2 <- anova(fm2)) 397s > # (sfm2 <- summary(fm2)) 397s > # 397s > # save(fm1, an1, sfm1, fm2, an2, sfm2, 397s > # file="~/GitHub/lmerTestR/package/inst/testdata/legacy_fits.RData") 397s > 397s > 397s > ####################################### 397s > ### Check that arguments for merModLmerTest and lmerModLmerTest methods match up: 397s > 397s > stopifnot( 397s + isTRUE(all.equal(formals(lmerTest:::anova.merModLmerTest), 397s + formals(lmerTest:::anova.lmerModLmerTest))), 397s + isTRUE(all.equal(formals(lmerTest:::summary.merModLmerTest), 397s + formals(lmerTest:::summary.lmerModLmerTest))), 397s + isTRUE(all.equal(formals(lmerTest:::drop1.merModLmerTest), 397s + formals(lmerTest:::drop1.lmerModLmerTest))), 397s + isTRUE(all.equal(formals(lmerTest:::step.merModLmerTest), 397s + formals(lmerTest:::step.lmerModLmerTest))), 397s + isTRUE(all.equal(formals(lmerTest:::ls_means.merModLmerTest), 397s + formals(lmerTest:::ls_means.lmerModLmerTest))), 397s + isTRUE(all.equal(formals(lmerTest:::difflsmeans.merModLmerTest), 397s + formals(lmerTest:::difflsmeans.lmerModLmerTest)))) 397s > 397s > 397s > ####################################### 397s > ## Tests for fm1: 397s > 397s > (an1new <- anova(fm1)) 397s Type III Analysis of Variance Table with Satterthwaite's method 397s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 397s Days 30031 30031 1 17 45.853 3.264e-06 *** 397s --- 397s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 397s > (sfm1new <- summary(fm1)) 397s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 397s lmerModLmerTest] 397s Formula: Reaction ~ Days + (Days | Subject) 397s Data: sleepstudy 397s 397s REML criterion at convergence: 1743.6 397s 397s Scaled residuals: 397s Min 1Q Median 3Q Max 397s -3.9536 -0.4634 0.0231 0.4634 5.1793 397s 397s Random effects: 397s Groups Name Variance Std.Dev. Corr 397s Subject (Intercept) 612.09 24.740 397s Days 35.07 5.922 0.07 397s Residual 654.94 25.592 397s Number of obs: 180, groups: Subject, 18 397s 397s Fixed effects: 397s Estimate Std. Error df t value Pr(>|t|) 397s (Intercept) 251.405 6.825 17.000 36.838 < 2e-16 *** 397s Days 10.467 1.546 17.000 6.771 3.26e-06 *** 397s --- 397s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 397s 397s Correlation of Fixed Effects: 397s (Intr) 397s Days -0.138 397s > 397s > stopifnot( 397s + isTRUE(all.equal(an1new, an1, check.attributes=FALSE, tol=TOL)), 397s + isTRUE(all.equal(coef(sfm1new), coef(sfm1), tol=TOL)) 397s + ) 397s > 397s > contest(fm1, c(0, 1)) 397s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 397s 1 30031.01 30031.01 1 17 45.853 3.26379e-06 397s > contest(fm1, c(0, 1), joint=FALSE) 397s Estimate Std. Error df t value lower upper Pr(>|t|) 397s 1 10.46729 1.545789 17 6.771485 7.205956 13.72862 3.26379e-06 397s > drop1(fm1) 397s Single term deletions using Satterthwaite's method: 397s 397s Model: 397s Reaction ~ Days + (Days | Subject) 397s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 397s Days 30031 30031 1 17 45.853 3.264e-06 *** 397s --- 397s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 397s > ranova(fm1) 397s ANOVA-like table for random-effects: Single term deletions 397s 397s Model: 397s Reaction ~ Days + (Days | Subject) 397s npar logLik AIC LRT Df Pr(>Chisq) 397s 6 -871.81 1755.6 397s Days in (Days | Subject) 4 -893.23 1794.5 42.837 2 4.99e-10 *** 397s --- 397s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 397s > step(fm1) 397s Backward reduced random-effect table: 397s 397s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 397s 6 -871.81 1755.6 397s Days in (Days | Subject) 0 4 -893.23 1794.5 42.837 2 4.99e-10 397s 397s 397s Days in (Days | Subject) *** 397s --- 397s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 397s 397s Backward reduced fixed-effect table: 397s Degrees of freedom method: Satterthwaite 397s 397s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 397s Days 0 30031 30031 1 17 45.853 3.264e-06 *** 397s --- 397s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 397s 397s Model found: 397s Reaction ~ Days + (Days | Subject) 397s > 397s > fm1new <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy, 397s + control=lmerControl(optimizer="bobyqa")) 397s > stopifnot( 397s + isTRUE(all.equal(drop1(fm1), drop1(fm1new), tol=TOL)), 397s + isTRUE(all.equal(ranova(fm1), ranova(fm1new), tol=TOL)), 397s + isTRUE(all.equal(contest(fm1, c(0, 1)), contest(fm1new, c(0, 1)), tol=TOL)), 397s + isTRUE(all.equal(contest(fm1, c(0, 1), joint=FALSE), 397s + contest(fm1new, c(0, 1), joint=FALSE), tol=TOL)) 397s + ) 398s > 398s > # Test that lme4 methods work: 398s > coef(fm1) 398s $Subject 398s (Intercept) Days 398s 308 253.6637 19.6662579 398s 309 211.0065 1.8475828 398s 310 212.4449 5.0184061 398s 330 275.0956 5.6529547 398s 331 273.6653 7.3973914 398s 332 260.4446 10.1951153 398s 333 268.2455 10.2436615 398s 334 244.1725 11.5418620 398s 335 251.0714 -0.2848731 398s 337 286.2955 19.0955699 398s 349 226.1950 11.6407002 398s 350 238.3351 17.0814910 398s 351 255.9829 7.4520288 398s 352 272.2687 14.0032993 398s 369 254.6806 11.3395026 398s 370 225.7922 15.2897506 398s 371 252.2121 9.4791309 398s 372 263.7196 11.7513157 398s 398s attr(,"class") 398s [1] "coef.mer" 398s > fixef(fm1) 398s (Intercept) Days 398s 251.40510 10.46729 398s > resid(fm1) 398s 1 2 3 4 5 6 398s -4.1036703 -14.6252282 -42.1955860 8.7773561 24.5231982 62.6951403 398s 7 8 9 10 11 12 398s 10.5425825 -101.1788754 19.5915667 35.6935088 11.7273721 -7.5883107 398s 13 14 15 16 17 18 398s -11.7238935 -11.8422762 -10.6807590 -4.2826418 -8.4617246 -6.2124074 398s 19 20 21 22 23 24 398s -1.4914902 9.6794271 -13.3909590 -23.1310650 11.8383289 5.3415228 398s 25 26 27 28 29 30 398s -3.2110832 -17.0789893 -7.1344953 8.1773986 8.4203926 -10.0952135 398s 31 32 33 34 35 36 398s 46.4469967 19.6516420 -2.5450126 -6.9214673 -11.9101220 -5.7748766 398s 37 38 39 40 41 42 398s -28.7737313 3.5950141 -14.9697406 28.0765048 13.9425924 3.9373010 398s 43 44 45 46 47 48 398s 13.3605097 24.2578183 13.0224270 -17.3335644 -27.9746558 9.3706529 398s 49 50 51 52 53 54 398s -39.0975385 31.3392701 -25.5840308 -27.8279461 -7.8735614 18.7388233 398s 55 56 57 58 59 60 398s 16.2378080 -1.4226073 132.5465774 15.0206621 -11.7052532 -98.3362685 398s 61 62 63 64 65 66 398s 15.5968640 11.0658025 -11.9635591 0.8331794 -12.0491821 18.7026564 398s 67 68 69 70 71 72 398s 2.3189949 8.8887334 -16.8348282 1.6043103 21.3005744 20.4868123 398s 73 74 75 76 77 78 398s -23.8915497 -24.1258118 -11.3155738 -17.6906358 -7.8988979 6.5573401 398s 79 80 81 82 83 84 398s -0.7605219 29.2497160 -9.4631090 23.1606642 3.9890373 20.5853104 398s 85 86 87 88 89 90 398s 1.5199836 4.9891567 -3.9098701 -13.7662970 -13.0383239 -11.2609507 398s 91 92 93 94 95 96 398s 26.0711443 8.4147744 -32.8753955 2.5400346 3.0546647 10.0651947 398s 97 98 99 100 101 102 398s 3.3912248 -3.2721451 16.8042850 0.7611151 9.9082056 -7.5189947 398s 103 104 105 106 107 108 398s -10.5507949 -6.1950951 -22.0474953 -14.6240955 -14.4743957 0.4221041 398s 109 110 111 112 113 114 398s 16.9600039 20.6838037 17.9616518 -11.9623391 -16.2935301 -34.0525210 398s 115 116 117 118 119 120 398s -37.7446120 5.9820971 38.6204061 5.0128151 19.5001242 -3.0158668 398s 121 122 123 124 125 126 398s -5.4564400 36.6226312 -0.9930976 2.2500737 -13.9636551 11.3905161 398s 127 128 129 130 131 132 398s -12.9485127 -41.5516414 5.9426298 24.5143010 -50.5915973 11.9219034 398s 133 134 135 136 137 138 398s 26.6032041 32.5769048 20.4583056 10.5435063 -1.8618930 -9.8591922 398s 139 140 141 142 143 144 398s -8.6544915 -9.7566908 17.2429421 2.4168396 -20.1171630 -11.0424656 398s 145 146 147 148 149 150 398s 14.7836319 5.8354293 -24.5822732 14.0658242 -5.1165783 9.7770191 398s 151 152 153 154 155 156 398s -0.5282354 -6.5584860 -17.4709366 -31.1884871 -19.4139377 41.9527117 398s 157 158 159 160 161 162 398s -36.3826389 14.7650105 17.0527600 8.8288094 17.6682554 10.7515245 398s 163 164 165 166 167 168 398s 6.7284937 1.1399628 -10.9581681 -15.0957989 -49.8211298 -13.9354607 398s 169 170 171 172 173 174 398s 22.7355085 31.9448776 5.6920558 -1.9969599 10.3745244 11.6580087 398s 175 176 177 178 179 180 398s -23.5523070 7.1313773 0.2542616 -2.7589541 11.4115302 -5.3578855 398s > 398s > ####################################### 398s > ## Tests for fm2: 398s > (an2new <- anova(fm2)) 398s Type III Analysis of Variance Table with Satterthwaite's method 398s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 398s Product 17.6984 5.8995 3 319 3.5029 0.01577 * 398s Information 6.5201 6.5201 1 323 3.8714 0.04997 * 398s Gender 1.8634 1.8634 1 319 1.1064 0.29366 398s --- 398s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 398s > (sfm2new <- summary(fm2)) 398s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 398s lmerModLmerTest] 398s Formula: 398s Informed.liking ~ Product + Information + Gender + (1 | Product:Consumer) 398s Data: ham 398s 398s REML criterion at convergence: 2712.2 398s 398s Scaled residuals: 398s Min 1Q Median 3Q Max 398s -3.1568 -0.5087 0.0338 0.4913 3.1623 398s 398s Random effects: 398s Groups Name Variance Std.Dev. 398s Product:Consumer (Intercept) 3.526 1.878 398s Residual 1.684 1.298 398s Number of obs: 648, groups: Product:Consumer, 324 398s 398s Fixed effects: 398s Estimate Std. Error df t value Pr(>|t|) 398s (Intercept) 5.8290 0.2640 343.6885 22.082 <2e-16 *** 398s Product2 -0.7037 0.3284 319.0000 -2.143 0.0329 * 398s Product3 0.2840 0.3284 319.0000 0.865 0.3879 398s Product4 0.1173 0.3284 319.0000 0.357 0.7212 398s Information2 0.2006 0.1020 323.0000 1.968 0.0500 * 398s Gender2 -0.2443 0.2322 319.0000 -1.052 0.2937 398s --- 398s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 398s 398s Correlation of Fixed Effects: 398s (Intr) Prdct2 Prdct3 Prdct4 Infrm2 398s Product2 -0.622 398s Product3 -0.622 0.500 398s Product4 -0.622 0.500 0.500 398s Informatin2 -0.193 0.000 0.000 0.000 398s Gender2 -0.434 0.000 0.000 0.000 0.000 398s > 398s > stopifnot( 398s + isTRUE(all.equal(an2new, an2, check.attributes=FALSE, tol=TOL)), 398s + isTRUE(all.equal(coef(sfm2new), coef(sfm2), tol=TOL)) 398s + ) 398s > 398s > drop1(fm2) 398s Single term deletions using Satterthwaite's method: 398s 398s Model: 398s Informed.liking ~ Product + Information + Gender + (1 | Product:Consumer) 398s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 398s Product 17.6984 5.8995 3 319 3.5029 0.01577 * 398s Information 6.5201 6.5201 1 323 3.8714 0.04997 * 398s Gender 1.8634 1.8634 1 319 1.1064 0.29366 398s --- 398s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 398s > ranova(fm2) 398s ANOVA-like table for random-effects: Single term deletions 398s 398s Model: 398s Informed.liking ~ Product + Information + Gender + (1 | Product:Consumer) 398s npar logLik AIC LRT Df Pr(>Chisq) 398s 8 -1356.1 2728.2 398s (1 | Product:Consumer) 7 -1454.7 2923.4 197.19 1 < 2.2e-16 *** 398s --- 398s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 398s > ls_means(fm2) 398s Least Squares Means table: 398s 398s Estimate Std. Error df t value lower upper Pr(>|t|) 398s Product1 5.80713 0.23223 319.0 25.006 5.35025 6.26402 < 2.2e-16 *** 398s Product2 5.10343 0.23223 319.0 21.976 4.64654 5.56032 < 2.2e-16 *** 398s Product3 6.09108 0.23223 319.0 26.229 5.63420 6.54797 < 2.2e-16 *** 398s Product4 5.92442 0.23223 319.0 25.511 5.46753 6.38131 < 2.2e-16 *** 398s Information1 5.63121 0.12682 437.8 44.404 5.38196 5.88046 < 2.2e-16 *** 398s Information2 5.83183 0.12682 437.8 45.986 5.58258 6.08107 < 2.2e-16 *** 398s Gender1 5.85366 0.16320 319.0 35.868 5.53257 6.17475 < 2.2e-16 *** 398s Gender2 5.60937 0.16523 319.0 33.949 5.28430 5.93445 < 2.2e-16 *** 398s --- 398s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 398s 398s Confidence level: 95% 398s Degrees of freedom method: Satterthwaite 398s > difflsmeans(fm2) 398s Least Squares Means table: 398s 398s Estimate Std. Error df t value lower 398s Product1 - Product2 7.0370e-01 3.2841e-01 319 2.1428 5.7578e-02 398s Product1 - Product3 -2.8395e-01 3.2841e-01 319 -0.8646 -9.3008e-01 398s Product1 - Product4 -1.1728e-01 3.2841e-01 319 -0.3571 -7.6341e-01 398s Product2 - Product3 -9.8765e-01 3.2841e-01 319 -3.0074 -1.6338e+00 398s Product2 - Product4 -8.2099e-01 3.2841e-01 319 -2.4999 -1.4671e+00 398s Product3 - Product4 1.6667e-01 3.2841e-01 319 0.5075 -4.7946e-01 398s Information1 - Information2 -2.0062e-01 1.0196e-01 323 -1.9676 -4.0121e-01 398s Gender1 - Gender2 2.4428e-01 2.3224e-01 319 1.0519 -2.1263e-01 398s upper Pr(>|t|) 398s Product1 - Product2 1.3498e+00 0.032890 * 398s Product1 - Product3 3.6218e-01 0.387898 398s Product1 - Product4 5.2884e-01 0.721234 398s Product2 - Product3 -3.4153e-01 0.002845 ** 398s Product2 - Product4 -1.7486e-01 0.012926 * 398s Product3 - Product4 8.1279e-01 0.612159 398s Information1 - Information2 -2.6433e-05 0.049970 * 398s Gender1 - Gender2 7.0120e-01 0.293660 398s --- 398s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 398s 398s Confidence level: 95% 398s Degrees of freedom method: Satterthwaite 398s > nbeta <- length(fixef(fm2)) 398s > L <- diag(nbeta) 398s > L[1:4, ] <- 0 398s > contest(fm2, L) 398s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 398s 1 8.383419 4.19171 2 320.9875 2.488919 0.08460028 398s > contest(fm2, diag(nbeta), joint=FALSE) 398s Estimate Std. Error df t value lower upper 398s 1 5.8289672 0.2639677 343.6885 22.0821233 5.309772e+00 6.34816269 398s 2 -0.7037037 0.3284114 319.0000 -2.1427506 -1.349830e+00 -0.05757783 398s 3 0.2839506 0.3284114 319.0000 0.8646187 -3.621753e-01 0.93007650 398s 4 0.1172840 0.3284114 319.0000 0.3571251 -5.288419e-01 0.76340983 398s 5 0.2006173 0.1019607 323.0000 1.9675949 2.643318e-05 0.40120813 398s 6 -0.2442835 0.2322396 319.0000 -1.0518599 -7.011983e-01 0.21263128 398s Pr(>|t|) 398s 1 6.753241e-68 398s 2 3.288952e-02 398s 3 3.878978e-01 398s 4 7.212343e-01 398s 5 4.997000e-02 398s 6 2.936600e-01 398s > step(fm2) 398s Backward reduced random-effect table: 398s 398s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 398s 8 -1356.1 2728.2 398s (1 | Product:Consumer) 0 7 -1454.7 2923.4 197.19 1 < 2.2e-16 *** 398s --- 398s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 398s 398s Backward reduced fixed-effect table: 398s Degrees of freedom method: Satterthwaite 398s 398s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 398s Gender 1 1.8634 1.8634 1 319 1.1064 0.29366 398s Product 0 17.6926 5.8975 3 320 3.5018 0.01579 * 398s Information 0 6.5201 6.5201 1 323 3.8714 0.04997 * 398s --- 398s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 398s 398s Model found: 398s Informed.liking ~ Product + Information + (1 | Product:Consumer) 398s > 398s > fm2new <- lmer(Informed.liking ~ Product + Information + Gender + 398s + (1|Product:Consumer), data=ham) 398s > stopifnot( 398s + isTRUE(all.equal(drop1(fm2), drop1(fm2new), tol=TOL)), 398s + isTRUE(all.equal(ranova(fm2), ranova(fm2new), tol=TOL)), 398s + isTRUE(all.equal(ls_means(fm2), ls_means(fm2new), tol=TOL)), 398s + isTRUE(all.equal(difflsmeans(fm2), difflsmeans(fm2new), tol=TOL)) 398s + ) 398s > 398s > # Test that lme4 methods work: 398s > coef(fm2) 398s $`Product:Consumer` 398s (Intercept) Product2 Product3 Product4 Information2 Gender2 398s 1:1 5.078836 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:2 5.276027 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:3 6.693279 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:4 6.693279 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:5 4.468805 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:6 5.078836 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:7 8.101302 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:8 6.289668 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:9 6.289668 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:10 5.482447 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:11 8.504912 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:12 3.661584 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:13 7.697691 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:14 8.101302 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:15 4.675225 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:16 4.872416 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:17 7.096889 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:18 7.500500 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:19 8.307721 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:20 6.693279 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:21 6.693279 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:22 6.083248 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:23 6.486859 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:24 7.500500 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:25 5.078836 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:26 7.294080 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:29 4.872416 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:30 6.083248 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:31 6.289668 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:32 7.697691 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:33 4.271615 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:34 4.675225 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:35 6.486859 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:36 6.083248 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:37 3.464393 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:38 6.289668 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:39 6.693279 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:40 3.661584 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:41 5.886057 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:42 5.482447 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:43 7.096889 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:44 6.083248 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:45 8.504912 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:46 5.078836 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:47 2.047141 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:48 6.890469 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:49 3.464393 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:50 3.257973 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:51 6.083248 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:52 8.504912 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:53 5.078836 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:54 3.661584 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:55 4.675225 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:56 6.486859 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:57 5.078836 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:58 5.482447 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:59 5.482447 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:60 5.482447 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:61 7.096889 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:62 5.276027 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:63 5.679637 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:64 4.872416 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:65 7.500500 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:66 6.083248 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:67 5.886057 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:68 7.294080 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:69 4.872416 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:70 6.486859 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:71 5.078836 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:73 2.854363 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:74 6.486859 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:75 4.675225 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 1:76 4.872416 -0.7037037 0.2839506 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0.2006173 -0.2442835 398s 4:33 4.176940 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:34 7.002215 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:35 6.795795 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:36 6.795795 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:37 5.387772 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:38 4.580551 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:39 4.176940 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:40 7.603017 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:41 4.580551 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:42 7.809437 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:43 5.387772 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:44 2.759689 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:45 5.181353 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:46 1.755276 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:47 1.952467 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:48 5.988574 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:49 7.002215 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:50 6.392185 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:51 8.410238 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:52 3.970521 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:53 7.002215 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:54 7.603017 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:55 5.387772 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:56 2.759689 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:57 7.002215 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:58 7.405826 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:59 6.194994 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:60 4.580551 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:61 6.194994 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:62 8.006627 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:63 5.584963 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:64 5.584963 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:65 3.369719 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:66 5.988574 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:67 6.194994 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:68 5.584963 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:69 6.795795 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:70 6.795795 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:71 4.984162 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:73 5.988574 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:74 8.410238 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:75 7.405826 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:76 8.410238 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:77 8.410238 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:78 7.405826 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:79 5.988574 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:80 3.970521 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:81 4.580551 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:82 5.988574 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:83 5.791383 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 4:84 4.580551 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 398s 398s attr(,"class") 398s [1] "coef.mer" 398s > fixef(fm2) 398s (Intercept) Product2 Product3 Product4 Information2 Gender2 398s 5.8289672 -0.7037037 0.2839506 0.1172840 0.2006173 -0.2442835 398s > resid(fm2) 398s 1 2 3 4 5 6 398s -0.07883589 -0.27945318 -0.13595549 -0.33657278 -1.13357551 0.66580721 398s 7 8 9 10 11 12 398s 0.09133291 -0.10928437 -0.03174324 -0.23236053 0.27864107 1.07802378 398s 13 14 15 16 17 18 398s 0.49185308 0.29123580 0.33120421 0.13058692 0.30672140 0.10610412 398s 19 20 21 22 23 24 398s -1.94317685 1.85620587 -0.15162889 0.64775382 2.09133291 -2.10928437 398s 25 26 27 28 29 30 398s 0.30672140 0.10610412 0.07487654 -1.12574075 -0.13357551 -0.33419279 398s 31 32 33 34 35 36 398s -0.50505641 0.29432631 -1.22452189 0.57486083 -0.28164149 -0.48225877 398s 37 38 39 40 41 42 398s -0.89370421 0.90567850 0.73481489 -0.46580240 -0.07883589 -0.27945318 398s 43 44 45 46 47 48 398s 0.46043383 -0.74018345 0.44476043 0.24414315 -2.10144573 1.69793698 398s 49 50 51 52 53 54 398s 1.14298202 -0.05763526 -1.07080946 -0.27142674 -0.10453624 0.69484647 398s 55 56 57 58 59 60 398s 0.15647895 -1.04413834 -0.28966792 0.50971479 -0.34678752 0.45259519 398s 61 62 63 64 65 66 398s -1.15162889 1.64775382 0.47689021 0.27627292 -0.28966792 0.50971479 398s 67 68 69 70 71 72 398s -0.34678752 0.45259519 0.44476043 0.24414315 -1.31227776 1.48710495 398s 73 74 75 76 77 78 398s 0.51755343 -0.68306385 0.23154842 1.03093113 -0.55523957 1.24414315 398s 79 80 81 82 83 84 398s 0.28411156 0.08349428 0.73937134 0.53875406 -0.66719878 -0.86781607 398s 85 86 87 88 89 90 398s 3.10629579 -3.09432150 0.73481489 -0.46580240 -0.41730054 -0.61791782 398s 91 92 93 94 95 96 398s -0.66719878 -0.86781607 -0.29731489 0.50206783 0.52398286 0.32336557 398s 97 98 99 100 101 102 398s 0.54659270 0.34597541 -0.66719878 -0.86781607 0.50990646 -0.69071082 398s 103 104 105 106 107 108 398s 0.52398286 0.32336557 1.14298202 -0.05763526 -0.66719878 -0.86781607 398s 109 110 111 112 113 114 398s -0.87565083 -0.07626811 1.13842556 -1.06219172 -0.67522522 0.12415750 398s 115 116 117 118 119 120 398s -0.15400888 0.64537384 0.25198178 0.05136450 -0.11949912 0.67988360 398s 121 122 123 124 125 126 398s 2.37186743 -2.82874985 -0.66719878 -0.86781607 -0.89370421 0.90567850 398s 127 128 129 130 131 132 398s -1.26518511 1.53419760 -0.09688928 0.70249344 0.05682315 -0.14379413 398s 133 134 135 136 137 138 398s -0.15162889 0.64775382 0.10938630 -1.09123099 1.49950005 -0.70111724 398s 139 140 141 142 143 144 398s 0.07487654 -1.12574075 0.05920314 -0.14141415 -0.11949912 0.67988360 398s 145 146 147 148 149 150 398s 0.69227869 0.49166141 -0.71429143 -0.91490872 -0.90469010 -1.10530738 398s 151 152 153 154 155 156 398s -0.10144573 -0.30206302 0.30672140 0.10610412 -0.52151279 -0.72213007 398s 157 158 159 160 161 162 398s -0.15162889 0.64775382 0.89855427 -1.30206302 0.30672140 0.10610412 398s 163 164 165 166 167 168 398s -1.11790211 -0.31851939 0.07725652 -1.12336076 -0.69783506 0.10154766 398s 169 170 171 172 173 174 398s 2.16103540 -2.03958188 -0.66719878 -0.86781607 1.12434917 -2.07626811 398s 175 176 177 178 179 180 398s 0.15647895 -1.04413834 0.75742473 -0.44319256 -0.66719878 -0.86781607 398s 181 182 183 184 185 186 398s -0.66481880 -0.86543608 1.15647895 -2.04413834 0.49950005 0.29888276 398s 187 188 189 190 191 192 398s 0.44238045 0.24176316 1.04114975 -0.15946753 -0.11949912 0.67988360 398s 193 194 195 196 197 198 398s -0.07883589 -0.27945318 -0.15400888 0.64537384 -0.34440754 0.45497518 398s 199 200 201 202 203 204 398s -0.11949912 0.67988360 0.95020337 -0.25041391 -0.66719878 -0.86781607 398s 205 206 207 208 209 210 398s -0.70092557 1.09845715 1.34925759 -1.85135969 -3.62813257 3.17125015 398s 211 212 213 214 215 216 398s -0.66719878 -0.86781607 0.29907443 0.09845715 -1.22907835 -0.42969563 398s 217 218 219 220 221 222 398s 0.16103540 -0.03958188 1.08586242 -0.11475486 -0.29731489 0.50206783 398s 223 224 225 226 227 228 398s 0.73481489 -0.46580240 -0.28966792 0.50971479 1.03876977 -0.16184751 398s 229 230 231 232 233 234 398s 0.84837111 -0.35224618 0.47689021 0.27627292 0.54659270 0.34597541 398s 235 236 237 238 239 240 398s -0.49247352 0.30690920 0.49185308 0.29123580 -0.86157444 0.93780828 398s 241 242 243 244 245 246 398s -1.27161454 0.52776818 -0.71429143 -0.91490872 -1.71191145 0.08747127 398s 247 248 249 250 251 252 398s 1.70577562 -2.49484166 -0.67522522 0.12415750 -0.15400888 0.64537384 398s 253 254 255 256 257 258 398s 0.65559246 -0.54502482 -0.11949912 0.67988360 -1.24257527 1.55680744 398s 259 260 261 262 263 264 398s -1.08886284 0.71051987 -1.29731489 1.50206783 0.33120421 0.13058692 398s 265 266 267 268 269 270 398s 0.16103540 -0.03958188 0.27864107 1.07802378 0.29907443 0.09845715 398s 271 272 273 274 275 276 398s 1.33120421 -0.86941308 -1.46439319 0.33498953 -0.15400888 0.64537384 398s 277 278 279 280 281 282 398s 0.84837111 -0.35224618 -0.50505641 0.29432631 0.71033208 -0.49028521 398s 283 284 285 286 287 288 398s -0.13595549 -0.33657278 0.67364584 -1.52697144 0.30216494 -0.89845234 398s 289 290 291 292 293 294 398s -0.69327860 1.10610412 -0.55761955 1.24176316 -0.94079686 0.85858585 398s 295 296 297 298 299 300 398s -0.29422438 -0.49484166 -2.41730054 1.38208218 -0.87803081 -0.07864810 398s 301 302 303 304 305 306 398s 0.49185308 0.29123580 1.52398286 -0.67663443 0.11394275 -0.08667453 398s 307 308 309 310 311 312 398s -0.53956617 0.25981655 0.46281381 -0.73780347 0.30216494 -0.89845234 398s 313 314 315 316 317 318 398s -0.48244657 0.31693615 -0.15400888 0.64537384 -0.15162889 0.64775382 398s 319 320 321 322 323 324 398s 0.07327953 0.87266225 0.90311072 -0.29750656 1.26765518 -1.93296210 398s 325 326 327 328 329 330 398s -0.15162889 0.64775382 0.49494359 -0.70567369 -1.83896460 1.96041812 398s 331 332 333 334 335 336 398s -1.08886284 0.71051987 -0.27926151 -0.47987879 -0.63268902 -0.83330631 398s 337 338 339 340 341 342 398s 0.73937134 0.53875406 -1.49247352 1.30690920 -0.66481880 -0.86543608 398s 343 344 345 346 347 348 398s 0.94564692 -1.25497037 1.92116411 -2.27945318 1.23154842 0.03093113 398s 349 350 351 352 353 354 398s -2.53718619 2.26219653 -0.87256032 -1.07317760 -0.80285783 -1.00347511 398s 355 356 357 358 359 360 398s 4.10391580 -4.09670148 1.10629579 -1.09432150 -0.82546767 -1.02608496 398s 361 362 363 364 365 366 398s 0.35381405 0.15319677 -0.66719878 -0.86781607 -0.49009354 0.30928918 398s 367 368 369 370 371 372 398s 0.13842556 -0.06219172 -0.46439319 -0.66501047 -0.55761955 1.24176316 398s 373 374 375 376 377 378 398s -0.74801822 1.05136450 -0.11949912 0.67988360 -0.01368986 -1.21430714 398s 379 380 381 382 383 384 398s 0.08586242 0.88524514 0.68463173 0.48401444 -0.26518511 0.53419760 398s 385 386 387 388 389 390 398s -0.83896460 0.96041812 -0.31774826 1.48163446 0.68463173 0.48401444 398s 391 392 393 394 395 396 398s 0.71676150 0.51614422 0.73937134 0.53875406 0.10391580 -0.09670148 398s 397 398 399 400 401 402 398s -0.29731489 0.50206783 -0.84352105 -0.04413834 -0.07883589 -0.27945318 398s 403 404 405 406 407 408 398s 1.63515909 -0.56545819 -0.13357551 -0.33419279 0.88050088 -0.32011640 398s 409 410 411 412 413 414 398s -0.41730054 -0.61791782 0.08586242 0.88524514 -0.10453624 0.69484647 398s 415 416 417 418 419 420 398s 0.52398286 0.32336557 1.32477478 -1.87584250 -2.53956617 2.25981655 398s 421 422 423 424 425 426 398s 1.25198178 -0.94863550 -2.50505641 2.29432631 -0.24257527 0.55680744 398s 427 428 429 430 431 432 398s -0.10691623 0.69246649 -0.87565083 -0.07626811 -0.63268902 -0.83330631 398s 433 434 435 436 437 438 398s -0.07883589 -0.27945318 -0.15400888 0.64537384 -1.15162889 1.64775382 398s 439 440 441 442 443 444 398s -0.11949912 0.67988360 0.51755343 -0.68306385 0.23154842 1.03093113 398s 445 446 447 448 449 450 398s -0.55523957 1.24414315 0.47689021 0.27627292 -0.48244657 0.31693615 398s 451 452 453 454 455 456 398s -0.36484091 1.43454181 1.04114975 -0.15946753 0.68772224 -0.51289505 398s 457 458 459 460 461 462 398s 0.51755343 -0.68306385 0.46043383 -0.74018345 0.86642449 -1.33419279 398s 463 464 465 466 467 468 398s 1.30216494 -1.89845234 0.90311072 -0.29750656 -0.13595549 -0.33657278 398s 469 470 471 472 473 474 398s -0.13357551 -0.33419279 0.68772224 -0.51289505 -0.03174324 -0.23236053 398s 475 476 477 478 479 480 398s 0.27864107 1.07802378 1.08824240 -0.11237488 1.12037218 -0.08024511 398s 481 482 483 484 485 486 398s 0.56464608 -0.63597120 1.08586242 -0.11475486 -0.89370421 0.90567850 398s 487 488 489 490 491 492 398s 0.54203624 -0.65858105 1.37186743 -1.82874985 1.08586242 -0.11475486 398s 493 494 495 496 497 498 398s -0.29731489 0.50206783 0.54203624 -0.65858105 0.49950005 0.29888276 398s 499 500 501 502 503 504 398s -0.73234482 0.06703790 0.07725652 -1.12336076 -0.48700303 -0.68762031 398s 505 506 507 508 509 510 398s -0.83896460 0.96041812 2.10391580 -2.09670148 -2.87565083 1.92373189 398s 511 512 513 514 515 516 398s 2.13842556 -2.06219172 0.11394275 -0.08667453 1.03876977 -0.16184751 398s 517 518 519 520 521 522 398s 0.84837111 -0.35224618 -0.31227776 0.48710495 1.95020337 -1.25041391 398s 523 524 525 526 527 528 398s -0.87803081 -0.07864810 -0.85759745 -1.05821473 2.54203624 -2.65858105 398s 529 530 531 532 533 534 398s -0.62813257 0.17125015 0.48947310 0.28885581 -0.70092557 1.09845715 398s 535 536 537 538 539 540 398s 0.33120421 0.13058692 -0.24257527 0.55680744 -1.28164149 0.51774123 398s 541 542 543 544 545 546 398s -0.06842948 -1.26904676 -0.66879579 1.13058692 1.92116411 -2.27945318 398s 547 548 549 550 551 552 398s 0.03876977 0.83815249 0.63753908 0.43692179 -0.10144573 -0.30206302 398s 553 554 555 556 557 558 398s -1.61007918 0.18930353 0.87503039 0.67441311 0.68463173 0.48401444 398s 559 560 561 562 563 564 398s 0.13842556 -0.06219172 -0.24257527 0.55680744 -0.70330555 1.09607717 398s 565 566 567 568 569 570 398s 0.68463173 0.48401444 0.71676150 0.51614422 -0.67522522 0.12415750 398s 571 572 573 574 575 576 398s 0.82793774 0.62732046 -0.51913280 -0.71975009 0.47689021 0.27627292 398s 577 578 579 580 581 582 398s -2.62813257 2.17125015 -0.31774826 1.48163446 -2.89370421 2.90567850 398s 583 584 585 586 587 588 398s 0.71676150 0.51614422 -2.01368986 0.78569286 -0.31774826 1.48163446 398s 589 590 591 592 593 594 398s 0.29907443 0.09845715 0.71676150 0.51614422 0.92116411 -1.27945318 398s 595 596 597 598 599 600 398s -1.34678752 1.45259519 0.63753908 0.43692179 0.47689021 0.27627292 398s 601 602 603 604 605 606 398s -0.04979663 0.74958609 0.48947310 0.28885581 -0.27926151 -0.47987879 398s 607 608 609 610 611 612 398s 0.13842556 -0.06219172 -0.04979663 0.74958609 1.89308377 -1.30753351 398s 613 614 615 616 617 618 398s 0.93157052 -2.26904676 -0.84352105 -0.04413834 0.11394275 -0.08667453 398s 619 620 621 622 623 624 398s -0.32873414 -0.52935142 -0.92274348 -0.12336076 -1.69783506 1.10154766 398s 625 626 627 628 629 630 398s 2.35381405 -1.84680323 1.27864107 0.07802378 1.49185308 -0.70876420 398s 631 632 633 634 635 636 398s 0.13842556 -0.06219172 -2.86800386 1.93137885 -2.34678752 2.45259519 398s 637 638 639 640 641 642 398s -1.13357551 0.66580721 1.09133291 -1.10928437 0.51755343 -0.68306385 398s 643 644 645 646 647 648 398s 0.24960180 0.04898452 -1.94079686 1.85858585 0.30216494 -0.89845234 398s > 398s > 398s BEGIN TEST test_lmer.R 398s 398s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 398s Copyright (C) 2025 The R Foundation for Statistical Computing 398s Platform: aarch64-unknown-linux-gnu 398s 398s R is free software and comes with ABSOLUTELY NO WARRANTY. 398s You are welcome to redistribute it under certain conditions. 398s Type 'license()' or 'licence()' for distribution details. 398s 398s R is a collaborative project with many contributors. 398s Type 'contributors()' for more information and 398s 'citation()' on how to cite R or R packages in publications. 398s 398s Type 'demo()' for some demos, 'help()' for on-line help, or 398s 'help.start()' for an HTML browser interface to help. 398s Type 'q()' to quit R. 398s 398s > # test_lmer.R 398s > 398s > stopifnot(!"lmerTest" %in% .packages()) # ensure that lmerTest is NOT attached 398s > data("sleepstudy", package="lme4") 398s > f <- function(form, data) lmerTest::lmer(form, data=data) 398s > form <- "Reaction ~ Days + (Days|Subject)" 398s > fm <- f(form, data=sleepstudy) 401s > anova(fm) 401s Type III Analysis of Variance Table with Satterthwaite's method 401s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 401s Days 30031 30031 1 17 45.853 3.264e-06 *** 401s --- 401s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 401s > summary(fm) 401s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 401s lmerModLmerTest] 401s Formula: form 401s Data: data 401s 401s REML criterion at convergence: 1743.6 401s 401s Scaled residuals: 401s Min 1Q Median 3Q Max 401s -3.9536 -0.4634 0.0231 0.4634 5.1793 401s 401s Random effects: 401s Groups Name Variance Std.Dev. Corr 401s Subject (Intercept) 612.10 24.741 401s Days 35.07 5.922 0.07 401s Residual 654.94 25.592 401s Number of obs: 180, groups: Subject, 18 401s 401s Fixed effects: 401s Estimate Std. Error df t value Pr(>|t|) 401s (Intercept) 251.405 6.825 17.000 36.838 < 2e-16 *** 401s Days 10.467 1.546 17.000 6.771 3.26e-06 *** 401s --- 401s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 401s 401s Correlation of Fixed Effects: 401s (Intr) 401s Days -0.138 401s > 401s > # cf. GitHub issue #2: 401s > test <- function() { 401s + tmp <- sleepstudy 401s + m <- lmerTest::lmer(Reaction ~ Days + (Days | Subject), data = tmp) 401s + summary(m) 401s + } 401s > test() 401s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 401s lmerModLmerTest] 401s Formula: Reaction ~ Days + (Days | Subject) 401s Data: tmp 401s 401s REML criterion at convergence: 1743.6 401s 401s Scaled residuals: 401s Min 1Q Median 3Q Max 401s -3.9536 -0.4634 0.0231 0.4634 5.1793 401s 401s Random effects: 401s Groups Name Variance Std.Dev. Corr 401s Subject (Intercept) 612.10 24.741 401s Days 35.07 5.922 0.07 401s Residual 654.94 25.592 401s Number of obs: 180, groups: Subject, 18 401s 401s Fixed effects: 401s Estimate Std. Error df t value Pr(>|t|) 401s (Intercept) 251.405 6.825 17.000 36.838 < 2e-16 *** 401s Days 10.467 1.546 17.000 6.771 3.26e-06 *** 401s --- 401s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 401s 401s Correlation of Fixed Effects: 401s (Intr) 401s Days -0.138 401s > test <- function() { 401s + tmp <- sleepstudy 401s + m <- lme4::lmer(Reaction ~ Days + (Days | Subject), data = tmp) 401s + if(requireNamespace("lmerTest", quietly = TRUE)) { 401s + summary(lmerTest::as_lmerModLmerTest(m)) 401s + } 401s + } 401s > test() 401s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 401s lmerModLmerTest] 401s Formula: Reaction ~ Days + (Days | Subject) 401s Data: tmp 401s 401s REML criterion at convergence: 1743.6 401s 401s Scaled residuals: 401s Min 1Q Median 3Q Max 401s -3.9536 -0.4634 0.0231 0.4634 5.1793 401s 401s Random effects: 401s Groups Name Variance Std.Dev. Corr 401s Subject (Intercept) 612.10 24.741 401s Days 35.07 5.922 0.07 401s Residual 654.94 25.592 401s Number of obs: 180, groups: Subject, 18 401s 401s Fixed effects: 401s Estimate Std. Error df t value Pr(>|t|) 401s (Intercept) 251.405 6.825 17.000 36.838 < 2e-16 *** 401s Days 10.467 1.546 17.000 6.771 3.26e-06 *** 401s --- 401s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 401s 401s Correlation of Fixed Effects: 401s (Intr) 401s Days -0.138 401s > 401s > library(lmerTest) 401s Loading required package: lme4 401s Loading required package: Matrix 401s 401s Attaching package: 'lmerTest' 401s 401s > 401s > # WRE says "using if(requireNamespace("pkgname")) is preferred, if possible." 401s > # even in tests: 401s > assertError <- function(expr, ...) 401s + if(requireNamespace("tools")) tools::assertError(expr, ...) else invisible() 401s > assertWarning <- function(expr, ...) 401s + if(requireNamespace("tools")) tools::assertWarning(expr, ...) else invisible() 401s > 401s > TOL <- 1e-4 401s > 401s > ##################################################################### 401s > # Check that lme4::lmer and lmerTest::lmer have the same arguments 401s > 401s > lmer_args <- formals(lme4::lmer) 401s > names(lmer_args) 401s [1] "formula" "data" "REML" "control" "start" 401s [6] "verbose" "subset" "weights" "na.action" "offset" 401s [11] "contrasts" "devFunOnly" 401s > lmerTest_args <- formals(lmerTest::lmer) 401s > seq_args <- seq_along(lmerTest_args) 401s > if(packageVersion("lme4") > '1.1.21') { 401s + stopifnot( 401s + all.equal(names(lmer_args), names(lmerTest_args)), 401s + all.equal(lmer_args, lmerTest_args) 401s + ) 401s + } else { # Older versions of 'lme4' has a "..." argument: 401s + stopifnot( 401s + all.equal(names(lmer_args)[seq_args], names(lmerTest_args[seq_args])), 401s + all.equal(lmer_args[seq_args], lmerTest_args[seq_args]) 401s + ) 401s + } 401s > 401s > ##################################################################### 401s > # Test evaluation of update inside a function: 401s > myupdate <- function(m, ...) { 401s + update(m, ...) 401s + } 401s > 401s > data("sleepstudy", package="lme4") 401s > fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy) 401s The following object is masked from 'package:lme4': 401s 401s lmer 401s 401s The following object is masked from 'package:stats': 401s 401s step 401s 401s > tmp <- sleepstudy 401s > rm(sleepstudy) 401s > fmA <- update(fm1, data = tmp) # works 401s > fmB <- myupdate(fm1, data = tmp) # also works 401s > # Same except for 'call': 401s > fmB@call <- fmA@call 401s > stopifnot(isTRUE(all.equal(fmA, fmB, tolerance=TOL))) 401s > # Based on bug-report by Henrik Singmann, github issue #3 401s > 401s > ##################################################################### 401s > # Test update when formula is a character vector: 401s > 401s > form <- "Informed.liking ~ Product+Information+ 401s + (1|Consumer) + (1|Product:Consumer) + (1|Information:Consumer)" 401s > m <- lmer(form, data=ham) 401s > class(m) 401s [1] "lmerModLmerTest" 401s attr(,"package") 401s [1] "lmerTest" 401s > class(update(m, ~.- Product)) 401s [1] "lmerModLmerTest" 401s attr(,"package") 401s [1] "lmerTest" 401s > stopifnot(inherits(update(m, ~.- Product), "lmerModLmerTest")) 401s > 401s > # In version < 3.0-1.9002 class(update(m, ~.- Product)) was "lmerMod" 401s > ##################################################################### 401s > # Test error message from as_lmerModLmerTest: 401s > data("sleepstudy", package="lme4") 401s > myfit <- function(formula, data) { 401s + lme4::lmer(formula = formula, data = data) 401s + } 401s > fm2 <- myfit(Reaction ~ Days + (Days|Subject), sleepstudy) 401s > m <- assertError(as_lmerModLmerTest(fm2)) 401s > stopifnot( 401s + grepl("Unable to extract deviance function from model fit", m[[1]], fixed=TRUE) 401s + ) 401s > 401s > ##################################################################### 401s > # Check that devFunOnly argument works: 401s > data("sleepstudy", package="lme4") 401s > fun <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy, devFunOnly = TRUE) 401s > stopifnot(is.function(fun)) # && names(formals(fun)[1]) == "theta") 401s > fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy) 401s > fun <- update(fm1, devFunOnly=TRUE) 402s > stopifnot(is.function(fun)) # && names(formals(fun)[1]) == "theta") 402s > # devFunOnly = FALSE: 402s > notfun <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy, devFunOnly = FALSE) 402s > stopifnot(inherits(notfun, "lmerModLmerTest")) 402s > # Partial matching: 402s > notfun <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy, devFun = FALSE) 402s > stopifnot(inherits(notfun, "lmerModLmerTest")) 402s > 402s > ##################################################################### 402s > # Use of as_lmerModLmerTest 402s > data("sleepstudy", package="lme4") 402s > m <- lme4::lmer(Reaction ~ Days + (Days | Subject), sleepstudy) 402s > bm <- lmerTest:::as_lmerModLmerTest(m) 402s > stopifnot( 402s + inherits(bm, "lmerModLmerTest"), 402s + !inherits(m, "lmerModLmerTest"), 402s + inherits(bm, "lmerMod"), 402s + all(c("vcov_varpar", "Jac_list", "vcov_beta", "sigma") %in% slotNames(bm)) 402s + ) 402s > 402s > ##################################################################### 402s > # Update method 402s > 402s > m <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy) 402s > m1 <- update(m, ~.-Days) 402s > m2 <- lmer(Reaction ~ (Days | Subject), sleepstudy) 402s > 402s > stopifnot( 402s + inherits(m, "lmerModLmerTest"), 402s + inherits(m1, "lmerModLmerTest"), 402s + inherits(m2, "lmerModLmerTest"), 402s + all.equal(m1, m2, tolerance=1e-6) 402s + ) 402s > 402s > 402s BEGIN TEST test_lmerTest_paper.R 402s 402s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 402s Copyright (C) 2025 The R Foundation for Statistical Computing 402s Platform: aarch64-unknown-linux-gnu 402s 402s R is free software and comes with ABSOLUTELY NO WARRANTY. 402s You are welcome to redistribute it under certain conditions. 402s Type 'license()' or 'licence()' for distribution details. 402s 402s R is a collaborative project with many contributors. 402s Type 'contributors()' for more information and 402s 'citation()' on how to cite R or R packages in publications. 402s 402s Type 'demo()' for some demos, 'help()' for on-line help, or 402s 'help.start()' for an HTML browser interface to help. 402s Type 'q()' to quit R. 402s 402s > # test_lmerTest_paper.R 402s > 402s > library(lmerTest) 402s Loading required package: lme4 402s Loading required package: Matrix 404s 404s Attaching package: 'lmerTest' 404s 404s The following object is masked from 'package:lme4': 404s 404s lmer 404s 404s The following object is masked from 'package:stats': 404s 404s step 404s 404s > 404s > # Kenward-Roger only available with pbkrtest and only then validated in R >= 3.3.3 404s > # (faulty results for R < 3.3.3 may be due to unstated dependencies in pbkrtest) 404s > has_pbkrtest <- requireNamespace("pbkrtest", quietly = TRUE) && getRversion() >= "3.3.3" 404s > 404s > # Read in data set 404s > load(system.file("testdata","test_paper_objects.RData", package="lmerTest")) 404s > 404s > # Evaluate code from paper: 404s > ## Section 8.2: 404s > tv <- lmer(Sharpnessofmovement ~ TVset * Picture + (1 | Assessor) + 404s + (1 | Assessor:TVset) + (1 | Assessor:Picture), data = TVbo, 404s + control=lmerControl(optimizer="bobyqa")) 404s > 404s > (an8.2 <- anova(tv)) 404s Type III Analysis of Variance Table with Satterthwaite's method 404s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 404s TVset 1.765 0.8825 2 14 0.2437 0.7869818 404s Picture 51.857 17.2857 3 21 4.7735 0.0108785 * 404s TVset:Picture 90.767 15.1279 6 138 4.1777 0.0006845 *** 404s --- 404s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 404s > 404s > if(has_pbkrtest) 404s + (ankr8.2 <- anova(tv, type=2, ddf="Kenward-Roger")) 405s Type II Analysis of Variance Table with Kenward-Roger's method 405s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 405s TVset 1.765 0.8825 2 14 0.2437 0.7869818 405s Picture 51.857 17.2857 3 21 4.7735 0.0108785 * 405s TVset:Picture 90.767 15.1279 6 138 4.1777 0.0006845 *** 405s --- 405s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 405s > 405s > ## Section 8.3: 405s > m.carrots <- lmer(Preference ~ sens1 + sens2 + (1 + sens1 + sens2 | Consumer) + 405s + (1 | Product), data=carrots, 405s + control=lmerControl(optimizer="bobyqa")) 405s boundary (singular) fit: see help('isSingular') 405s > (sum8.3 <- coef(summary(m.carrots))) 405s Estimate Std. Error df t value Pr(>|t|) 405s (Intercept) 4.79911155 0.07529214 20.721910 63.7398768 2.918945e-25 405s sens1 0.01082919 0.01502840 9.168029 0.7205818 4.891315e-01 405s sens2 0.07064553 0.01727799 10.944477 4.0887589 1.812020e-03 405s > 405s > ## Section 8.4: 405s > tv <- lmer(Sharpnessofmovement ~ TVset * Picture + 405s + (1 | Assessor:TVset) + (1 | Assessor:Picture) + 405s + (1 | Assessor:Picture:TVset) + (1 | Repeat) + (1 | Repeat:Picture) + 405s + (1 | Repeat:TVset) + (1 | Repeat:TVset:Picture) + (1 | Assessor), 405s + data = TVbo, 405s + control=lmerControl(optimizer="bobyqa")) 406s boundary (singular) fit: see help('isSingular') 406s > st <- step(tv) 406s boundary (singular) fit: see help('isSingular') 406s boundary (singular) fit: see help('isSingular') 407s boundary (singular) fit: see help('isSingular') 407s boundary (singular) fit: see help('isSingular') 407s boundary (singular) fit: see help('isSingular') 408s boundary (singular) fit: see help('isSingular') 408s boundary (singular) fit: see help('isSingular') 408s boundary (singular) fit: see help('isSingular') 408s boundary (singular) fit: see help('isSingular') 409s boundary (singular) fit: see help('isSingular') 409s boundary (singular) fit: see help('isSingular') 409s boundary (singular) fit: see help('isSingular') 409s boundary (singular) fit: see help('isSingular') 410s boundary (singular) fit: see help('isSingular') 410s boundary (singular) fit: see help('isSingular') 410s boundary (singular) fit: see help('isSingular') 410s boundary (singular) fit: see help('isSingular') 410s boundary (singular) fit: see help('isSingular') 411s boundary (singular) fit: see help('isSingular') 411s boundary (singular) fit: see help('isSingular') 411s boundary (singular) fit: see help('isSingular') 411s boundary (singular) fit: see help('isSingular') 411s boundary (singular) fit: see help('isSingular') 411s boundary (singular) fit: see help('isSingular') 412s boundary (singular) fit: see help('isSingular') 412s boundary (singular) fit: see help('isSingular') 412s boundary (singular) fit: see help('isSingular') 412s boundary (singular) fit: see help('isSingular') 412s boundary (singular) fit: see help('isSingular') 412s boundary (singular) fit: see help('isSingular') 412s boundary (singular) fit: see help('isSingular') 412s boundary (singular) fit: see help('isSingular') 413s boundary (singular) fit: see help('isSingular') 413s > (elim_tab_random8.4 <- st$random) 413s Backward reduced random-effect table: 413s 413s Eliminated npar logLik AIC LRT Df 413s 21 -412.70 867.41 413s (1 | Assessor:Picture:TVset) 1 20 -412.70 865.41 0.0000 1 413s (1 | Repeat:Picture) 2 19 -412.70 863.41 0.0000 1 413s (1 | Repeat) 3 18 -412.70 861.41 0.0000 1 413s (1 | Repeat:TVset:Picture) 4 17 -412.70 859.41 0.0000 1 413s (1 | Repeat:TVset) 5 16 -412.70 857.41 0.0000 1 413s (1 | Assessor:TVset) 0 15 -414.10 858.20 2.7891 1 413s (1 | Assessor:Picture) 0 15 -418.88 867.76 12.3473 1 413s (1 | Assessor) 0 15 -416.44 862.88 7.4698 1 413s Pr(>Chisq) 413s 413s (1 | Assessor:Picture:TVset) 1.0000000 413s (1 | Repeat:Picture) 0.9999997 413s (1 | Repeat) 1.0000000 413s (1 | Repeat:TVset:Picture) 1.0000000 413s (1 | Repeat:TVset) 0.9999997 413s (1 | Assessor:TVset) 0.0949061 . 413s (1 | Assessor:Picture) 0.0004416 *** 413s (1 | Assessor) 0.0062742 ** 413s --- 413s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 413s > (elim_tab_fixed8.4 <- st$fixed) 413s Backward reduced fixed-effect table: 413s Degrees of freedom method: Satterthwaite 413s 413s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 413s TVset:Picture 0 90.767 15.128 6 138 4.1777 0.0006845 *** 413s --- 413s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 413s > (an8.4 <- anova(get_model(st))) 413s Type III Analysis of Variance Table with Satterthwaite's method 413s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 413s TVset 1.765 0.8825 2 14 0.2437 0.7869818 413s Picture 51.857 17.2857 3 21 4.7735 0.0108785 * 413s TVset:Picture 90.767 15.1279 6 138 4.1777 0.0006845 *** 413s --- 413s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 413s > 413s > ## Section 8.5: 413s > # L <- matrix(0, ncol = 12, nrow = 6) 413s > # L[1, 7] <- L[2, 8] <- L[3, 9] <- L[4, 10] <- L[5, 11] <- L[6, 12] <- 1 413s > L <- cbind(array(0, dim=c(6, 6)), diag(6)) 413s > (con1_8.5 <- calcSatterth(tv, L)) 413s $denom 413s [1] 138 413s 413s $Fstat 413s [,1] 413s [1,] 4.177655 413s 413s $pvalue 413s [,1] 413s [1,] 0.0006844792 413s 413s $ndf 413s [1] 6 413s 413s > (con2_8.5 <- contest(tv, L)) 413s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 413s 1 90.76719 15.12786 6 138 4.177655 0.0006844792 413s > 413s > ## Section C: 413s > # m.carrots <- lmer(Preference ~ sens1 + sens2 + (1 + sens1 + sens2 | Consumer) + 413s > # (1 | product), data = carrots) 413s > # step(m.carrots, reduce.fixed = FALSE) 413s > (ran_C <- ranova(m.carrots)) 413s boundary (singular) fit: see help('isSingular') 413s boundary (singular) fit: see help('isSingular') 414s ANOVA-like table for random-effects: Single term deletions 414s 414s Model: 414s Preference ~ sens1 + sens2 + (1 + sens1 + sens2 | Consumer) + (1 | Product) 414s npar logLik AIC LRT Df 414s 11 -1869.7 3761.5 414s sens1 in (1 + sens1 + sens2 | Consumer) 8 -1870.7 3757.3 1.8274 3 414s sens2 in (1 + sens1 + sens2 | Consumer) 8Warning message: 414s Model failed to converge with 1 negative eigenvalue: -1.6e+03 414s -1874.5 3765.0 9.5464 3 414s (1 | Product) 10 -1878.7 3777.4 17.9080 1 414s Pr(>Chisq) 414s 414s sens1 in (1 + sens1 + sens2 | Consumer) 0.60899 414s sens2 in (1 + sens1 + sens2 | Consumer) 0.02284 * 414s (1 | Product) 2.318e-05 *** 414s --- 414s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 414s > 414s > # Compare to validated outputs: 414s > TOL <- 1e-4 414s > stopifnot( 414s + isTRUE(all.equal(an8.2_save, an8.2, check.attributes = FALSE, tolerance=TOL)), 414s + isTRUE(all.equal(sum8.3_save, sum8.3, check.attributes = FALSE, tolerance=TOL)), 414s + isTRUE(all.equal(elim_tab_random8.4_save, elim_tab_random8.4, 414s + check.attributes = FALSE, tolerance=TOL)), 414s + isTRUE(all.equal(elim_tab_fixed8.4_save, elim_tab_fixed8.4, 414s + check.attributes = FALSE, tolerance=TOL)), 414s + isTRUE(all.equal(an8.4_save, an8.4, check.attributes = FALSE, tolerance=TOL)), 414s + isTRUE(all.equal(con1_8.5_save, con1_8.5, check.attributes = FALSE, tolerance=TOL)), 414s + isTRUE(all.equal(con2_8.5_save, con2_8.5, check.attributes = FALSE, tolerance=TOL)) 414s + ) 414s > if(has_pbkrtest) { 414s + stopifnot( 414s + isTRUE(all.equal(ankr8.2_save, ankr8.2, check.attributes = FALSE, tolerance=TOL)) 414s + ) 414s + } 414s > 414s > 414s BEGIN TEST test_ls_means.R 414s 414s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 414s Copyright (C) 2025 The R Foundation for Statistical Computing 414s Platform: aarch64-unknown-linux-gnu 414s 414s R is free software and comes with ABSOLUTELY NO WARRANTY. 414s You are welcome to redistribute it under certain conditions. 414s Type 'license()' or 'licence()' for distribution details. 414s 414s R is a collaborative project with many contributors. 414s Type 'contributors()' for more information and 414s 'citation()' on how to cite R or R packages in publications. 414s 414s Type 'demo()' for some demos, 'help()' for on-line help, or 414s 'help.start()' for an HTML browser interface to help. 414s Type 'q()' to quit R. 414s 414s > # test_lsmeans.R 414s > 414s > library(lmerTest) 414s Loading required package: lme4 414s Loading required package: Matrix 416s 416s Attaching package: 'lmerTest' 416s 416s The following object is masked from 'package:lme4': 416s 416s lmer 416s 416s > 416s > The following object is masked from 'package:stats': 416s 416s step 416s 416s TOL <- 1e-4 416s > # Kenward-Roger only available with pbkrtest and only then validated in R >= 3.3.3 416s > # (faulty results for R < 3.3.3 may be due to unstated dependencies in pbkrtest) 416s > has_pbkrtest <- requireNamespace("pbkrtest", quietly = TRUE) && getRversion() >= "3.3.3" 416s > 416s > ########### Basic model structures: 416s > 416s > # Factor * covariate: 416s > data("cake", package="lme4") 416s > model <- lmer(angle ~ recipe * temp + (1|recipe:replicate), cake) 416s > (lsm <- ls_means(model)) 416s Least Squares Means table: 416s 416s Estimate Std. Error df t value lower upper Pr(>|t|) 416s recipeA 33.1222 1.7368 42 19.070 29.6172 36.6273 < 2.2e-16 *** 416s recipeB 31.6444 1.7368 42 18.220 28.1394 35.1495 < 2.2e-16 *** 416s recipeC 31.6000 1.7368 42 18.194 28.0949 35.1051 < 2.2e-16 *** 416s --- 416s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 416s 416s Confidence level: 95% 416s Degrees of freedom method: Satterthwaite 416s > stopifnot( 416s + nrow(lsm) == 3L, 416s + ncol(lsm) == 7L, 416s + # Balanced, so LS-means equal raw means: 416s + isTRUE(all.equal(c(with(cake, tapply(angle, recipe, mean))), lsm[, "Estimate"], 416s + check.attributes=FALSE, tolerance=TOL)) 416s + ) 416s > 416s > # Pairwise differences of LS-means: 416s > plsm <- ls_means(model, pairwise = TRUE) 416s > plsm2 <- difflsmeans(model) 416s > C <- as.matrix(lmerTest:::get_pairs(rownames(lsm))) 416s > stopifnot( 416s + isTRUE(all.equal(plsm, plsm2, tolerance=TOL)), 416s + isTRUE(all.equal(plsm[, "Estimate"], c(lsm[, "Estimate"] %*% C), 416s + check.attributes=FALSE, tolerance=TOL)) 416s + ) 416s > 416s > # Contrasts vectors: 416s > show_tests(lsm) 416s $recipe 416s (Intercept) recipeB recipeC temp recipeB:temp recipeC:temp 416s recipeA 1 0 0 200 0 0 416s recipeB 1 1 0 200 200 0 416s recipeC 1 0 1 200 0 200 416s 416s > show_tests(plsm) 416s $recipe 416s (Intercept) recipeB recipeC temp recipeB:temp recipeC:temp 416s recipeA - recipeB 0 -1 0 0 -200 0 416s recipeA - recipeC 0 0 -1 0 0 -200 416s recipeB - recipeC 0 1 -1 0 200 -200 416s 416s > 416s > # Factor * Ordered: 416s > model <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake) 416s > (lsm2 <- ls_means(model)) 416s Least Squares Means table: 416s 416s Estimate Std. Error df t value lower upper 416s recipeA 33.1222 1.7368 42.0 19.070 29.6172 36.6273 416s recipeB 31.6444 1.7368 42.0 18.220 28.1394 35.1495 416s recipeC 31.6000 1.7368 42.0 18.194 28.0949 35.1051 416s temperature175 27.9778 1.1767 77.4 23.776 25.6349 30.3207 416s temperature185 29.9556 1.1767 77.4 25.457 27.6127 32.2985 416s temperature195 31.4222 1.1767 77.4 26.704 29.0793 33.7651 416s temperature205 32.1778 1.1767 77.4 27.346 29.8349 34.5207 416s temperature215 35.8444 1.1767 77.4 30.462 33.5015 38.1873 416s temperature225 35.3556 1.1767 77.4 30.046 33.0127 37.6985 416s recipeA:temperature175 29.1333 2.0381 77.4 14.294 25.0753 33.1913 416s recipeB:temperature175 26.8667 2.0381 77.4 13.182 22.8087 30.9247 416s recipeC:temperature175 27.9333 2.0381 77.4 13.706 23.8753 31.9913 416s recipeA:temperature185 31.5333 2.0381 77.4 15.472 27.4753 35.5913 416s recipeB:temperature185 29.4000 2.0381 77.4 14.425 25.3420 33.4580 416s recipeC:temperature185 28.9333 2.0381 77.4 14.196 24.8753 32.9913 416s recipeA:temperature195 30.8000 2.0381 77.4 15.112 26.7420 34.8580 416s recipeB:temperature195 31.7333 2.0381 77.4 15.570 27.6753 35.7913 416s recipeC:temperature195 31.7333 2.0381 77.4 15.570 27.6753 35.7913 416s recipeA:temperature205 33.5333 2.0381 77.4 16.453 29.4753 37.5913 416s recipeB:temperature205 32.1333 2.0381 77.4 15.766 28.0753 36.1913 416s recipeC:temperature205 30.8667 2.0381 77.4 15.145 26.8087 34.9247 416s recipeA:temperature215 38.6667 2.0381 77.4 18.972 34.6087 42.7247 416s recipeB:temperature215 34.4667 2.0381 77.4 16.911 30.4087 38.5247 416s recipeC:temperature215 34.4000 2.0381 77.4 16.878 30.3420 38.4580 416s recipeA:temperature225 35.0667 2.0381 77.4 17.206 31.0087 39.1247 416s recipeB:temperature225 35.2667 2.0381 77.4 17.304 31.2087 39.3247 416s recipeC:temperature225 35.7333 2.0381 77.4 17.533 31.6753 39.7913 416s Pr(>|t|) 416s recipeA < 2.2e-16 *** 416s recipeB < 2.2e-16 *** 416s recipeC < 2.2e-16 *** 416s temperature175 < 2.2e-16 *** 416s temperature185 < 2.2e-16 *** 416s temperature195 < 2.2e-16 *** 416s temperature205 < 2.2e-16 *** 416s temperature215 < 2.2e-16 *** 416s temperature225 < 2.2e-16 *** 416s recipeA:temperature175 < 2.2e-16 *** 416s recipeB:temperature175 < 2.2e-16 *** 416s recipeC:temperature175 < 2.2e-16 *** 416s recipeA:temperature185 < 2.2e-16 *** 416s recipeB:temperature185 < 2.2e-16 *** 416s recipeC:temperature185 < 2.2e-16 *** 416s recipeA:temperature195 < 2.2e-16 *** 416s recipeB:temperature195 < 2.2e-16 *** 416s recipeC:temperature195 < 2.2e-16 *** 416s recipeA:temperature205 < 2.2e-16 *** 416s recipeB:temperature205 < 2.2e-16 *** 416s recipeC:temperature205 < 2.2e-16 *** 416s recipeA:temperature215 < 2.2e-16 *** 416s recipeB:temperature215 < 2.2e-16 *** 416s recipeC:temperature215 < 2.2e-16 *** 416s recipeA:temperature225 < 2.2e-16 *** 416s recipeB:temperature225 < 2.2e-16 *** 416s recipeC:temperature225 < 2.2e-16 *** 416s --- 416s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 416s 416s Confidence level: 95% 416s Degrees of freedom method: Satterthwaite 416s > stopifnot( 416s + nrow(lsm2) == 3 + 6 + 3*6, 416s + ncol(lsm) == 7L, 416s + # Balanced, so LS-means equal raw means: 416s + isTRUE(all.equal(lsm[1:3, ], lsm2[1:3, ], 416s + check.attributes=FALSE, tolerance=TOL)) 416s + ) 416s > 416s > 416s > # Factor * Factor: 416s > cake2 <- cake 416s > cake2$temperature <- factor(cake2$temperature, ordered = FALSE) 416s > model <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake2) 416s > (lsm3 <- ls_means(model)) 416s Least Squares Means table: 416s 416s Estimate Std. Error df t value lower upper 416s recipeA 33.1222 1.7368 42.0 19.070 29.6172 36.6273 416s recipeB 31.6444 1.7368 42.0 18.220 28.1394 35.1495 416s recipeC 31.6000 1.7368 42.0 18.194 28.0949 35.1051 416s temperature175 27.9778 1.1767 77.4 23.776 25.6349 30.3207 416s temperature185 29.9556 1.1767 77.4 25.457 27.6127 32.2985 416s temperature195 31.4222 1.1767 77.4 26.704 29.0793 33.7651 416s temperature205 32.1778 1.1767 77.4 27.346 29.8349 34.5207 416s temperature215 35.8444 1.1767 77.4 30.462 33.5015 38.1873 416s temperature225 35.3556 1.1767 77.4 30.046 33.0127 37.6985 416s recipeA:temperature175 29.1333 2.0381 77.4 14.294 25.0753 33.1913 416s recipeB:temperature175 26.8667 2.0381 77.4 13.182 22.8087 30.9247 416s recipeC:temperature175 27.9333 2.0381 77.4 13.706 23.8753 31.9913 416s recipeA:temperature185 31.5333 2.0381 77.4 15.472 27.4753 35.5913 416s recipeB:temperature185 29.4000 2.0381 77.4 14.425 25.3420 33.4580 416s recipeC:temperature185 28.9333 2.0381 77.4 14.196 24.8753 32.9913 416s recipeA:temperature195 30.8000 2.0381 77.4 15.112 26.7420 34.8580 416s recipeB:temperature195 31.7333 2.0381 77.4 15.570 27.6753 35.7913 416s recipeC:temperature195 31.7333 2.0381 77.4 15.570 27.6753 35.7913 416s recipeA:temperature205 33.5333 2.0381 77.4 16.453 29.4753 37.5913 416s recipeB:temperature205 32.1333 2.0381 77.4 15.766 28.0753 36.1913 416s recipeC:temperature205 30.8667 2.0381 77.4 15.145 26.8087 34.9247 416s recipeA:temperature215 38.6667 2.0381 77.4 18.972 34.6087 42.7247 416s recipeB:temperature215 34.4667 2.0381 77.4 16.911 30.4087 38.5247 416s recipeC:temperature215 34.4000 2.0381 77.4 16.878 30.3420 38.4580 416s recipeA:temperature225 35.0667 2.0381 77.4 17.206 31.0087 39.1247 416s recipeB:temperature225 35.2667 2.0381 77.4 17.304 31.2087 39.3247 416s recipeC:temperature225 35.7333 2.0381 77.4 17.533 31.6753 39.7913 416s Pr(>|t|) 416s recipeA < 2.2e-16 *** 416s recipeB < 2.2e-16 *** 416s recipeC < 2.2e-16 *** 416s temperature175 < 2.2e-16 *** 416s temperature185 < 2.2e-16 *** 416s temperature195 < 2.2e-16 *** 416s temperature205 < 2.2e-16 *** 416s temperature215 < 2.2e-16 *** 416s temperature225 < 2.2e-16 *** 416s recipeA:temperature175 < 2.2e-16 *** 416s recipeB:temperature175 < 2.2e-16 *** 416s recipeC:temperature175 < 2.2e-16 *** 416s recipeA:temperature185 < 2.2e-16 *** 416s recipeB:temperature185 < 2.2e-16 *** 416s recipeC:temperature185 < 2.2e-16 *** 416s recipeA:temperature195 < 2.2e-16 *** 416s recipeB:temperature195 < 2.2e-16 *** 416s recipeC:temperature195 < 2.2e-16 *** 416s recipeA:temperature205 < 2.2e-16 *** 416s recipeB:temperature205 < 2.2e-16 *** 416s recipeC:temperature205 < 2.2e-16 *** 416s recipeA:temperature215 < 2.2e-16 *** 416s recipeB:temperature215 < 2.2e-16 *** 416s recipeC:temperature215 < 2.2e-16 *** 416s recipeA:temperature225 < 2.2e-16 *** 416s recipeB:temperature225 < 2.2e-16 *** 416s recipeC:temperature225 < 2.2e-16 *** 416s --- 416s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 416s 416s Confidence level: 95% 416s Degrees of freedom method: Satterthwaite 416s > stopifnot( 416s + isTRUE(all.equal(lsm2, lsm3, check.attributes=FALSE, tolerance=TOL)) 416s + ) 416s > 416s > # Covariate (only): 416s > data("sleepstudy", package="lme4") 416s > m <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy) 416s > (lsm <- ls_means(m)) 416s Least Squares Means table: 416s 416s Estimate Std. Error df t value lower upper Pr(>|t|) 416s 416s Confidence level: 95% 416s Degrees of freedom method: Satterthwaite 416s > stopifnot( 416s + nrow(lsm) == 0L, 416s + ncol(lsm) == 7L 416s + ) 416s > 416s > # No fixef: 416s > m <- lmer(Reaction ~ 0 + (Days | Subject), sleepstudy) 417s > (lsm <- ls_means(m)) 417s Least Squares Means table: 417s 417s Estimate Std. Error df t value lower upper Pr(>|t|) 417s 417s Confidence level: 95% 417s Degrees of freedom method: Satterthwaite 417s > stopifnot( 417s + nrow(lsm) == 0L, 417s + ncol(lsm) == 7L 417s + ) 417s > 417s > ########### Arguments and options: 417s > 417s > # which 417s > model <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake2) 417s > (lsm4 <- ls_means(model, which = "recipe")) 417s Least Squares Means table: 417s 417s Estimate Std. Error df t value lower upper Pr(>|t|) 417s recipeA 33.1222 1.7368 42 19.070 29.6172 36.6273 < 2.2e-16 *** 417s recipeB 31.6444 1.7368 42 18.220 28.1394 35.1495 < 2.2e-16 *** 417s recipeC 31.6000 1.7368 42 18.194 28.0949 35.1051 < 2.2e-16 *** 417s --- 417s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 417s 417s Confidence level: 95% 417s Degrees of freedom method: Satterthwaite 417s > stopifnot( 417s + nrow(lsm4) == 3L, 417s + ncol(lsm4) == 7L, 417s + isTRUE(all.equal(lsm3[1:3, ], lsm4, check.attributes=FALSE, tolerance=TOL)) 417s + ) 417s > 417s > # KR: 417s > if(has_pbkrtest) 417s + (lsm5 <- ls_means(model, which = "recipe", ddf = "Kenward-Roger")) 417s Least Squares Means table: 417s 417s Estimate Std. Error df t value lower upper Pr(>|t|) 417s recipeA 33.1222 1.7368 42 19.070 29.6172 36.6273 < 2.2e-16 *** 417s recipeB 31.6444 1.7368 42 18.220 28.1394 35.1495 < 2.2e-16 *** 417s recipeC 31.6000 1.7368 42 18.194 28.0949 35.1051 < 2.2e-16 *** 417s --- 417s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 417s 417s Confidence level: 95% 417s Degrees of freedom method: Kenward-Roger 417s > 417s > # level: 417s > (lsm6 <- ls_means(model, which = "recipe", level=0.99)) 417s Least Squares Means table: 417s 417s Estimate Std. Error df t value lower upper Pr(>|t|) 417s recipeA 33.1222 1.7368 42 19.070 28.4361 37.8083 < 2.2e-16 *** 417s recipeB 31.6444 1.7368 42 18.220 26.9584 36.3305 < 2.2e-16 *** 417s recipeC 31.6000 1.7368 42 18.194 26.9139 36.2861 < 2.2e-16 *** 417s --- 417s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 417s 417s Confidence level: 99% 417s Degrees of freedom method: Satterthwaite 417s > 417s > stopifnot( 417s + all(lsm6[, "lower"] < lsm4[, "lower"]), 417s + all(lsm6[, "upper"] > lsm4[, "upper"]) 417s + ) 417s > 417s > 417s > 417s > ########### Missing cels -> unestimable contrasts: 417s > 417s > # Missing cell: 417s > cake3 <- cake 417s > cake3$temperature <- factor(cake3$temperature, ordered=FALSE) 417s > cake3 <- droplevels(subset(cake3, temperature %in% levels(cake3$temperature)[1:3])) 417s > cake3 <- droplevels(subset(cake3, !(recipe == "C" & temperature == "195") )) 417s > str(cake3) 417s 'data.frame': 120 obs. of 5 variables: 417s $ replicate : Factor w/ 15 levels "1","2","3","4",..: 1 1 1 1 1 1 1 1 2 2 ... 417s $ recipe : Factor w/ 3 levels "A","B","C": 1 1 1 2 2 2 3 3 1 1 ... 417s $ temperature: Factor w/ 3 levels "175","185","195": 1 2 3 1 2 3 1 2 1 2 ... 417s $ angle : int 42 46 47 39 46 51 46 44 47 29 ... 417s $ temp : num 175 185 195 175 185 195 175 185 175 185 ... 417s > with(cake3, table(recipe, temperature)) 417s temperature 417s recipe 175 185 195 417s A 15 15 15 417s B 15 15 15 417s C 15 15 0 417s > model <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake3) 417s fixed-effect model matrix is rank deficient so dropping 1 column / coefficient 417s > (lsm7 <- ls_means(model)) 417s Least Squares Means table: 417s 417s Estimate Std. Error df t value lower upper 417s recipeA 30.4889 1.7407 40.3 17.515 26.9716 34.0062 417s recipeB 29.3333 1.7407 40.3 16.851 25.8160 32.8506 417s recipeC NA NA NA NA NA NA 417s temperature175 27.9778 1.1016 57.2 25.398 25.7720 30.1835 417s temperature185 29.9556 1.1016 57.2 27.193 27.7498 32.1613 417s temperature195 NA NA NA NA NA NA 417s recipeA:temperature175 29.1333 1.9080 57.2 15.269 25.3129 32.9538 417s recipeB:temperature175 26.8667 1.9080 57.2 14.081 23.0462 30.6871 417s recipeC:temperature175 27.9333 1.9080 57.2 14.640 24.1129 31.7538 417s recipeA:temperature185 31.5333 1.9080 57.2 16.527 27.7129 35.3538 417s recipeB:temperature185 29.4000 1.9080 57.2 15.409 25.5795 33.2205 417s recipeC:temperature185 28.9333 1.9080 57.2 15.164 25.1129 32.7538 417s recipeA:temperature195 30.8000 1.9080 57.2 16.143 26.9795 34.6205 417s recipeB:temperature195 31.7333 1.9080 57.2 16.632 27.9129 35.5538 417s recipeC:temperature195 NA NA NA NA NA NA 417s Pr(>|t|) 417s recipeA < 2.2e-16 *** 417s recipeB < 2.2e-16 *** 417s recipeC NA 417s temperature175 < 2.2e-16 *** 417s temperature185 < 2.2e-16 *** 417s temperature195 NA 417s recipeA:temperature175 < 2.2e-16 *** 417s recipeB:temperature175 < 2.2e-16 *** 417s recipeC:temperature175 < 2.2e-16 *** 417s recipeA:temperature185 < 2.2e-16 *** 417s recipeB:temperature185 < 2.2e-16 *** 417s recipeC:temperature185 < 2.2e-16 *** 417s recipeA:temperature195 < 2.2e-16 *** 417s recipeB:temperature195 < 2.2e-16 *** 417s recipeC:temperature195 NA 417s --- 417s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 417s 417s Confidence level: 95% 417s Degrees of freedom method: Satterthwaite 417s > 417s > # Using show_tests with options: 417s > show_tests(lsm7, fractions = TRUE) 417s $recipe 417s (Intercept) recipeB recipeC temperature185 temperature195 417s recipeA 1 0 0 1/3 1/3 417s recipeB 1 1 0 1/3 1/3 417s recipeC 1 0 1 1/3 1/3 417s recipeB:temperature185 recipeC:temperature185 recipeB:temperature195 417s recipeA 0 0 0 417s recipeB 1/3 0 1/3 417s recipeC 0 1/3 0 417s recipeC:temperature195 417s recipeA 0 417s recipeB 0 417s recipeC 1/3 417s 417s $temperature 417s (Intercept) recipeB recipeC temperature185 temperature195 417s temperature175 1 1/3 1/3 0 0 417s temperature185 1 1/3 1/3 1 0 417s temperature195 1 1/3 1/3 0 1 417s recipeB:temperature185 recipeC:temperature185 417s temperature175 0 0 417s temperature185 1/3 1/3 417s temperature195 0 0 417s recipeB:temperature195 recipeC:temperature195 417s temperature175 0 0 417s temperature185 0 0 417s temperature195 1/3 1/3 417s 417s $`recipe:temperature` 417s (Intercept) recipeB recipeC temperature185 417s recipeA:temperature175 1 0 0 0 417s recipeB:temperature175 1 1 0 0 417s recipeC:temperature175 1 0 1 0 417s recipeA:temperature185 1 0 0 1 417s recipeB:temperature185 1 1 0 1 417s recipeC:temperature185 1 0 1 1 417s recipeA:temperature195 1 0 0 0 417s recipeB:temperature195 1 1 0 0 417s recipeC:temperature195 1 0 1 0 417s temperature195 recipeB:temperature185 417s recipeA:temperature175 0 0 417s recipeB:temperature175 0 0 417s recipeC:temperature175 0 0 417s recipeA:temperature185 0 0 417s recipeB:temperature185 0 1 417s recipeC:temperature185 0 0 417s recipeA:temperature195 1 0 417s recipeB:temperature195 1 0 417s recipeC:temperature195 1 0 417s recipeC:temperature185 recipeB:temperature195 417s recipeA:temperature175 0 0 417s recipeB:temperature175 0 0 417s recipeC:temperature175 0 0 417s recipeA:temperature185 0 0 417s recipeB:temperature185 0 0 417s recipeC:temperature185 1 0 417s recipeA:temperature195 0 0 417s recipeB:temperature195 0 1 417s recipeC:temperature195 0 0 417s recipeC:temperature195 417s recipeA:temperature175 0 417s recipeB:temperature175 0 417s recipeC:temperature175 0 417s recipeA:temperature185 0 417s recipeB:temperature185 0 417s recipeC:temperature185 0 417s recipeA:temperature195 0 417s recipeB:temperature195 0 417s recipeC:temperature195 1 417s 417s > show_tests(lsm7, fractions = TRUE, names = FALSE) 417s $recipe 417s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] 417s [1,] 1 0 0 1/3 1/3 0 0 0 0 417s [2,] 1 1 0 1/3 1/3 1/3 0 1/3 0 417s [3,] 1 0 1 1/3 1/3 0 1/3 0 1/3 417s 417s $temperature 417s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] 417s [1,] 1 1/3 1/3 0 0 0 0 0 0 417s [2,] 1 1/3 1/3 1 0 1/3 1/3 0 0 417s [3,] 1 1/3 1/3 0 1 0 0 1/3 1/3 417s 417s $`recipe:temperature` 417s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] 417s [1,] 1 0 0 0 0 0 0 0 0 417s [2,] 1 1 0 0 0 0 0 0 0 417s [3,] 1 0 1 0 0 0 0 0 0 417s [4,] 1 0 0 1 0 0 0 0 0 417s [5,] 1 1 0 1 0 1 0 0 0 417s [6,] 1 0 1 1 0 0 1 0 0 417s [7,] 1 0 0 0 1 0 0 0 0 417s [8,] 1 1 0 0 1 0 0 1 0 417s [9,] 1 0 1 0 1 0 0 0 1 417s 417s > 417s > # Missing diagonal: 417s > cake4 <- cake 417s > cake4$temperature <- factor(cake4$temperature, ordered=FALSE) 417s > cake4 <- droplevels(subset(cake4, temperature %in% levels(cake4$temperature)[1:3])) 417s > cake4 <- droplevels(subset(cake4, !((recipe == "A" & temperature == "175") | 417s + (recipe == "B" & temperature == "185") | 417s + (recipe == "C" & temperature == "195") ))) 417s > # str(cake4) 417s > with(cake4, table(recipe, temperature)) 417s temperature 417s recipe 175 185 195 417s A 0 15 15 417s B 15 0 15 417s C 15 15 0 417s > model <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake4) 417s fixed-effect model matrix is rank deficient so dropping 3 columns / coefficients 417s > ls_means(model) 417s Least Squares Means table: 417s 417s Estimate Std. Error df t value lower upper 417s recipeA NA NA NA NA NA NA 417s recipeB NA NA NA NA NA NA 417s recipeC NA NA NA NA NA NA 417s temperature175 NA NA NA NA NA NA 417s temperature185 NA NA NA NA NA NA 417s temperature195 NA NA NA NA NA NA 417s recipeA:temperature175 NA NA NA NA NA NA 417s recipeB:temperature175 26.8667 1.8908 53.5 14.209 23.0750 30.6584 417s recipeC:temperature175 27.9333 1.8908 53.5 14.773 24.1416 31.7250 417s recipeA:temperature185 31.5333 1.8908 53.5 16.677 27.7416 35.3250 417s recipeB:temperature185 NA NA NA NA NA NA 417s recipeC:temperature185 28.9333 1.8908 53.5 15.302 25.1416 32.7250 417s recipeA:temperature195 30.8000 1.8908 53.5 16.289 27.0083 34.5917 417s recipeB:temperature195 31.7333 1.8908 53.5 16.783 27.9416 35.5250 417s recipeC:temperature195 NA NA NA NA NA NA 417s Pr(>|t|) 417s recipeA NA 417s recipeB NA 417s recipeC NA 417s temperature175 NA 417s temperature185 NA 417s temperature195 NA 417s recipeA:temperature175 NA 417s recipeB:temperature175 < 2.2e-16 *** 417s recipeC:temperature175 < 2.2e-16 *** 417s recipeA:temperature185 < 2.2e-16 *** 417s recipeB:temperature185 NA 417s recipeC:temperature185 < 2.2e-16 *** 417s recipeA:temperature195 < 2.2e-16 *** 417s recipeB:temperature195 < 2.2e-16 *** 417s recipeC:temperature195 NA 417s --- 417s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 417s 417s Confidence level: 95% 417s Degrees of freedom method: Satterthwaite 417s > 417s > 417s > ########### Various contrasts codings: 417s > 417s > model <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake3, 417s + contrasts = list(recipe="contr.sum", temperature="contr.helmert")) 417s fixed-effect model matrix is rank deficient so dropping 1 column / coefficient 417s > (lsm8 <- ls_means(model)) 417s Least Squares Means table: 417s 417s Estimate Std. Error df t value lower upper 417s recipeA 30.4889 1.7407 40.3 17.515 26.9716 34.0062 417s recipeB 29.3333 1.7407 40.3 16.851 25.8160 32.8506 417s recipeC NA NA NA NA NA NA 417s temperature175 27.9778 1.1016 57.2 25.398 25.7720 30.1835 417s temperature185 29.9556 1.1016 57.2 27.193 27.7498 32.1613 417s temperature195 NA NA NA NA NA NA 417s recipeA:temperature175 29.1333 1.9080 57.2 15.269 25.3129 32.9538 417s recipeB:temperature175 26.8667 1.9080 57.2 14.081 23.0462 30.6871 417s recipeC:temperature175 27.9333 1.9080 57.2 14.640 24.1129 31.7538 417s recipeA:temperature185 31.5333 1.9080 57.2 16.527 27.7129 35.3538 417s recipeB:temperature185 29.4000 1.9080 57.2 15.409 25.5795 33.2205 417s recipeC:temperature185 28.9333 1.9080 57.2 15.164 25.1129 32.7538 417s recipeA:temperature195 30.8000 1.9080 57.2 16.143 26.9795 34.6205 417s recipeB:temperature195 31.7333 1.9080 57.2 16.632 27.9129 35.5538 417s recipeC:temperature195 NA NA NA NA NA NA 417s Pr(>|t|) 417s recipeA < 2.2e-16 *** 417s recipeB < 2.2e-16 *** 417s recipeC NA 417s temperature175 < 2.2e-16 *** 417s temperature185 < 2.2e-16 *** 417s temperature195 NA 417s recipeA:temperature175 < 2.2e-16 *** 417s recipeB:temperature175 < 2.2e-16 *** 417s recipeC:temperature175 < 2.2e-16 *** 417s recipeA:temperature185 < 2.2e-16 *** 417s recipeB:temperature185 < 2.2e-16 *** 417s recipeC:temperature185 < 2.2e-16 *** 417s recipeA:temperature195 < 2.2e-16 *** 417s recipeB:temperature195 < 2.2e-16 *** 417s recipeC:temperature195 NA 417s --- 417s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 417s 417s Confidence level: 95% 417s Degrees of freedom method: Satterthwaite 417s > # show_tests(lsm7) 417s > # show_tests(lsm8) 417s > stopifnot( 417s + isTRUE(all.equal(lsm7, lsm8, check.attributes=FALSE, tolerance=TOL)) 417s + ) 417s > 417s > # ambient contrasts not contr.treatment: 417s > options("contrasts") 417s $contrasts 417s unordered ordered 417s "contr.treatment" "contr.poly" 417s 417s > options(contrasts = c("contr.sum", "contr.poly")) 417s > model <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake3) 417s fixed-effect model matrix is rank deficient so dropping 1 column / coefficient 417s > (lsm9 <- ls_means(model)) 417s Least Squares Means table: 417s 417s Estimate Std. Error df t value lower upper 417s recipeA 30.4889 1.7407 40.3 17.515 26.9716 34.0062 417s recipeB 29.3333 1.7407 40.3 16.851 25.8160 32.8506 417s recipeC NA NA NA NA NA NA 417s temperature175 27.9778 1.1016 57.2 25.398 25.7720 30.1835 417s temperature185 29.9556 1.1016 57.2 27.193 27.7498 32.1613 417s temperature195 NA NA NA NA NA NA 417s recipeA:temperature175 29.1333 1.9080 57.2 15.269 25.3129 32.9538 417s recipeB:temperature175 26.8667 1.9080 57.2 14.081 23.0462 30.6871 417s recipeC:temperature175 27.9333 1.9080 57.2 14.640 24.1129 31.7538 417s recipeA:temperature185 31.5333 1.9080 57.2 16.527 27.7129 35.3538 417s recipeB:temperature185 29.4000 1.9080 57.2 15.409 25.5795 33.2205 417s recipeC:temperature185 28.9333 1.9080 57.2 15.164 25.1129 32.7538 417s recipeA:temperature195 30.8000 1.9080 57.2 16.143 26.9795 34.6205 417s recipeB:temperature195 31.7333 1.9080 57.2 16.632 27.9129 35.5538 417s recipeC:temperature195 NA NA NA NA NA NA 417s Pr(>|t|) 417s recipeA < 2.2e-16 *** 417s recipeB < 2.2e-16 *** 417s recipeC NA 417s temperature175 < 2.2e-16 *** 417s temperature185 < 2.2e-16 *** 417s temperature195 NA 417s recipeA:temperature175 < 2.2e-16 *** 417s recipeB:temperature175 < 2.2e-16 *** 417s recipeC:temperature175 < 2.2e-16 *** 417s recipeA:temperature185 < 2.2e-16 *** 417s recipeB:temperature185 < 2.2e-16 *** 417s recipeC:temperature185 < 2.2e-16 *** 417s recipeA:temperature195 < 2.2e-16 *** 417s recipeB:temperature195 < 2.2e-16 *** 417s recipeC:temperature195 NA 417s --- 417s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 417s 417s Confidence level: 95% 417s Degrees of freedom method: Satterthwaite 417s > options(contrasts = c("contr.treatment", "contr.poly")) 417s > options("contrasts") 417s $contrasts 417s [1] "contr.treatment" "contr.poly" 417s 417s > stopifnot( 417s + isTRUE(all.equal(lsm7, lsm9, check.attributes=FALSE, tolerance=TOL)) 417s + ) 417s > 417s > 417s > 417s BEGIN TEST test_ranova_step.R 417s 417s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 417s Copyright (C) 2025 The R Foundation for Statistical Computing 417s Platform: aarch64-unknown-linux-gnu 417s 417s R is free software and comes with ABSOLUTELY NO WARRANTY. 417s You are welcome to redistribute it under certain conditions. 417s Type 'license()' or 'licence()' for distribution details. 417s 417s R is a collaborative project with many contributors. 417s Type 'contributors()' for more information and 417s 'citation()' on how to cite R or R packages in publications. 417s 417s Type 'demo()' for some demos, 'help()' for on-line help, or 417s 'help.start()' for an HTML browser interface to help. 417s Type 'q()' to quit R. 417s 417s > # test_ranova.R 417s > 417s > # Test functionality _before_ attaching lmerTest 417s > stopifnot(!"lmerTest" %in% .packages()) # ensure that lmerTest is NOT attached 417s > data("sleepstudy", package="lme4") 417s > f <- function(form, data) lmerTest::lmer(form, data=data) 417s > form <- "Reaction ~ Days + (Days|Subject)" 417s > fm <- f(form, data=sleepstudy) 419s > lmerTest::ranova(fm) 419s ANOVA-like table for random-effects: Single term deletions 419s 419s Model: 419s Reaction ~ Days + (Days | Subject) 419s npar logLik AIC LRT Df Pr(>Chisq) 419s 6 -871.81 1755.6 419s Days in (Days | Subject) 4 -893.23 1794.5 42.837 2 4.99e-10 *** 419s --- 419s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 419s > lmerTest::rand(fm) 420s ANOVA-like table for random-effects: Single term deletions 420s 420s Model: 420s Reaction ~ Days + (Days | Subject) 420s npar logLik AIC LRT Df Pr(>Chisq) 420s 6 -871.81 1755.6 420s Days in (Days | Subject) 4 -893.23 1794.5 42.837 2 4.99e-10 *** 420s --- 420s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 420s > lmerTest::step(fm) 420s Backward reduced random-effect table: 420s 420s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 420s 6 -871.81 1755.6 420s Days in (Days | Subject) 0 4 -893.23 1794.5 42.837 2 4.99e-10 420s 420s 420s Days in (Days | Subject) *** 420s --- 420s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 420s 420s Backward reduced fixed-effect table: 420s Degrees of freedom method: Satterthwaite 420s 420s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 420s Days 0 30031 30031 1 17 45.853 3.264e-06 *** 420s --- 420s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 420s 420s Model found: 420s Reaction ~ Days + (Days | Subject) 420s > 420s > library(lmerTest) 420s Loading required package: lme4 420s Loading required package: Matrix 420s 420s Attaching package: 'lmerTest' 420s 420s The following object is masked from 'package:lme4': 420s 420s lmer 420s 420s The following object is masked from 'package:stats': 420s 420s step 420s 420s > 420s > # WRE says "using if(requireNamespace("pkgname")) is preferred, if possible." 420s > # even in tests: 420s > assertError <- function(expr, ...) 420s + if(requireNamespace("tools")) tools::assertError(expr, ...) else invisible() 420s > assertWarning <- function(expr, ...) 420s + if(requireNamespace("tools")) tools::assertWarning(expr, ...) else invisible() 420s > 420s > TOL <- 1e-4 420s > ##################################################################### 420s > data("sleepstudy", package="lme4") 420s > 420s > # Test reduction of (Days | Subject) to (1 | Subject): 420s > fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy) 420s > (an <- rand(fm1)) # 2 df test 420s ANOVA-like table for random-effects: Single term deletions 420s 420s Model: 420s Reaction ~ Days + (Days | Subject) 420s npar logLik AIC LRT Df Pr(>Chisq) 420s 6 -871.81 1755.6 420s Days in (Days | Subject) 4 -893.23 1794.5 42.837 2 4.99e-10 *** 420s --- 420s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 420s > (an <- ranova(fm1)) # 2 df test 420s ANOVA-like table for random-effects: Single term deletions 420s 420s Model: 420s Reaction ~ Days + (Days | Subject) 420s npar logLik AIC LRT Df Pr(>Chisq) 420s 6 -871.81 1755.6 420s Days in (Days | Subject) 4 -893.23 1794.5 42.837 2 4.99e-10 *** 420s --- 420s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 420s > step(fm1) 420s Backward reduced random-effect table: 420s 420s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 420s 6 -871.81 1755.6 420s Days in (Days | Subject) 0 4 -893.23 1794.5 42.837 2 4.99e-10 420s 420s 420s Days in (Days | Subject) *** 420s --- 420s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 420s 420s Backward reduced fixed-effect table: 420s Degrees of freedom method: Satterthwaite 420s 420s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 420s Days 0 30031 30031 1 17 45.853 3.264e-06 *** 420s --- 420s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 420s 420s Model found: 420s Reaction ~ Days + (Days | Subject) 420s > stopifnot( 420s + nrow(an) == 2L, 420s + an[2L, "Df"] == 2L 420s + ) 420s > 420s > # This test can also be achieved with anova(): 420s > fm2 <- lmer(Reaction ~ Days + (1|Subject), sleepstudy) 420s > (stp <- step(fm2)) 420s Backward reduced random-effect table: 420s 420s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 420s 4 -893.23 1794.5 420s (1 | Subject) 0 3 -946.83 1899.7 107.2 1 < 2.2e-16 *** 420s --- 420s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 420s 420s Backward reduced fixed-effect table: 420s Degrees of freedom method: Satterthwaite 420s 420s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 420s Days 0 162703 162703 1 161 169.4 < 2.2e-16 *** 420s --- 420s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 420s 420s Model found: 420s Reaction ~ Days + (1 | Subject) 420s > get_model(stp) 420s Linear mixed model fit by REML ['lmerModLmerTest'] 420s Formula: Reaction ~ Days + (1 | Subject) 420s Data: sleepstudy 420s REML criterion at convergence: 1786.465 420s Random effects: 420s Groups Name Std.Dev. 420s Subject (Intercept) 37.12 420s Residual 30.99 420s Number of obs: 180, groups: Subject, 18 420s Fixed Effects: 420s (Intercept) Days 420s 251.41 10.47 420s > (ana <- anova(fm1, fm2, refit=FALSE)) 420s Data: sleepstudy 420s Models: 420s fm2: Reaction ~ Days + (1 | Subject) 420s fm1: Reaction ~ Days + (Days | Subject) 420s npar AIC BIC logLik -2*log(L) Chisq Df Pr(>Chisq) 420s fm2 4 1794.5 1807.2 -893.23 1786.5 420s fm1 6 1755.6 1774.8 -871.81 1743.6 42.837 2 4.99e-10 *** 420s --- 420s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 420s > 420s > stopifnot( 420s + all.equal(an[2L, "LRT"], ana[2L, "Chisq"], tolerance=TOL) 420s + ) 420s > 420s > # Illustrate complete.test argument: 420s > # Test removal of (Days | Subject): 420s > (an <- ranova(fm1, reduce.terms = FALSE)) # 3 df test 420s ANOVA-like table for random-effects: Single term deletions 420s 420s Model: 420s Reaction ~ Days + (Days | Subject) 420s npar logLik AIC LRT Df Pr(>Chisq) 420s 6 -871.81 1755.6 420s (Days | Subject) 3 -946.83 1899.7 150.03 3 < 2.2e-16 *** 420s --- 420s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 420s > 420s > # The likelihood ratio test statistic is in this case: 420s > fm3 <- lm(Reaction ~ Days, sleepstudy) 420s > LRT <- 2*c(logLik(fm1, REML=TRUE) - logLik(fm3, REML=TRUE)) # LRT 420s > stopifnot( 420s + nrow(an) == 2L, 420s + an[2L, "Df"] == 3L, 420s + all.equal(an[2L, "LRT"], LRT, tolerance=TOL) 420s + ) 420s > 420s > ## _NULL_ model: 420s > fm <- lmer(Reaction ~ -1 + (1|Subject), sleepstudy) 420s > step(fm) 420s Backward reduced random-effect table: 420s 420s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 420s 2 -992.84 1989.7 420s (1 | Subject) 0 1 -1284.32 2570.7 582.97 1 < 2.2e-16 *** 420s --- 420s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 420s 420s Backward reduced fixed-effect table: 420s Degrees of freedom method: Satterthwaite 420s 420s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 420s 420s Model found: 420s Reaction ~ -1 + (1 | Subject) 420s > ranova(fm) 420s ANOVA-like table for random-effects: Single term deletions 420s 420s Model: 420s Reaction ~ -1 + (1 | Subject) 420s npar logLik AIC LRT Df Pr(>Chisq) 420s 2 -992.84 1989.7 420s (1 | Subject) 1 -1284.32 2570.7 582.97 1 < 2.2e-16 *** 420s --- 420s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 420s > lm1 <- lm(Reaction ~ 0, data=sleepstudy) 420s > LRT <- 2*c(logLik(fm, REML=FALSE) - logLik(lm1, REML=FALSE)) 420s > 420s > ## Tests of ML-fits agree with anova(): 420s > fm1 <- lmer(Reaction ~ Days + (1|Subject), sleepstudy, REML=FALSE) 420s > step(fm1) 420s Backward reduced random-effect table: 420s 420s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 420s 4 -897.04 1802.1 420s (1 | Subject) 0 3 -950.15 1906.3 106.21 1 < 2.2e-16 *** 420s --- 420s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 420s 420s Backward reduced fixed-effect table: 420s Degrees of freedom method: Satterthwaite 420s 420s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 420s Days 0 162703 162703 1 162 170.45 < 2.2e-16 *** 420s --- 420s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 420s 420s Model found: 420s Reaction ~ Days + (1 | Subject) 420s > lm2 <- lm(Reaction ~ Days, sleepstudy) 420s > (an1 <- ranova(fm1)) 420s ANOVA-like table for random-effects: Single term deletions 420s 420s Model: 420s Reaction ~ Days + (1 | Subject) 420s npar logLik AIC LRT Df Pr(>Chisq) 420s 4 -897.04 1802.1 420s (1 | Subject) 3 -950.15 1906.3 106.21 1 < 2.2e-16 *** 420s --- 420s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 420s > (an2 <- anova(fm1, lm2)) 420s Data: sleepstudy 420s Models: 420s lm2: Reaction ~ Days 420s fm1: Reaction ~ Days + (1 | Subject) 420s npar AIC BIC logLik -2*log(L) Chisq Df Pr(>Chisq) 420s lm2 3 1906.3 1915.9 -950.15 1900.3 420s fm1 4 1802.1 1814.8 -897.04 1794.1 106.21 1 < 2.2e-16 *** 420s --- 420s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 420s > j <- grep("Chi Df|Df", colnames(an2)) 420s > stopifnot( 420s + all.equal(an1[2, "LRT"], an2[2, "Chisq"], tolerance=TOL), 420s + all.equal(an1[2, "Df"], an2[2, j[length(j)]], tolerance=TOL), 420s + all.equal(an1[1:2, "logLik"], an2[2:1, "logLik"], tolerance=TOL) 420s + ) 420s > ## Note that lme4 version <1.1-22 use "Chi Df" while >=1.1-22 use "Df" 420s > 420s > # Expect warnings when old (version < 3.0-0) arguments are used: 420s > assertWarning(step(fm, reduce.fixed = FALSE, reduce.random = FALSE, 420s + type=3, fixed.calc = FALSE, lsmeans.calc = FALSE, 420s + difflsmeans.calc = TRUE, test.effs = 42, keep.e="save")) 420s > assertWarning(step(fm, reduce.fixed = FALSE, reduce.random = FALSE, 420s + lsmeans=3)) 420s > 420s > 420s > check_nrow <- function(obj, expect_nrow) { 420s + stopifnot( 420s + is.numeric(expect_nrow), 420s + nrow(obj) == expect_nrow 420s + ) 420s + } 420s > 420s > # Statistical nonsense, but it works: 420s > fm1 <- lmer(Reaction ~ Days + (1 | Subject) + (0 + Days|Subject), sleepstudy) 420s > step(fm1) 420s Backward reduced random-effect table: 420s 420s Eliminated npar logLik AIC LRT Df 420s 5 -871.83 1753.7 420s (1 | Subject) 0 4 -883.26 1774.5 22.856 1 420s Days in (0 + Days | Subject) 0 4 -893.23 1794.5 42.796 1 420s Pr(>Chisq) 420s 420s (1 | Subject) 1.746e-06 *** 420s Days in (0 + Days | Subject) 6.076e-11 *** 420s --- 420s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 420s 420s Backward reduced fixed-effect table: 420s Degrees of freedom method: Satterthwaite 420s 420s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 420s Days 0 29442 29442 1 18.156 45.046 2.594e-06 *** 420s --- 420s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 420s 420s Model found: 420s Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 420s > (an <- ranova(fm1)) 420s ANOVA-like table for random-effects: Single term deletions 420s 420s Model: 420s Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 420s npar logLik AIC LRT Df Pr(>Chisq) 420s 5 -871.83 1753.7 420s (1 | Subject) 4 -883.26 1774.5 22.856 1 1.746e-06 *** 420s Days in (0 + Days | Subject) 4 -893.23 1794.5 42.796 1 6.076e-11 *** 420s --- 420s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 420s > check_nrow(an, 3) 420s > ranova(fm1, reduce.terms = FALSE) 420s ANOVA-like table for random-effects: Single term deletions 420s 420s Model: 420s Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 420s npar logLik AIC LRT Df Pr(>Chisq) 420s 5 -871.83 1753.7 420s (1 | Subject) 4 -883.26 1774.5 22.856 1 1.746e-06 *** 420s (0 + Days | Subject) 4 -893.23 1794.5 42.796 1 6.076e-11 *** 420s --- 420s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 420s > 420s > # Statistical nonsense, but it works: 420s > fm1 <- lmer(Reaction ~ Days + (0 + Days|Subject), sleepstudy) 421s > step(fm1) 421s Backward reduced random-effect table: 421s 421s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 421s 4 -883.26 1774.5 421s Days in (0 + Days | Subject) 0 4 -893.23 1794.5 19.94 0 421s 421s Backward reduced fixed-effect table: 421s Degrees of freedom method: Satterthwaite 421s 421s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 421s Days 0 26395 26395 1 21.679 31.347 1.32e-05 *** 421s --- 421s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 421s 421s Model found: 421s Reaction ~ Days + (0 + Days | Subject) 421s > (an <- ranova(fm1)) # no test of non-nested models 421s ANOVA-like table for random-effects: Single term deletions 421s 421s Model: 421s Reaction ~ Days + (0 + Days | Subject) 421s npar logLik AIC LRT Df Pr(>Chisq) 421s 4 -883.26 1774.5 421s Days in (0 + Days | Subject) 4 -893.23 1794.5 19.94 0 421s > stopifnot( 421s + nrow(an) == 2L, 421s + an[2L, "Df"] == 0, 421s + all(is.na(an[2L, "Pr(>Chisq)"])) 421s + ) 421s > fm0 <- lmer(Reaction ~ Days + (1|Subject), sleepstudy) 421s > step(fm0) 421s Backward reduced random-effect table: 421s 421s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 421s 4 -893.23 1794.5 421s (1 | Subject) 0 3 -946.83 1899.7 107.2 1 < 2.2e-16 *** 421s --- 421s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 421s 421s Backward reduced fixed-effect table: 421s Degrees of freedom method: Satterthwaite 421s 421s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 421s Days 0 162703 162703 1 161 169.4 < 2.2e-16 *** 421s --- 421s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 421s 421s Model found: 421s Reaction ~ Days + (1 | Subject) 421s > (an2 <- anova(fm1, fm0, refit=FALSE)) 421s Data: sleepstudy 421s Models: 421s fm1: Reaction ~ Days + (0 + Days | Subject) 421s fm0: Reaction ~ Days + (1 | Subject) 421s npar AIC BIC logLik -2*log(L) Chisq Df Pr(>Chisq) 421s fm1 4 1774.5 1787.3 -883.26 1766.5 421s fm0 4 1794.5 1807.2 -893.23 1786.5 0 0 421s > stopifnot( 421s + (packageVersion("lme4")<="1.1.23" && an2[2L, "Pr(>Chisq)"] == 1) || 421s + is.na(an2[2L, "Pr(>Chisq)"]) 421s + ) 421s > ranova(fm1, reduce.terms = FALSE) 421s ANOVA-like table for random-effects: Single term deletions 421s 421s Model: 421s Reaction ~ Days + (0 + Days | Subject) 421s npar logLik AIC LRT Df Pr(>Chisq) 421s 4 -883.26 1774.5 421s (0 + Days | Subject) 3 -946.83 1899.7 127.14 1 < 2.2e-16 *** 421s --- 421s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 421s > 421s > fm1 <- lmer(Reaction ~ Days + (-1 + Days|Subject), sleepstudy) 421s > step(fm1) 421s Backward reduced random-effect table: 421s 421s Eliminated npar logLik AIC LRT Df 421s 4 -883.26 1774.5 421s Days in (-1 + Days | Subject) 0 4 -893.23 1794.5 19.94 0 421s Pr(>Chisq) 421s 421s Days in (-1 + Days | Subject) 421s 421s Backward reduced fixed-effect table: 421s Degrees of freedom method: Satterthwaite 421s 421s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 421s Days 0 26395 26395 1 21.679 31.347 1.32e-05 *** 421s --- 421s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 421s 421s Model found: 421s Reaction ~ Days + (-1 + Days | Subject) 421s > (an3 <- ranova(fm1)) # no test of non-nested models 421s ANOVA-like table for random-effects: Single term deletions 421s 421s Model: 421s Reaction ~ Days + (-1 + Days | Subject) 421s npar logLik AIC LRT Df Pr(>Chisq) 421s 4 -883.26 1774.5 421s Days in (-1 + Days | Subject) 4 -893.23 1794.5 19.94 0 421s > stopifnot( 421s + all.equal(an, an3, check.attributes=FALSE, tolerance=TOL) 421s + ) 421s > 421s > # Example where comparison of non-nested models is generated 421s > fm <- lmer(Reaction ~ poly(Days, 2) + (0 + poly(Days, 2) | Subject), sleepstudy) 421s boundary (singular) fit: see help('isSingular') 421s > step(fm) 421s Backward reduced random-effect table: 421s 421s Eliminated npar logLik AIC 421s 7 -937.05 1888.1 421s poly(Days, 2) in (0 + poly(Days, 2) | Subject) 1 5 -884.67 1779.3 421s (1 | Subject) 0 4 -938.16 1884.3 421s LRT Df Pr(>Chisq) 421s 421s poly(Days, 2) in (0 + poly(Days, 2) | Subject) -104.77 2 1 421s (1 | Subject) 106.98 1 <2e-16 *** 421s --- 421s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 421s 421s Backward reduced fixed-effect table: 421s Degrees of freedom method: Satterthwaite 421s 421s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 421s poly(Days, 2) 0 163782 81891 2 160 85.329 < 2.2e-16 *** 421s --- 421s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 421s 421s Model found: 421s Reaction ~ poly(Days, 2) + (1 | Subject) 421s > an <- ranova(fm) 421s > stopifnot( 421s + nrow(an) == 2L, 421s + an[2, "Pr(>Chisq)"] == 1 421s + ) 421s > ranova(fm, reduce.terms = FALSE) # test of nested models 421s ANOVA-like table for random-effects: Single term deletions 421s 421s Model: 421s Reaction ~ poly(Days, 2) + (0 + poly(Days, 2) | Subject) 421s npar logLik AIC LRT Df Pr(>Chisq) 421s 7 -937.05 1888.1 421s (0 + poly(Days, 2) | Subject) 4 -938.16 1884.3 2.2153 3 0.5289 421s > 421s > # These models are nested, though: 421s > fm <- lmer(Reaction ~ poly(Days, 2) + (1 + poly(Days, 2) | Subject), sleepstudy) 421s > step(fm) 421s Backward reduced random-effect table: 421s 421s Eliminated npar logLik AIC 421s 10 -856.40 1732.8 421s poly(Days, 2) in (1 + poly(Days, 2) | Subject) 0 5 -884.67 1779.3 421s LRT Df Pr(>Chisq) 421s 421s poly(Days, 2) in (1 + poly(Days, 2) | Subject) 56.524 5 6.338e-11 *** 421s --- 421s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 421s 421s Backward reduced fixed-effect table: 421s Degrees of freedom method: Satterthwaite 421s 421s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 421s poly(Days, 2) 0 24215 12108 2 17 23.366 1.323e-05 *** 421s --- 421s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 421s 421s Model found: 421s Reaction ~ poly(Days, 2) + (1 + poly(Days, 2) | Subject) 421s > ranova(fm) 422s ANOVA-like table for random-effects: Single term deletions 422s 422s Model: 422s Reaction ~ poly(Days, 2) + (1 + poly(Days, 2) | Subject) 422s npar logLik AIC LRT Df 422s 10 -856.40 1732.8 422s poly(Days, 2) in (1 + poly(Days, 2) | Subject) 5 -884.67 1779.3 56.524 5 422s Pr(>Chisq) 422s 422s poly(Days, 2) in (1 + poly(Days, 2) | Subject) 6.338e-11 *** 422s --- 422s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 422s > fm0 <- lmer(Reaction ~ poly(Days, 2) + (1 | Subject), sleepstudy) 422s > step(fm0) 422s Backward reduced random-effect table: 422s 422s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 422s 5 -884.67 1779.3 422s (1 | Subject) 0 4 -938.16 1884.3 106.98 1 < 2.2e-16 *** 422s --- 422s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 422s 422s Backward reduced fixed-effect table: 422s Degrees of freedom method: Satterthwaite 422s 422s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 422s poly(Days, 2) 0 163782 81891 2 160 85.329 < 2.2e-16 *** 422s --- 422s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 422s 422s Model found: 422s Reaction ~ poly(Days, 2) + (1 | Subject) 422s > anova(fm0, fm, refit=FALSE) 422s Data: sleepstudy 422s Models: 422s fm0: Reaction ~ poly(Days, 2) + (1 | Subject) 422s fm: Reaction ~ poly(Days, 2) + (1 + poly(Days, 2) | Subject) 422s npar AIC BIC logLik -2*log(L) Chisq Df Pr(>Chisq) 422s fm0 5 1779.3 1795.3 -884.67 1769.3 422s fm 10 1732.8 1764.7 -856.40 1712.8 56.524 5 6.338e-11 *** 422s --- 422s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 422s > ranova(fm, reduce.terms = FALSE) 422s ANOVA-like table for random-effects: Single term deletions 422s 422s Model: 422s Reaction ~ poly(Days, 2) + (1 + poly(Days, 2) | Subject) 422s npar logLik AIC LRT Df Pr(>Chisq) 422s 10 -856.40 1732.8 422s (1 + poly(Days, 2) | Subject) 4 -938.16 1884.3 163.51 6 < 2.2e-16 *** 422s --- 422s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 422s > 422s > # A model with ||-notation: 422s > fm1 <- lmer(Reaction ~ Days + (Days||Subject), sleepstudy) 422s > step(fm1) 422s Backward reduced random-effect table: 422s 422s Eliminated npar logLik AIC LRT Df 422s 5 -871.83 1753.7 422s (1 | Subject) 0 4 -883.26 1774.5 22.856 1 422s Days in (0 + Days | Subject) 0 4 -893.23 1794.5 42.796 1 422s Pr(>Chisq) 422s 422s (1 | Subject) 1.746e-06 *** 422s Days in (0 + Days | Subject) 6.076e-11 *** 422s --- 422s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 422s 422s Backward reduced fixed-effect table: 422s Degrees of freedom method: Satterthwaite 422s 422s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 422s Days 0 29442 29442 1 18.156 45.046 2.594e-06 *** 422s --- 422s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 422s 422s Model found: 422s Reaction ~ Days + ((1 | Subject) + (0 + Days | Subject)) 422s > ranova(fm1) 422s ANOVA-like table for random-effects: Single term deletions 422s 422s Model: 422s Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 422s npar logLik AIC LRT Df Pr(>Chisq) 422s 5 -871.83 1753.7 422s (1 | Subject) 4 -883.26 1774.5 22.856 1 1.746e-06 *** 422s Days in (0 + Days | Subject) 4 -893.23 1794.5 42.796 1 6.076e-11 *** 422s --- 422s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 422s > 422s > # What about models with nested factors? 422s > fm <- lmer(Coloursaturation ~ TVset*Picture + (1|Assessor:TVset) + (1|Assessor), 422s + data=TVbo) 422s > step(fm) 422s Backward reduced random-effect table: 422s 422s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 422s 15 -280.22 590.44 422s (1 | Assessor) 1 14 -280.27 588.53 0.090 1 0.7643 422s (1 | Assessor:TVset) 0 13 -312.24 650.47 63.941 1 1.282e-15 *** 422s --- 422s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 422s 422s Backward reduced fixed-effect table: 422s Degrees of freedom method: Satterthwaite 422s 422s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 422s TVset:Picture 0 13.8 2.2999 6 159 2.6761 0.01679 * 422s --- 422s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 422s 422s Model found: 422s Coloursaturation ~ TVset + Picture + (1 | Assessor:TVset) + TVset:Picture 422s > (an1 <- ranova(fm)) 422s ANOVA-like table for random-effects: Single term deletions 422s 422s Model: 422s Coloursaturation ~ TVset * Picture + (1 | Assessor:TVset) + (1 | Assessor) 422s npar logLik AIC LRT Df Pr(>Chisq) 422s 15 -280.22 590.44 422s (1 | Assessor:TVset) 14 -302.61 633.22 44.777 1 2.208e-11 *** 422s (1 | Assessor) 14 -280.27 588.53 0.090 1 0.7643 422s --- 422s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 422s > 422s > fm <- lmer(Coloursaturation ~ TVset * Picture + 422s + (1|Assessor/TVset), data=TVbo) 422s > step(fm) 423s Backward reduced random-effect table: 423s 423s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 423s 15 -280.22 590.44 423s (1 | Assessor) 1 14 -280.27 588.53 0.090 1 0.7643 423s (1 | TVset:Assessor) 0 13 -312.24 650.47 63.941 1 1.282e-15 *** 423s --- 423s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 423s 423s Backward reduced fixed-effect table: 423s Degrees of freedom method: Satterthwaite 423s 423s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 423s TVset:Picture 0 13.8 2.2999 6 159 2.6761 0.01679 * 423s --- 423s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 423s 423s Model found: 423s Coloursaturation ~ TVset + Picture + (1 | TVset:Assessor) + TVset:Picture 423s > (an2 <- ranova(fm)) 423s ANOVA-like table for random-effects: Single term deletions 423s 423s Model: 423s Coloursaturation ~ TVset * Picture + (1 | TVset:Assessor) + (1 | Assessor) 423s npar logLik AIC LRT Df Pr(>Chisq) 423s 15 -280.22 590.44 423s (1 | TVset:Assessor) 14 -302.61 633.22 44.777 1 2.208e-11 *** 423s (1 | Assessor) 14 -280.27 588.53 0.090 1 0.7643 423s --- 423s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 423s > stopifnot( 423s + all.equal(an1, an2, check.attributes=FALSE, tolerance=TOL) 423s + ) 423s > 423s > ##################################################################### 423s > # Test evaluation within functions, i.e. in other environments etc. 423s > attach(sleepstudy) 423s > fm <- lmer(Reaction ~ Days + (Days|Subject)) 423s > step(fm) 423s Backward reduced random-effect table: 423s 423s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 423s 6 -871.81 1755.6 423s Days in (Days | Subject) 0 4 -893.23 1794.5 42.837 2 4.99e-10 423s 423s 423s Days in (Days | Subject) *** 423s --- 423s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 423s 423s Backward reduced fixed-effect table: 423s Degrees of freedom method: Satterthwaite 423s 423s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 423s Days 0 30031 30031 1 17 45.853 3.264e-06 *** 423s --- 423s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 423s 423s Model found: 423s Reaction ~ Days + (Days | Subject) 423s > ranova(fm) # OK 423s ANOVA-like table for random-effects: Single term deletions 423s 423s Model: 423s Reaction ~ Days + (Days | Subject) 423s npar logLik AIC LRT Df Pr(>Chisq) 423s 6 -871.81 1755.6 423s Days in (Days | Subject) 4 -893.23 1794.5 42.837 2 4.99e-10 *** 423s --- 423s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 423s > detach(sleepstudy) 423s > 423s > # Evaluating in a function works: 423s > f <- function(form, data) lmer(form, data=data) 423s > form <- "Informed.liking ~ Product+Information+ 423s + (1|Consumer) + (1|Product:Consumer) + (1|Information:Consumer)" 423s > fm <- f(form, data=ham) 423s > ranova(fm) 423s boundary (singular) fit: see help('isSingular') 423s ANOVA-like table for random-effects: Single term deletions 423s 423s Model: 423s Informed.liking ~ Product + Information + (1 | Consumer) + (1 | Product:Consumer) + (1 | Information:Consumer) 423s npar logLik AIC LRT Df Pr(>Chisq) 423s 9 -1353.9 2725.8 423s (1 | Consumer) 8 -1355.1 2726.1 2.295 1 0.1298 423s (1 | Product:Consumer) 8 -1436.3 2888.6 164.753 1 <2e-16 *** 423s (1 | Information:Consumer) 8 -1354.5 2725.1 1.255 1 0.2626 423s --- 423s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 423s > step_res <- step(fm) 423s boundary (singular) fit: see help('isSingular') 424s > stopifnot( 424s + all(c("Sum Sq", "Mean Sq", "NumDF", "DenDF", "F value", "Pr(>F)") %in% 424s + colnames(step_res$fixed)) 424s + ) 424s > 424s > ########################### 424s > # Evaluation in function without the formula: 424s > # Reported by Uwe Ligges 2025-01-16. 424s > f <- function(data) { 424s + lmer(Petal.Length ~ Sepal.Length + (1|Species), data=data) 424s + } 424s > 424s > res <- f(iris) 424s > ranova(res) # used to fail - now it works 424s ANOVA-like table for random-effects: Single term deletions 424s 424s Model: 424s Petal.Length ~ Sepal.Length + (1 | Species) 424s npar logLik AIC LRT Df Pr(>Chisq) 424s 4 -34.66 77.32 424s (1 | Species) 3 -193.84 393.68 318.36 1 < 2.2e-16 *** 424s --- 424s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 424s > 424s > data <- iris 424s > ranova(res) # now it works 424s ANOVA-like table for random-effects: Single term deletions 424s 424s Model: 424s Petal.Length ~ Sepal.Length + (1 | Species) 424s npar logLik AIC LRT Df Pr(>Chisq) 424s 4 -34.66 77.32 424s (1 | Species) 3 -193.84 393.68 318.36 1 < 2.2e-16 *** 424s --- 424s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 424s > ########################### 424s > # Evaluation in function without the formula(2): 424s > # A model with ||-notation: 424s > f2 <- function(data) { 424s + lmer(Reaction ~ Days + (Days||Subject), data) 424s + } 424s > res <- f2(sleepstudy) 424s > ranova(res) 424s ANOVA-like table for random-effects: Single term deletions 424s 424s Model: 424s Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 424s npar logLik AIC LRT Df Pr(>Chisq) 424s 5 -871.83 1753.7 424s (1 | Subject) 4 -883.26 1774.5 22.856 1 1.746e-06 *** 424s Days in (0 + Days | Subject) 4 -893.23 1794.5 42.796 1 6.076e-11 *** 424s --- 424s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 424s > 424s > # A model with multiple RE terms: 424s > f3 <- function(data) { 424s + lmer(Coloursaturation ~ TVset*Picture + (1|Assessor:TVset) + (1|Assessor), data) 424s + } 424s > res <- f3(TVbo) 424s > ranova(res) 424s ANOVA-like table for random-effects: Single term deletions 424s 424s Model: 424s Coloursaturation ~ TVset * Picture + (1 | Assessor:TVset) + (1 | Assessor) 424s npar logLik AIC LRT Df Pr(>Chisq) 424s 15 -280.22 590.44 424s (1 | Assessor:TVset) 14 -302.61 633.22 44.777 1 2.208e-11 *** 424s (1 | Assessor) 14 -280.27 588.53 0.090 1 0.7643 424s --- 424s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 424s > ########################### 424s > 424s > # Check that step works when form is a character vector 424s > m <- lmer(form, data=ham) 424s > step_res <- step(m) 425s boundary (singular) fit: see help('isSingular') 425s > (drop1_table <- attr(step_res, "drop1")) 425s Single term deletions using Satterthwaite's method: 425s 425s Model: 425s Informed.liking ~ Product + Information + (1 | Consumer) + (1 | Product:Consumer) 425s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 425s Product 19.3466 6.4489 3 240 3.8291 0.01048 * 425s Information 6.5201 6.5201 1 323 3.8714 0.04997 * 425s --- 425s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 425s > stopifnot( 425s + all(c("Sum Sq", "Mean Sq", "NumDF", "DenDF", "F value", "Pr(>F)") %in% 425s + colnames(drop1_table)) 425s + ) 425s > # In version < 3.0-1.9002 attr(step_res, "drop1") picked up lme4::drop1.merMod 425s > # and returned an AIC table after the model had been update'd. 425s > 425s > ##################################################################### 425s > # Model with 2 ranef covarites: 425s > 425s > # Model of the form (x1 + x2 | gr): 425s > model <- lmer(Preference ~ sens2 + Homesize + (sens1 + sens2 | Consumer) 425s + , data=carrots) 425s boundary (singular) fit: see help('isSingular') 425s Warning message: 425s Model failed to converge with 1 negative eigenvalue: -3.1e+02 425s > step(model) 425s boundary (singular) fit: see help('isSingular') 426s Backward reduced random-effect table: 426s 426s Eliminated npar logLik AIC LRT Df 426s 10 -1874.4 3768.8 426s sens1 in (sens1 + sens2 | Consumer) 1 7 -1874.5 3762.9 0.1333 3 426s sens2 in (sens2 | Consumer) 0 5 -1878.0 3765.9 6.9944 2 426s Pr(>Chisq) 426s 426s sens1 in (sens1 + sens2 | Consumer) 0.98757 426s sens2 in (sens2 | Consumer) 0.03028 * 426s --- 426s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 426s 426s Backward reduced fixed-effect table: 426s Degrees of freedom method: Satterthwaite 426s 426s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 426s sens2 0 58.685 58.685 1 102.02 54.8236 3.888e-11 *** 426s Homesize 0 5.979 5.979 1 100.95 5.5852 0.02003 * 426s --- 426s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 426s 426s Model found: 426s Preference ~ sens2 + Homesize + (sens2 | Consumer) 426s > stopifnot( 426s + nrow(ranova(model)) == 3L, 426s + nrow(ranova(model, reduce.terms = FALSE)) == 2L 426s + ) 426s boundary (singular) fit: see help('isSingular') 426s > 426s > # Model of the form (f1 + f2 | gr): 426s > model <- lmer(Preference ~ sens2 + Homesize + Gender + 426s + (Gender+Homesize|Consumer), data=carrots) 426s boundary (singular) fit: see help('isSingular') 426s > step(model) 426s Backward reduced random-effect table: 426s 426s Eliminated npar logLik AIC LRT 426s 11 -1872.3 3766.5 426s Gender in (Gender + Homesize | Consumer) 1 8 -1875.1 3766.3 5.7408 426s Homesize in (Homesize | Consumer) 0 6 -1878.4 3768.7 6.4705 426s Df Pr(>Chisq) 426s 426s Gender in (Gender + Homesize | Consumer) 3 0.12493 426s Homesize in (Homesize | Consumer) 2 0.03935 * 426s --- 426s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 426s 426s Backward reduced fixed-effect table: 426s Degrees of freedom method: Satterthwaite 426s 426s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 426s Gender 1 0.632 0.632 1 91.80 0.5686 0.45275 426s sens2 Warning messages: 426s 1: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, : 426s Model is nearly unidentifiable: large eigenvalue ratio 426s - Rescale variables? 426s 2: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, : 426s Model is nearly unidentifiable: large eigenvalue ratio 426s - Rescale variables? 426s 3: Model failed to converge with 1 negative eigenvalue: -2.7e-04 426s 0 83.385 83.385 1 1129.09 75.0490 < 2e-16 *** 426s Homesize 0 6.212 6.212 1 97.82 5.5910 0.02003 * 426s --- 426s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 426s 426s Model found: 426s Preference ~ sens2 + Homesize + (Homesize | Consumer) 426s > stopifnot( 426s + nrow(ranova(model)) == 3L, 426s + nrow(ranova(model, reduce.terms = FALSE)) == 2L 426s + ) 427s Warning message: 427s In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, : 427s Model is nearly unidentifiable: large eigenvalue ratio 427s - Rescale variables? 427s > 427s > # Model of the form (-1 + f2 | gr): 427s > model <- lmer(Preference ~ sens2 + Homesize + Gender + 427s + (Gender -1 |Consumer), data=carrots) 427s > step(model) 427s Backward reduced random-effect table: 427s 427s Eliminated npar logLik AIC LRT Df 427s 8 -1876.4 3768.9 427s Gender in (Gender - 1 | Consumer) 1 6 -1878.4 3768.7 3.863 2 427s (1 | Consumer) 0 5 -1917.2 3844.5 77.714 1 427s Pr(>Chisq) 427s 427s Gender in (Gender - 1 | Consumer) 0.145 427s (1 | Consumer) <2e-16 *** 427s --- 427s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 427s 427s Backward reduced fixed-effect table: 427s Degrees of freedom method: Satterthwaite 427s 427s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 427s Gender 1 1.879 1.879 1 99.98 1.6909 0.19647 427s sens2 0 83.363 83.363 1 1129.00 75.0256 < 2e-16 *** 427s Homesize 0 5.729 5.729 1 100.97 5.1557 0.02529 * 427s --- 427s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 427s 427s Model found: 427s Preference ~ sens2 + Homesize + (1 | Consumer) 427s > an1 <- ranova(model) 427s > an1b <- ranova(model, reduce.terms = FALSE) 427s > 427s > model <- lmer(Preference ~ sens2 + Homesize + Gender + 427s + (0 + Gender|Consumer), data=carrots) 427s > step(model) 427s Backward reduced random-effect table: 427s 427s Eliminated npar logLik AIC LRT Df 427s 8 -1876.4 3768.9 427s Gender in (0 + Gender | Consumer) 1 6 -1878.4 3768.7 3.863 2 427s (1 | Consumer) 0 5 -1917.2 3844.5 77.714 1 427s Pr(>Chisq) 427s 427s Gender in (0 + Gender | Consumer) 0.145 427s (1 | Consumer) <2e-16 *** 427s --- 427s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 427s 427s Backward reduced fixed-effect table: 427s Degrees of freedom method: Satterthwaite 427s 427s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 427s Gender 1 1.879 1.879 1 99.98 1.6909 0.19647 427s sens2 0 83.363 83.363 1 1129.00 75.0256 < 2e-16 *** 427s Homesize 0 5.729 5.729 1 100.97 5.1557 0.02529 * 427s --- 427s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 427s 427s Model found: 427s Preference ~ sens2 + Homesize + (1 | Consumer) 427s > an2 <- ranova(model) 427s > an2b <- ranova(model, reduce.terms = FALSE) 428s > 428s > stopifnot( 428s + all.equal(an1, an2, check.attributes=FALSE, tolerance=TOL), 428s + all.equal(an1b, an2b, check.attributes=FALSE, tolerance=TOL) 428s + ) 428s > 428s > ####### Polynomial terms: 428s > model <- lmer(Preference ~ sens2 + Gender + (poly(sens2, 2) | Consumer), 428s + data=carrots) 428s > (an <- ranova(model)) 428s ANOVA-like table for random-effects: Single term deletions 428s 428s Model: 428s Preference ~ sens2 + Gender + (poly(sens2, 2) | Consumer) 428s npar logLik AIC LRT Df 428s 10 -1874.1 3768.2 428s poly(sens2, 2) in (poly(sens2, 2) | Consumer) 5 -1879.9 3769.7 11.552 5 428s Pr(>Chisq) 428s 428s poly(sens2, 2) in (poly(sens2, 2) | Consumer) 0.04147 * 428s --- 428s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 428s > step(model) 429s Backward reduced random-effect table: 429s 429s Eliminated npar logLik AIC 429s 10 -1874.1 3768.2 429s poly(sens2, 2) in (poly(sens2, 2) | Consumer) 0 5 -1879.9 3769.7 429s LRT Df Pr(>Chisq) 429s 429s poly(sens2, 2) in (poly(sens2, 2) | Consumer) 11.552 5 0.04147 * 429s --- 429s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 429s 429s Backward reduced fixed-effect table: 429s Degrees of freedom method: Satterthwaite 429s 429s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 429s Gender 1 1.188 1.188 1 101.03 1.1263 0.2911 429s sens2 0 53.435 53.435 1 110.68 50.6799 1.153e-10 *** 429s --- 429s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 429s 429s Model found: 429s Preference ~ sens2 + (poly(sens2, 2) | Consumer) 429s > 429s > model <- lmer(Preference ~ sens2 + Gender + (sens2 + I(sens2^2) | Consumer), 429s + data=carrots) 429s Warning message: 429s In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, : 429s Model failed to converge with max|grad| = 0.00950416 (tol = 0.002, component 1) 429s See ?lme4::convergence and ?lme4::troubleshooting. 429s Warning message: 429s In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, : 429s Model failed to converge with max|grad| = 0.174608 (tol = 0.002, component 1) 429s See ?lme4::convergence and ?lme4::troubleshooting. 429s > (an2 <- ranova(model)) 429s boundary (singular) fit: see help('isSingular') 429s ANOVA-like table for random-effects: Single term deletions 429s 429s Model: 429s Preference ~ sens2 + Gender + (sens2 + I(sens2^2) | Consumer) 429s npar logLik AIC LRT Df 429s 10 -1874.1 3768.2 429s sens2 in (sens2 + I(sens2^2) | Consumer) 7 -1879.8 3773.5 11.3609 3 429s I(sens2^2) in (sens2 + I(sens2^2) | Consumer) 7 -1876.5 3767.0 4.8727 3 429s Pr(>Chisq) 429s 429s sens2 in (sens2 + I(sens2^2) | Consumer) 0.009926 ** 429s I(sens2^2) in (sens2 + I(sens2^2) | Consumer) 0.181363 429s --- 429s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 429s > step(model) 429s boundary (singular) fit: see help('isSingular') 429s Backward reduced random-effect table: 429s 429s Eliminated npar logLik AIC 429s 10 -1874.1 3768.2 429s I(sens2^2) in (sens2 + I(sens2^2) | Consumer) 1 7 -1876.5 3767.0 429s sens2 in (sens2 | Consumer) 0 5 -1879.9 3769.7 429s LRT Df Pr(>Chisq) 429s 429s I(sens2^2) in (sens2 + I(sens2^2) | Consumer) 4.8727 3 0.18136 429s sens2 in (sens2 | Consumer) 6.6735 2 0.03555 * 429s --- 429s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 429s 429s Backward reduced fixed-effect table: 429s Degrees of freedom method: Satterthwaite 429s 429s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 429s Gender 1 1.211 1.211 1 101.02 1.1309 0.2901 429s sens2 0 58.688 58.688 1 102.01 54.8276 3.883e-11 *** 429s --- 429s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 429s 429s Model found: 429s Preference ~ sens2 + (sens2 | Consumer) 429s > stopifnot( 429s + nrow(an) == 2L, 429s + an[2L, "Df"] == 5L, 429s + nrow(an2) == 3L, 429s + all(an2[2:3, "Df"] == 3L) 429s + ) 429s > 429s > ######## Functions of terms in random effects: 429s > model <- lmer(Preference ~ sens2 + Gender + (log(10+sens2) | Consumer), 429s + data=carrots) 430s > ranova(model) # Works 430s ANOVA-like table for random-effects: Single term deletions 430s 430s Model: 430s Preference ~ sens2 + Gender + (log(10 + sens2) | Consumer) 430s npar logLik AIC LRT Df 430s 7 -1875.3 3764.6 430s log(10 + sens2) in (log(10 + sens2) | Consumer) 5 -1879.9 3769.7 9.0854 2 430s Pr(>Chisq) 430s 430s log(10 + sens2) in (log(10 + sens2) | Consumer) 0.01064 * 430s --- 430s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 430s > step(model) 430s Backward reduced random-effect table: 430s 430s Eliminated npar logLik AIC 430s 7 -1875.3 3764.6 430s log(10 + sens2) in (log(10 + sens2) | Consumer) 0 5 -1879.9 3769.7 430s LRT Df Pr(>Chisq) 430s 430s log(10 + sens2) in (log(10 + sens2) | Consumer) 9.0854 2 0.01064 * 430s --- 430s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 430s 430s Backward reduced fixed-effect table: 430s Degrees of freedom method: Satterthwaite 430s 430s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 430s Gender 1 1.200 1.200 1 101.02 1.1295 0.2904 430s sens2 0 54.184 54.184 1 109.20 51.0012 1.083e-10 *** 430s --- 430s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 430s 430s Model found: 430s Preference ~ sens2 + (log(10 + sens2) | Consumer) 430s > 430s > ##################################################################### 430s > 430s > # Missing values changes the number of observations in use: 430s > m <- lmer(Preference ~ sens2 + Homesize + 430s + (1 |Consumer:Income), data=carrots) 430s > assertError(step(m)) 430s > ans <- try(ranova(m), silent = TRUE) 430s > stopifnot( 430s + inherits(ans, "try-error"), 430s + grepl("number of rows in use has changed", ans) 430s + ) 430s > 430s > ## Removing missing values solves the problem: 430s > m2 <- lmer(Preference ~ sens2 + Homesize + 430s + (1 |Consumer:Income), data=carrots[complete.cases(carrots), ]) 430s > ranova(m2) # Works 430s ANOVA-like table for random-effects: Single term deletions 430s 430s Model: 430s Preference ~ sens2 + Homesize + (1 | Consumer:Income) 430s npar logLik AIC LRT Df Pr(>Chisq) 430s 5 -1752.0 3513.9 430s (1 | Consumer:Income) 4 -1778.6 3565.2 53.272 1 2.904e-13 *** 430s --- 430s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 430s > step(m2) 430s Backward reduced random-effect table: 430s 430s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 430s 5 -1752.0 3513.9 430s (1 | Consumer:Income) 0 4 -1778.6 3565.2 53.272 1 2.904e-13 *** 430s --- 430s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 430s 430s Backward reduced fixed-effect table: 430s Degrees of freedom method: Satterthwaite 430s 430s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 430s sens2 0 77.308 77.308 1 1058.49 69.7915 < 2.2e-16 *** 430s Homesize 0 8.569 8.569 1 95.23 7.7355 0.006527 ** 430s --- 430s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 430s 430s Model found: 430s Preference ~ sens2 + Homesize + (1 | Consumer:Income) 430s > 430s > ## Including the variable with missing values (Income) among the fixed effects 430s > ## also solves the problem: 430s > m <- lmer(Preference ~ sens2 + Homesize + Income + #(1 + sens2 | Consumer) + 430s + (1 |Consumer:Income), data=carrots) 430s > ranova(m) 430s ANOVA-like table for random-effects: Single term deletions 430s 430s Model: 430s Preference ~ sens2 + Homesize + Income + (1 | Consumer:Income) 430s npar logLik AIC LRT Df Pr(>Chisq) 430s 8 -1766.0 3547.9 430s (1 | Consumer:Income) 7 -1791.1 3596.3 50.395 1 1.257e-12 *** 430s --- 430s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 430s > step(m) 430s Backward reduced random-effect table: 430s 430s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 430s 8 -1766.0 3547.9 430s (1 | Consumer:Income) 0 7 -1791.1 3596.3 50.395 1 1.257e-12 *** 430s --- 430s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 430s 430s Backward reduced fixed-effect table: 430s Degrees of freedom method: Satterthwaite 430s 430s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 430s Income 1 3.567 1.189 3 91.92 1.0627 0.368918 430s sens2 0 78.191 78.191 1 1062.96 69.8919 < 2.2e-16 *** 430s Homesize 0 7.983 7.983 1 94.93 7.1355 0.008894 ** 430s --- 430s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 430s 430s Model found: 430s Preference ~ sens2 + Homesize + (1 | Consumer:Income) 430s > 430s > # Missing values in a an insignificant fixed effect causes the an error in step: 430s > m0 <- lmer(Preference ~ sens2 + Homesize + Income + #(1 + sens2 | Consumer) + 430s + (1 |Consumer), data=carrots) 430s > ranova(m0) 430s ANOVA-like table for random-effects: Single term deletions 430s 430s Model: 430s Preference ~ sens2 + Homesize + Income + (1 | Consumer) 430s npar logLik AIC LRT Df Pr(>Chisq) 430s 8 -1766.0 3547.9 430s (1 | Consumer) 7 -1791.1 3596.3 50.395 1 1.257e-12 *** 430s --- 430s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 430s > ans <- try(step(m0), silent = TRUE) 430s > stopifnot( 430s + inherits(ans, "try-error"), 430s + grepl("number of rows in use has changed", ans) 430s + ) 430s > 430s > # Check that step still works for linear models (etc.) 430s > flm <- lm(Coloursaturation ~ TVset * Picture, data=TVbo) 430s > res <- step(flm, trace=0) 430s > stopifnot( 430s + inherits(res, "lm") 430s + ) 430s > 430s > ##################### Using reduce and keep args: 430s > # Fit a model to the ham dataset: 430s > m <- lmer(Informed.liking ~ Product*Information+ 430s + (1|Consumer) + (1|Product:Consumer) 430s + + (1|Information:Consumer), data=ham) 430s > 430s > # Backward elimination using terms with default alpha-levels: 430s > (step_res <- step(m)) 431s boundary (singular) fit: see help('isSingular') 431s Backward reduced random-effect table: 431s 431s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 431s 12 -1352.0 2728.1 431s (1 | Information:Consumer) 1 11 -1352.8 2727.5 1.444 1 0.22952 431s (1 | Consumer) 0 10 -1354.4 2728.7 3.184 1 0.07437 431s (1 | Product:Consumer) 0 10 -1435.0 2890.0 164.443 1 < 2e-16 431s 431s 431s (1 | Information:Consumer) 431s (1 | Consumer) . 431s (1 | Product:Consumer) *** 431s --- 431s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 431s 431s Backward reduced fixed-effect table: 431s Degrees of freedom method: Satterthwaite 431s 431s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 431s Product:Information 1 10.3873 3.4624 3 320 2.0765 0.10321 431s Product 0 19.3466 6.4489 3 240 3.8291 0.01048 * 431s Information 0 6.5201 6.5201 1 323 3.8714 0.04997 * 431s --- 431s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 431s 431s Model found: 431s Informed.liking ~ Product + Information + (1 | Consumer) + (1 | Product:Consumer) 431s > 431s > (step_res <- step(m, reduce.random = FALSE)) 431s boundary (singular) fit: see help('isSingular') 432s Backward reduced random-effect table: 432s 432s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 432s 12 -1352.0 2728.1 432s (1 | Consumer) 0 11 -1353.2 2728.3 2.252 1 0.1335 432s (1 | Product:Consumer) 0 11 -1435.0 2892.0 165.887 1 <2e-16 432s (1 | Information:Consumer) 0 11 -1352.8 2727.5 1.444 1 0.2295 432s 432s 432s (1 | Consumer) 432s (1 | Product:Consumer) *** 432s (1 | Information:Consumer) 432s --- 432s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 432s 432s Backward reduced fixed-effect table: 432s Degrees of freedom method: Satterthwaite 432s 432s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 432s Product:Information 1 10.3873 3.4624 3 240 2.2014 0.08855 . 432s Information 2 5.3335 5.3335 1 80 3.3414 0.07129 . 432s Product 0 18.3361 6.1120 3 240 3.8291 0.01048 * 432s --- 432s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 432s 432s Model found: 432s Informed.liking ~ Product + (1 | Consumer) + (1 | Product:Consumer) + (1 | Information:Consumer) 432s > (step_res <- step(m, reduce.fixed = FALSE)) 432s boundary (singular) fit: see help('isSingular') 432s Backward reduced random-effect table: 432s 432s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 432s 12 -1352.0 2728.1 432s (1 | Information:Consumer) 1 11 -1352.8 2727.5 1.444 1 0.22952 432s (1 | Consumer) 0 10 -1354.4 2728.7 3.184 1 0.07437 432s (1 | Product:Consumer) 0 10 -1435.0 2890.0 164.443 1 < 2e-16 432s 432s 432s (1 | Information:Consumer) 432s (1 | Consumer) . 432s (1 | Product:Consumer) *** 432s --- 432s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 432s 432s Backward reduced fixed-effect table: 432s Degrees of freedom method: Satterthwaite 432s 432s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 432s Product:Information 0 10.387 3.4624 3 320 2.0765 0.1032 432s 432s Model found: 432s Informed.liking ~ Product + Information + (1 | Consumer) + (1 | Product:Consumer) + Product:Information 432s > (step_res <- step(m, reduce.fixed = FALSE, reduce.random = FALSE)) 432s boundary (singular) fit: see help('isSingular') 432s Backward reduced random-effect table: 432s 432s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 432s 12 -1352.0 2728.1 432s (1 | Consumer) 0 11 -1353.2 2728.3 2.252 1 0.1335 432s (1 | Product:Consumer) 0 11 -1435.0 2892.0 165.887 1 <2e-16 432s (1 | Information:Consumer) 0 11 -1352.8 2727.5 1.444 1 0.2295 432s 432s 432s (1 | Consumer) 432s (1 | Product:Consumer) *** 432s (1 | Information:Consumer) 432s --- 432s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 432s 432s Backward reduced fixed-effect table: 432s Degrees of freedom method: Satterthwaite 432s 432s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 432s Product:Information 0 10.387 3.4624 3 240 2.2014 0.08855 . 432s --- 432s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 432s 432s Model found: 432s Informed.liking ~ Product * Information + (1 | Consumer) + (1 | Product:Consumer) + (1 | Information:Consumer) 432s > 432s > (step_res <- step(m, reduce.random = FALSE, keep="Information")) 433s boundary (singular) fit: see help('isSingular') 433s Backward reduced random-effect table: 433s 433s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 433s 12 -1352.0 2728.1 433s (1 | Consumer) 0 11 -1353.2 2728.3 2.252 1 0.1335 433s (1 | Product:Consumer) 0 11 -1435.0 2892.0 165.887 1 <2e-16 433s (1 | Information:Consumer) 0 11 -1352.8 2727.5 1.444 1 0.2295 433s 433s 433s (1 | Consumer) 433s (1 | Product:Consumer) *** 433s (1 | Information:Consumer) 433s --- 433s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 433s 433s Backward reduced fixed-effect table: 433s Degrees of freedom method: Satterthwaite 433s 433s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 433s Product:Information 1 10.3873 3.4624 3 240 2.2014 0.08855 . 433s Product 0 18.3363 6.1121 3 240 3.8292 0.01048 * 433s Information 0 5.3335 5.3335 1 80 3.3414 0.07129 . 433s --- 433s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 433s 433s Model found: 433s Informed.liking ~ Product + Information + (1 | Consumer) + (1 | Product:Consumer) + (1 | Information:Consumer) 433s > (step_res <- step(m, reduce.random = FALSE, keep="Product:Information")) 433s boundary (singular) fit: see help('isSingular') 433s Backward reduced random-effect table: 433s 433s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 433s 12 -1352.0 2728.1 433s (1 | Consumer) 0 11 -1353.2 2728.3 2.252 1 0.1335 433s (1 | Product:Consumer) 0 11 -1435.0 2892.0 165.887 1 <2e-16 433s (1 | Information:Consumer) 0 11 -1352.8 2727.5 1.444 1 0.2295 433s 433s 433s (1 | Consumer) 433s (1 | Product:Consumer) *** 433s (1 | Information:Consumer) 433s --- 433s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 433s 433s Backward reduced fixed-effect table: 433s Degrees of freedom method: Satterthwaite 433s 433s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 433s Product:Information 0 10.387 3.4624 3 240 2.2014 0.08855 . 433s --- 433s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 433s 433s Model found: 433s Informed.liking ~ Product * Information + (1 | Consumer) + (1 | Product:Consumer) + (1 | Information:Consumer) 433s > 433s > 433s > ########################### 433s > ## Test that `step` works even if all random terms are reduced away: 433s > set.seed(101) 433s > test <- data.frame(TM = factor(rep(rep(c("org","min"),each=3),3)), 433s + dep = runif(18,0,20), 433s + ind = runif(18,0,7), 433s + dorp = factor(rep(1:3,each=6))) 433s > full.model <- lmer(dep ~ TM + ind + (1 | dorp), data=test) 433s > res <- step(full.model) 433s > # res$random 433s > # res$fixed 433s > # attr(res, "model") 433s > # attr(res, "drop1") 433s > 433s > 433s > 433s BEGIN TEST test_re_covar_structures.R 433s 433s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 433s Copyright (C) 2025 The R Foundation for Statistical Computing 433s Platform: aarch64-unknown-linux-gnu 433s 433s R is free software and comes with ABSOLUTELY NO WARRANTY. 433s You are welcome to redistribute it under certain conditions. 433s Type 'license()' or 'licence()' for distribution details. 433s 433s R is a collaborative project with many contributors. 433s Type 'contributors()' for more information and 433s 'citation()' on how to cite R or R packages in publications. 433s 433s Type 'demo()' for some demos, 'help()' for on-line help, or 433s 'help.start()' for an HTML browser interface to help. 433s Type 'q()' to quit R. 433s 433s > # test_re_covar_structure.R 433s > library(lmerTest) 433s Loading required package: lme4 433s Loading required package: Matrix 435s 435s Attaching package: 'lmerTest' 435s 435s The following object is masked from 'package:lme4': 435s 435s lmer 435s 435s The following object is masked from 'package:stats': 435s 435s step 435s 435s > 435s > # WRE says "using if(requireNamespace("pkgname")) is preferred, if possible." 435s > # even in tests: 435s > assertError <- function(expr, ...) 435s + if(requireNamespace("tools")) tools::assertError(expr, ...) else invisible() 435s > assertWarning <- function(expr, ...) 435s + if(requireNamespace("tools")) tools::assertWarning(expr, ...) else invisible() 435s > 435s > # Kenward-Roger only available with pbkrtest and only then validated in R >= 3.3.3 435s > # (faulty results for R < 3.3.3 may be due to unstated dependencies in pbkrtest) 435s > has_pbkrtest <- requireNamespace("pbkrtest", quietly = TRUE) && getRversion() >= "3.3.3" 435s > 435s > data("sleepstudy", package="lme4") 435s > TOL <- 1e-4 435s > 435s > #################################### 435s > ## Test that lmerMod objects can be coerced to lmerModLmerTest and 435s > ## that the deviance function can be evaluated with expected results 435s > #################################### 435s > 435s > 435s > #################################### 435s > ## Basic tests of new (lme4 >= 2.0.0) covariance structure 435s > ## - simple sleepstudy data (random coefficient) 435s > #################################### 435s > 435s > has_pkgs <- requireNamespace("utils", quietly = TRUE) && 435s + requireNamespace("lme4", quietly = TRUE) && 435s + requireNamespace("pbkrtest", quietly = TRUE) && 435s + getRversion() >= "3.3.3" 435s > is_lme4_2_0_0 <- utils::packageVersion("lme4") >= "2.0.0" 435s > 435s > if(has_pkgs && is_lme4_2_0_0) { 435s + 435s + ## From the examples of ?`Covariance-class`: 435s + ## Unstructured 435s + fm1.us <- lmer(Reaction ~ Days + us(Days | Subject), sleepstudy) 435s + ## Diagional 435s + fm1.diag <- lmer(Reaction ~ Days + diag(Days | Subject), sleepstudy) 435s + fm1.diag.hom <- lmer(Reaction ~ Days + diag(Days | Subject, hom = TRUE), 435s + sleepstudy) 435s + ## Compound symmetry 435s + fm1.cs <- lmer(Reaction ~ Days + cs(1 + Days | Subject), sleepstudy) 435s + fm1.cs.hom <- lmer(Reaction ~ Days + cs(1 + Days | Subject, hom = TRUE), 435s + sleepstudy) 435s + ## Auto-regressive order 1 435s + sleepstudy$Daysf <- factor(sleepstudy$Days, ordered = TRUE) 435s + fm1.ar1 <- lmer(Reaction ~ Daysf + ar1(0 + Daysf | Subject, hom = TRUE), 435s + sleepstudy, REML = TRUE) 435s + 435s + ## Also adding a double-vertical-bar model (though not from 435s + ## 'Covariance-class' examples): 435s + fm1.bv <- lmer(Reaction ~ Days + (Days || Subject), sleepstudy) 435s + 435s + 435s + ltmodels <- namedList(fm1.us, 435s + fm1.diag, 435s + fm1.diag.hom, 435s + fm1.cs, 435s + fm1.cs.hom, 435s + fm1.ar1, 435s + fm1.bv) 435s + ## Run various methods on all models: 435s + for(model in ltmodels) { 435s + # model <- ltmodels[[5]] 435s + print(model) 435s + print(summary(model)) 435s + # model 435s + # summary(model) 435s + L <- diag(c(0, rep(1, length(fixef(model)) -1))) 435s + contest(model, L, joint = TRUE) 435s + contest(model, L[2, ], joint = FALSE) 435s + (an <- anova(model)) ## ddf is Satterthwaite 435s + anova(model, ddf = "Ken") 435s + anova(model, ddf="lme4") 435s + anova(model, type="I") 435s + anova(model, type="II") 435s + anova(model, type="III") 435s + show_tests(an) 435s + drop1(model) 435s + ranova(model) 435s + ranova(model, reduce.terms = FALSE) 435s + step(model) 435s + (lsm <- ls_means(model)) 435s + show_tests(lsm) 435s + (dlsm <- difflsmeans(model)) 435s + show_tests(dlsm) 435s + } 435s + } 435s > 435s > #################################### 435s > ## Basic tests of new (lme4 >= 2.0.0) covariance structure 435s > ## - Unbalanced categorical dataset with multiple RE terms 435s > #################################### 435s > 435s > 435s > 435s > 435s > 435s BEGIN TEST test_summary.R 435s 435s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 435s Copyright (C) 2025 The R Foundation for Statistical Computing 435s Platform: aarch64-unknown-linux-gnu 435s 435s R is free software and comes with ABSOLUTELY NO WARRANTY. 435s You are welcome to redistribute it under certain conditions. 435s Type 'license()' or 'licence()' for distribution details. 435s 435s R is a collaborative project with many contributors. 435s Type 'contributors()' for more information and 435s 'citation()' on how to cite R or R packages in publications. 435s 435s Type 'demo()' for some demos, 'help()' for on-line help, or 435s 'help.start()' for an HTML browser interface to help. 435s Type 'q()' to quit R. 435s 435s > # test_summary.R 435s > 435s > # WRE says "using if(requireNamespace("pkgname")) is preferred, if possible." 435s > # even in tests: 435s > assertError <- function(expr, ...) 435s + if(requireNamespace("tools")) tools::assertError(expr, ...) else invisible() 435s > assertWarning <- function(expr, ...) 435s + if(requireNamespace("tools")) tools::assertWarning(expr, ...) else invisible() 435s > 435s > # Kenward-Roger only available with pbkrtest and only then validated in R >= 3.3.3 435s > # (faulty results for R < 3.3.3 may be due to unstated dependencies in pbkrtest) 435s > has_pbkrtest <- requireNamespace("pbkrtest", quietly = TRUE) && getRversion() >= "3.3.3" 437s > 437s > library(lmerTest) 437s Loading required package: lme4 437s Loading required package: Matrix 437s 437s Attaching package: 'lmerTest' 437s 437s The following object is masked from 'package:lme4': 437s 437s lmer 437s 437s The following object is masked from 'package:stats': 437s 437s step 437s 437s > 437s > data("sleepstudy", package="lme4") 437s > data("cake", package="lme4") 437s > 437s > # Fit basic model and compute summary: 437s > fm <- lmer(Reaction ~ Days + (1|Subject) + (0+Days|Subject), sleepstudy) 438s > (sfm <- summary(fm)) 438s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 438s lmerModLmerTest] 438s Formula: Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 438s Data: sleepstudy 438s 438s REML criterion at convergence: 1743.7 438s 438s Scaled residuals: 438s Min 1Q Median 3Q Max 438s -3.9626 -0.4625 0.0204 0.4653 5.1860 438s 438s Random effects: 438s Groups Name Variance Std.Dev. 438s Subject (Intercept) 627.57 25.051 438s Subject.1 Days 35.86 5.988 438s Residual 653.58 25.565 438s Number of obs: 180, groups: Subject, 18 438s 438s Fixed effects: 438s Estimate Std. Error df t value Pr(>|t|) 438s (Intercept) 251.405 6.885 18.156 36.513 < 2e-16 *** 438s Days 10.467 1.560 18.156 6.712 2.59e-06 *** 438s --- 438s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 438s 438s Correlation of Fixed Effects: 438s (Intr) 438s Days -0.184 438s > 438s > ## Test class: 438s > stopifnot(all( 438s + class(sfm) == c("summary.lmerModLmerTest", "summary.merMod"), 438s + all(c("df", "Pr(>|t|)") %in% colnames(coef(sfm))) 438s + )) 438s > stopifnot(class(summary(fm, ddf="lme4")) == "summary.merMod") 438s > 438s > ## Test coefficient table names: 438s > mat <- coef(summary(fm)) 438s > stopifnot(all( # colnames 438s + colnames(mat) == c("Estimate", "Std. Error", "df", "t value", "Pr(>|t|)") 438s + )) 438s > stopifnot(all( # rownames 438s + names(fixef(fm)) == rownames(mat) 438s + )) 438s > 438s > ## Test pass of 'correlation' argument to lme4:::summary.merMod: 438s > x <- capture.output(summary(fm)) 438s > x_nocor <- capture.output(summary(fm, correlation=FALSE)) 438s > txt <- "Correlation of Fixed Effects:" 438s > stopifnot( 438s + any(grep(txt, x)), 438s + !any(grepl(txt, x_nocor)) 438s + ) 438s > 438s > # Test warning with unrecognized arguments (caught by lme4:::summary.merMod): 438s > assertWarning(summary(fm, false_arg=FALSE)) 438s > 438s > ## Test pass of extra arguments to lme4:::print.summary.merMod: 438s > x <- capture.output(print(summary(fm), signif.stars=TRUE)) 438s > x_nocor <- capture.output(print(summary(fm), signif.stars=FALSE)) 438s > txt <- "Signif. codes:" 438s > stopifnot( 438s + any(grep(txt, x)), 438s + !any(grepl(txt, x_nocor)) 438s + ) 438s > 438s > ####### ddf argument: 438s > (an1 <- summary(fm)) # Also testing print method. 438s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 438s lmerModLmerTest] 438s Formula: Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 438s Data: sleepstudy 438s 438s REML criterion at convergence: 1743.7 438s 438s Scaled residuals: 438s Min 1Q Median 3Q Max 438s -3.9626 -0.4625 0.0204 0.4653 5.1860 438s 438s Random effects: 438s Groups Name Variance Std.Dev. 438s Subject (Intercept) 627.57 25.051 438s Subject.1 Days 35.86 5.988 438s Residual 653.58 25.565 438s Number of obs: 180, groups: Subject, 18 438s 438s Fixed effects: 438s Estimate Std. Error df t value Pr(>|t|) 438s (Intercept) 251.405 6.885 18.156 36.513 < 2e-16 *** 438s Days 10.467 1.560 18.156 6.712 2.59e-06 *** 438s --- 438s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 438s 438s Correlation of Fixed Effects: 438s (Intr) 438s Days -0.184 438s > (an2 <- summary(fm, ddf="Satterthwaite")) 438s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 438s lmerModLmerTest] 438s Formula: Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 438s Data: sleepstudy 438s 438s REML criterion at convergence: 1743.7 438s 438s Scaled residuals: 438s Min 1Q Median 3Q Max 438s -3.9626 -0.4625 0.0204 0.4653 5.1860 438s 438s Random effects: 438s Groups Name Variance Std.Dev. 438s Subject (Intercept) 627.57 25.051 438s Subject.1 Days 35.86 5.988 438s Residual 653.58 25.565 438s Number of obs: 180, groups: Subject, 18 438s 438s Fixed effects: 438s Estimate Std. Error df t value Pr(>|t|) 438s (Intercept) 251.405 6.885 18.156 36.513 < 2e-16 *** 438s Days 10.467 1.560 18.156 6.712 2.59e-06 *** 438s --- 438s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 438s 438s Correlation of Fixed Effects: 438s (Intr) 438s Days -0.184 438s > stopifnot(isTRUE( 438s + all.equal(an1, an2) 438s + )) 438s > (an3 <- summary(fm, ddf="Sat")) ## Abbreviated argument 438s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 438s lmerModLmerTest] 438s Formula: Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 438s Data: sleepstudy 438s 438s REML criterion at convergence: 1743.7 438s 438s Scaled residuals: 438s Min 1Q Median 3Q Max 438s -3.9626 -0.4625 0.0204 0.4653 5.1860 438s 438s Random effects: 438s Groups Name Variance Std.Dev. 438s Subject (Intercept) 627.57 25.051 438s Subject.1 Days 35.86 5.988 438s Residual 653.58 25.565 438s Number of obs: 180, groups: Subject, 18 438s 438s Fixed effects: 438s Estimate Std. Error df t value Pr(>|t|) 438s (Intercept) 251.405 6.885 18.156 36.513 < 2e-16 *** 438s Days 10.467 1.560 18.156 6.712 2.59e-06 *** 438s --- 438s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 438s 438s Correlation of Fixed Effects: 438s (Intr) 438s Days -0.184 438s > stopifnot(isTRUE( 438s + all.equal(an1, an3) 438s + )) 438s > (summary(fm, ddf="lme4")) 438s Linear mixed model fit by REML ['lmerMod'] 438s Formula: Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 438s Data: sleepstudy 438s 438s REML criterion at convergence: 1743.7 438s 438s Scaled residuals: 438s Min 1Q Median 3Q Max 438s -3.9626 -0.4625 0.0204 0.4653 5.1860 438s 438s Random effects: 438s Groups Name Variance Std.Dev. 438s Subject (Intercept) 627.57 25.051 438s Subject.1 Days 35.86 5.988 438s Residual 653.58 25.565 438s Number of obs: 180, groups: Subject, 18 438s 438s Fixed effects: 438s Estimate Std. Error t value 438s (Intercept) 251.405 6.885 36.513 438s Days 10.467 1.560 6.712 438s 438s Correlation of Fixed Effects: 438s (Intr) 438s Days -0.184 438s > if(has_pbkrtest) { 438s + (summary(fm, ddf="Kenward-Roger")) 438s + assertError(summary(fm, ddf="KR")) ## Error on incorrect arg. 438s + } 438s > 438s > ## lme4 method: 438s > an1 <- summary(fm, ddf="lme4") 438s > an2 <- summary(as(fm, "lmerMod")) 438s > stopifnot(isTRUE( 438s + all.equal(an1, an2) 438s + )) 438s > 438s > 438s > # Test printed output 438s > # - Satterthwaite 438s > x <- capture.output(sfm) # equal to output of 'print(sfm)' 438s > txt <- c("lmerModLmerTest", "t-tests use Satterthwaite's method", 438s + "df", "t value", "Pr(>|t|)") 438s > stopifnot(all( 438s + sapply(txt, function(text) any(grepl(text, x))) 438s + )) 438s > 438s > # Test printed output 438s > # - KR 438s > if(has_pbkrtest) { 438s + (sfm <- summary(fm, ddf="Kenward-Roger")) 438s + x <- capture.output(sfm) 438s + txt <- c("lmerModLmerTest", "t-tests use Kenward-Roger's method", 438s + "df", "t value", "Pr(>|t|)") 438s + stopifnot(all( 438s + sapply(txt, function(text) any(grepl(text, x))) 438s + )) 438s + } 438s > 438s > #################################### 438s > ## Test 'boundary' fixef structures: 438s > #################################### 438s > 438s > # Example with no fixef: 438s > m <- lmer(Reaction ~ -1 + (Days | Subject), sleepstudy) 438s > # m <- lmer(Reaction ~ 0 + (Days | Subject), sleepstudy) # alternative 438s > stopifnot(length(fixef(m)) == 0L) 438s > stopifnot( 438s + nrow(coef(summary(m))) == 0L, 438s + nrow(coef(summary(m, ddf="lme4"))) == 0L 438s + ) 438s > if(has_pbkrtest){ 438s + stopifnot(nrow(coef(summary(m, ddf="Kenward-Roger"))) == 0L) 438s + } 438s > 438s > # Example with intercept only: 438s > m <- lmer(Reaction ~ (Days | Subject), sleepstudy) 438s > # m <- lmer(Reaction ~ 1 + (Days | Subject), sleepstudy) # alternative 438s > stopifnot(length(fixef(m)) == 1L, 438s + names(fixef(m)) == "(Intercept)") 438s > stopifnot( 438s + nrow(coef(summary(m))) == 1L, 438s + nrow(coef(summary(m, ddf="lme4"))) == 1L 438s + ) 438s > if(has_pbkrtest){ 438s + stopifnot(nrow(coef(summary(m, ddf="Kenward-Roger"))) == 1L) 438s + } 438s > 438s > # Example with >1 fixef without intercept: 438s > m <- lmer(Reaction ~ Days - 1 + I(Days^2) + (Days | Subject), sleepstudy) 438s > stopifnot(length(fixef(m)) == 2L, 438s + names(fixef(m)) == c("Days", "I(Days^2)")) 438s > stopifnot( 438s + nrow(coef(summary(m))) == 2L, 438s + nrow(coef(summary(m, ddf="lme4"))) == 2L 438s + ) 438s > if(has_pbkrtest){ 438s + stopifnot(nrow(coef(summary(m, ddf="Kenward-Roger"))) == 2L) 438s + } 438s > 438s > 438s BEGIN TEST test_zerovar.R 439s 439s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 439s Copyright (C) 2025 The R Foundation for Statistical Computing 439s Platform: aarch64-unknown-linux-gnu 439s 439s R is free software and comes with ABSOLUTELY NO WARRANTY. 439s You are welcome to redistribute it under certain conditions. 439s Type 'license()' or 'licence()' for distribution details. 439s 439s R is a collaborative project with many contributors. 439s Type 'contributors()' for more information and 439s 'citation()' on how to cite R or R packages in publications. 439s 439s Type 'demo()' for some demos, 'help()' for on-line help, or 439s 'help.start()' for an HTML browser interface to help. 439s Type 'q()' to quit R. 439s 439s > # test_zerovar.R 439s > 439s > library(lmerTest) 439s Loading required package: lme4 439s Loading required package: Matrix 441s 441s Attaching package: 'lmerTest' 441s 441s The following object is masked from 'package:lme4': 441s 441s lmer 441s 441s The following object is masked from 'package:stats': 441s 441s step 441s 441s > data("sleepstudy", package="lme4") 441s > 441s > # Baseline fit: 441s > m0 <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy, 441s + control=lmerControl(optimizer="bobyqa")) 441s > ## default optimizer does not converge proporly 441s > m0 441s Linear mixed model fit by REML ['lmerModLmerTest'] 441s Formula: Reaction ~ Days + (Days | Subject) 441s Data: sleepstudy 441s REML criterion at convergence: 1743.628 441s Random effects: 441s Groups Name Std.Dev. Corr 441s Subject (Intercept) 24.740 441s Days 5.922 0.07 441s Residual 25.592 441s Number of obs: 180, groups: Subject, 18 441s Fixed Effects: 441s (Intercept) Days 441s 251.41 10.47 441s > (an0 <- anova(m0)) 441s Type III Analysis of Variance Table with Satterthwaite's method 441s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 441s Days 30031 30031 1 17 45.853 3.264e-06 *** 441s --- 441s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 441s > 441s > # Make a fit with a zero variance estimate: 441s > n <- nrow(sleepstudy) 441s > g <- factor(rep(1:2, c(n - 10, 10))) 441s > m <- lmer(Reaction ~ Days + (Days | Subject) + (1|g), sleepstudy, 441s + control=lmerControl(optimizer="bobyqa")) 441s boundary (singular) fit: see help('isSingular') 441s > m 441s Linear mixed model fit by REML ['lmerModLmerTest'] 441s Formula: Reaction ~ Days + (Days | Subject) + (1 | g) 441s Data: sleepstudy 441s REML criterion at convergence: 1743.628 441s Random effects: 441s Groups Name Std.Dev. Corr 441s Subject (Intercept) 24.740 441s Days 5.922 0.07 441s g (Intercept) 0.000 441s Residual 25.592 441s Number of obs: 180, groups: Subject, 18; g, 2 441s Fixed Effects: 441s (Intercept) Days 441s 251.41 10.47 441s optimizer (bobyqa) convergence code: 0 (OK) ; 0 optimizer warnings; 1 lme4 warnings 441s > (an <- anova(m)) 441s Type III Analysis of Variance Table with Satterthwaite's method 441s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 441s Days 30031 30031 1 17 45.853 3.264e-06 *** 441s --- 441s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 441s > 441s > # check that fit has a zero variance 441s > vc <- as.data.frame(VarCorr(m)) 441s > stopifnot(isTRUE( 441s + all.equal(0, vc[vc$grp == "g", "sdcor"], tolerance=1e-4) 441s + )) 441s > # The hessian/vcov is actually positive definite: 441s > stopifnot(isTRUE( 441s + all(eigen(m@vcov_varpar, only.values = TRUE)$values > 0) 441s + )) 441s > 441s > # Check that ANOVA tables are the same: 441s > stopifnot(isTRUE( 441s + all.equal(an0[, 1:5], an[, 1:5], tolerance=1e-4) 441s + )) 441s > 441s > stopifnot(isTRUE( # Equality of summary tables 441s + all.equal(coef(summary(m0)), coef(summary(m)), tolerance=1e-4) 441s + )) 441s > stopifnot(isTRUE( # Equality of lme4-anova tables 441s + all.equal(anova(m0, ddf="lme4"), anova(m, ddf="lme4"), tolerance=1e-4) 441s + )) 441s > 441s > 441s BEGIN TEST zlmerTest_zeroDenom.R 441s 441s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 441s Copyright (C) 2025 The R Foundation for Statistical Computing 441s Platform: aarch64-unknown-linux-gnu 441s 441s R is free software and comes with ABSOLUTELY NO WARRANTY. 441s You are welcome to redistribute it under certain conditions. 441s Type 'license()' or 'licence()' for distribution details. 441s 441s R is a collaborative project with many contributors. 441s Type 'contributors()' for more information and 441s 'citation()' on how to cite R or R packages in publications. 441s 441s Type 'demo()' for some demos, 'help()' for on-line help, or 441s 'help.start()' for an HTML browser interface to help. 441s Type 'q()' to quit R. 441s 441s > library(lmerTest) 441s Loading required package: lme4 441s Loading required package: Matrix 443s 443s Attaching package: 'lmerTest' 443s 443s The following object is masked from 'package:lme4': 443s 443s lmer 443s 443s The following object is masked from 'package:stats': 443s 443s step 443s 443s > 443s > # Read in data set 443s > load(system.file("testdata","potdata.RData", package="lmerTest")) 443s > 443s > # Mixed model 443s > lmerout <- lmer(biomass ~ CO2*nutrients + (1|chamber),data=potdata) 443s > summary(lmerout) 443s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 443s lmerModLmerTest] 443s Formula: biomass ~ CO2 * nutrients + (1 | chamber) 443s Data: potdata 443s 443s REML criterion at convergence: 49.2 443s 443s Scaled residuals: 443s Min 1Q Median 3Q Max 443s -1.4159 -0.5588 0.0000 0.5588 1.4159 443s 443s Random effects: 443s Groups Name Variance Std.Dev. 443s chamber (Intercept) 0.2437 0.4936 443s Residual 1.5797 1.2568 443s Number of obs: 24, groups: chamber, 4 443s 443s Fixed effects: 443s Estimate Std. Error df t value Pr(>|t|) 443s (Intercept) 12.8500 0.9548 11.0163 13.458 3.49e-08 *** 443s CO2675 2.0000 1.3503 11.0163 1.481 0.166595 443s nutrients2 7.3500 1.2568 10.0000 5.848 0.000162 *** 443s nutrients3 10.4500 1.2568 10.0000 8.314 8.39e-06 *** 443s nutrients4 18.6500 1.2568 10.0000 14.839 3.88e-08 *** 443s nutrients5 25.0500 1.2568 10.0000 19.931 2.22e-09 *** 443s nutrients6 29.0000 1.2568 10.0000 23.074 5.28e-10 *** 443s CO2675:nutrients2 -0.5000 1.7775 10.0000 -0.281 0.784214 443s CO2675:nutrients3 1.9000 1.7775 10.0000 1.069 0.310218 443s CO2675:nutrients4 3.4500 1.7775 10.0000 1.941 0.080949 . 443s CO2675:nutrients5 5.9000 1.7775 10.0000 3.319 0.007756 ** 443s CO2675:nutrients6 5.2500 1.7775 10.0000 2.954 0.014444 * 443s --- 443s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 443s 443s Correlation of Fixed Effects: 443s (Intr) CO2675 ntrnt2 ntrnt3 ntrnt4 ntrnt5 ntrnt6 CO2675:2 CO2675:3 443s CO2675 -0.707 443s nutrients2 -0.658 0.465 443s nutrients3 -0.658 0.465 0.500 443s nutrients4 -0.658 0.465 0.500 0.500 443s nutrients5 -0.658 0.465 0.500 0.500 0.500 443s nutrients6 -0.658 0.465 0.500 0.500 0.500 0.500 443s CO2675:ntr2 0.465 -0.658 -0.707 -0.354 -0.354 -0.354 -0.354 443s CO2675:ntr3 0.465 -0.658 -0.354 -0.707 -0.354 -0.354 -0.354 0.500 443s CO2675:ntr4 0.465 -0.658 -0.354 -0.354 -0.707 -0.354 -0.354 0.500 0.500 443s CO2675:ntr5 0.465 -0.658 -0.354 -0.354 -0.354 -0.707 -0.354 0.500 0.500 443s CO2675:ntr6 0.465 -0.658 -0.354 -0.354 -0.354 -0.354 -0.707 0.500 0.500 443s CO2675:4 CO2675:5 443s CO2675 443s nutrients2 443s nutrients3 443s nutrients4 443s nutrients5 443s nutrients6 443s CO2675:ntr2 443s CO2675:ntr3 443s CO2675:ntr4 443s CO2675:ntr5 0.500 443s CO2675:ntr6 0.500 0.500 443s > 443s > an.sat <- anova(lmerout) 443s > anova(lmerout, ddf="lme4") 443s Analysis of Variance Table 443s npar Sum Sq Mean Sq F value 443s CO2 1 67.86 67.86 42.9589 443s nutrients 5 3050.44 610.09 386.2129 443s CO2:nutrients 5 35.47 7.09 4.4906 443s > TOL <- 1e-5 443s > stopifnot(isTRUE(all.equal( 443s + an.sat[,"DenDF"], c(2, 10, 10), tolerance=TOL 443s + ))) 443s > 443s > stopifnot(isTRUE( 443s + all.equal(an.sat[,"Pr(>F)"], c(0.0224955602, 1e-11, 0.020905569), tolerance=TOL) 443s + )) 443s > 443s > # if(require(pbkrtest)) 443s > # an.kr <- anova(lmerout, ddf="Kenward-Roger") 443s > # 443s > # TOL <- 1e-7 443s > # stopifnot(all.equal(an.kr[,"Pr(>F)"], c(0.0224955602, 1e-11, 0.020905569) , 443s > # tol=TOL), 443s > # all.equal(an.kr[,"DenDF"], 443s > # c(2, 10, 10) , tol=TOL), 443s > # TRUE) 443s > 443s autopkgtest [23:59:07]: test run-unit-test: -----------------------] 444s autopkgtest [23:59:08]: test run-unit-test: - 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to remove and 0 not upgraded. 633s Reading package lists... 633s Building dependency tree... 633s Reading state information... 634s Solving dependencies... 634s The following NEW packages will be installed: 634s build-essential cpp cpp-15 cpp-15-aarch64-linux-gnu cpp-aarch64-linux-gnu 634s dctrl-tools fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 634s fonts-glyphicons-halflings fonts-mathjax g++ g++-15 g++-15-aarch64-linux-gnu 634s g++-aarch64-linux-gnu gcc gcc-15 gcc-15-aarch64-linux-gnu 634s gcc-aarch64-linux-gnu gfortran gfortran-15 gfortran-15-aarch64-linux-gnu 634s gfortran-aarch64-linux-gnu icu-devtools libasan8 libblas-dev libblas3 634s libbz2-dev libc-dev-bin libc6-dev libcairo2 libcc1-0 libcrypt-dev libdatrie1 634s libdeflate-dev libdeflate0 libfontconfig1 libgcc-15-dev libgfortran-15-dev 634s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhwasan0 libice6 634s libicu-dev libisl23 libitm1 libjbig0 libjpeg-dev libjpeg-turbo8 634s libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libjs-bootstrap libjs-highlight.js 634s libjs-jquery libjs-jquery-datatables libjs-mathjax liblapack-dev liblapack3 634s liblerc4 liblsan0 liblzma-dev libmpc3 libncurses-dev libnlopt0 634s libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils 634s libpaper2 libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3 634s libpixman-1-0 libpkgconf3 libpng-dev libreadline-dev libsharpyuv0 libsm6 634s libstdc++-15-dev libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-dev 634s libtk8.6 libtsan2 libubsan1 libwebp7 libxcb-render0 libxcb-shm0 libxft2 634s libxrender1 libxss1 libxt6t64 libzstd-dev linux-libc-dev node-normalize.css 634s pkg-r-autopkgtest pkgconf pkgconf-bin r-base-core r-base-dev 634s r-cran-backports r-cran-boot r-cran-broom r-cran-cli r-cran-colorspace 634s r-cran-cowplot r-cran-cpp11 r-cran-curl r-cran-deriv r-cran-doby 634s r-cran-dplyr r-cran-evaluate r-cran-fansi r-cran-farver r-cran-forecast 634s r-cran-fracdiff r-cran-generics r-cran-ggplot2 r-cran-glue r-cran-gtable 634s r-cran-highr r-cran-isoband r-cran-jsonlite r-cran-knitr r-cran-labeling 634s r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-lme4 r-cran-lmertest 634s r-cran-lmtest r-cran-magrittr r-cran-mass r-cran-matrix 634s r-cran-microbenchmark r-cran-minqa r-cran-modelr r-cran-nlme r-cran-nloptr 634s r-cran-nnet r-cran-numderiv r-cran-pbkrtest r-cran-pillar r-cran-pkgconfig 634s r-cran-pkgkitten r-cran-purrr r-cran-quadprog r-cran-quantmod r-cran-r6 634s r-cran-rbibutils r-cran-rcolorbrewer r-cran-rcpp r-cran-rcpparmadillo 634s r-cran-rcppeigen r-cran-rdpack r-cran-reformulas r-cran-rlang r-cran-s7 634s r-cran-scales r-cran-statmod r-cran-stringi r-cran-stringr r-cran-tibble 634s r-cran-tidyr r-cran-tidyselect r-cran-timedate r-cran-tseries r-cran-ttr 634s r-cran-urca r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr 634s r-cran-xfun r-cran-xts r-cran-yaml r-cran-zoo rpcsvc-proto unzip x11-common 634s xdg-utils zip zlib1g-dev 634s 0 upgraded, 190 newly installed, 0 to remove and 0 not upgraded. 634s Need to get 215 MB of archives. 634s After this operation, 631 MB of additional disk space will be used. 634s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 libc-dev-bin arm64 2.42-2ubuntu4 [22.5 kB] 634s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 linux-libc-dev arm64 6.19.0-3.3 [1819 kB] 637s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libcrypt-dev arm64 1:4.5.1-1 [123 kB] 637s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 rpcsvc-proto arm64 1.4.3-1build1 [65.6 kB] 637s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 libc6-dev arm64 2.42-2ubuntu4 [1765 kB] 641s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libisl23 arm64 0.27-1build1 [676 kB] 642s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 libmpc3 arm64 1.3.1-2 [55.6 kB] 642s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp-15-aarch64-linux-gnu arm64 15.2.0-12ubuntu1 [11.7 MB] 667s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp-15 arm64 15.2.0-12ubuntu1 [1030 B] 667s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [5736 B] 667s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp arm64 4:15.2.0-4ubuntu1 [22.4 kB] 667s Get:12 http://ftpmaster.internal/ubuntu resolute/main arm64 libcc1-0 arm64 15.2.0-12ubuntu1 [49.0 kB] 667s Get:13 http://ftpmaster.internal/ubuntu resolute/main arm64 libgomp1 arm64 15.2.0-12ubuntu1 [147 kB] 667s Get:14 http://ftpmaster.internal/ubuntu resolute/main arm64 libitm1 arm64 15.2.0-12ubuntu1 [27.8 kB] 667s Get:15 http://ftpmaster.internal/ubuntu resolute/main arm64 libasan8 arm64 15.2.0-12ubuntu1 [2920 kB] 673s Get:16 http://ftpmaster.internal/ubuntu resolute/main arm64 liblsan0 arm64 15.2.0-12ubuntu1 [1316 kB] 675s Get:17 http://ftpmaster.internal/ubuntu resolute/main arm64 libtsan2 arm64 15.2.0-12ubuntu1 [2688 kB] 681s Get:18 http://ftpmaster.internal/ubuntu resolute/main arm64 libubsan1 arm64 15.2.0-12ubuntu1 [1175 kB] 685s Get:19 http://ftpmaster.internal/ubuntu resolute/main arm64 libhwasan0 arm64 15.2.0-12ubuntu1 [1638 kB] 692s Get:20 http://ftpmaster.internal/ubuntu resolute/main arm64 libgcc-15-dev arm64 15.2.0-12ubuntu1 [2600 kB] 701s Get:21 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc-15-aarch64-linux-gnu arm64 15.2.0-12ubuntu1 [23.1 MB] 745s Get:22 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc-15 arm64 15.2.0-12ubuntu1 [519 kB] 745s Get:23 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [1206 B] 745s Get:24 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc arm64 4:15.2.0-4ubuntu1 [5016 B] 746s Get:25 http://ftpmaster.internal/ubuntu resolute/main arm64 libstdc++-15-dev arm64 15.2.0-12ubuntu1 [2549 kB] 752s Get:26 http://ftpmaster.internal/ubuntu resolute/main arm64 g++-15-aarch64-linux-gnu arm64 15.2.0-12ubuntu1 [13.2 MB] 778s Get:27 http://ftpmaster.internal/ubuntu resolute/main arm64 g++-15 arm64 15.2.0-12ubuntu1 [25.3 kB] 778s Get:28 http://ftpmaster.internal/ubuntu resolute/main arm64 g++-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [956 B] 778s Get:29 http://ftpmaster.internal/ubuntu resolute/main arm64 g++ arm64 4:15.2.0-4ubuntu1 [1080 B] 778s Get:30 http://ftpmaster.internal/ubuntu resolute/main arm64 build-essential arm64 12.12ubuntu2 [5254 B] 778s Get:31 http://ftpmaster.internal/ubuntu resolute/main arm64 dctrl-tools arm64 2.24-3build4 [102 kB] 778s Get:32 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-mono all 2.37-8build1 [502 kB] 778s Get:33 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-core all 2.37-8build1 [834 kB] 779s Get:34 http://ftpmaster.internal/ubuntu resolute/main arm64 fontconfig-config arm64 2.17.1-3ubuntu1 [38.5 kB] 779s Get:35 http://ftpmaster.internal/ubuntu resolute/main arm64 libfontconfig1 arm64 2.17.1-3ubuntu1 [144 kB] 779s Get:36 http://ftpmaster.internal/ubuntu resolute/main arm64 fontconfig arm64 2.17.1-3ubuntu1 [181 kB] 779s Get:37 http://ftpmaster.internal/ubuntu resolute/universe arm64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-6 [119 kB] 779s Get:38 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-mathjax all 2.7.9+dfsg-1build1 [2283 kB] 783s Get:39 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran5 arm64 15.2.0-12ubuntu1 [451 kB] 783s Get:40 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran-15-dev arm64 15.2.0-12ubuntu1 [490 kB] 783s Get:41 http://ftpmaster.internal/ubuntu resolute/main arm64 gfortran-15-aarch64-linux-gnu arm64 15.2.0-12ubuntu1 [12.5 MB] 805s Get:42 http://ftpmaster.internal/ubuntu resolute/main arm64 gfortran-15 arm64 15.2.0-12ubuntu1 [18.1 kB] 805s Get:43 http://ftpmaster.internal/ubuntu resolute/main arm64 gfortran-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [1022 B] 805s Get:44 http://ftpmaster.internal/ubuntu resolute/main arm64 gfortran arm64 4:15.2.0-4ubuntu1 [1160 B] 805s Get:45 http://ftpmaster.internal/ubuntu resolute/main arm64 icu-devtools arm64 78.2-1ubuntu1 [207 kB] 805s Get:46 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas3 arm64 3.12.1-7ubuntu1 [181 kB] 805s Get:47 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas-dev arm64 3.12.1-7ubuntu1 [160 kB] 805s Get:48 http://ftpmaster.internal/ubuntu resolute/main arm64 libbz2-dev arm64 1.0.8-6build2 [34.9 kB] 805s Get:49 http://ftpmaster.internal/ubuntu resolute/main arm64 libpixman-1-0 arm64 0.46.4-1 [204 kB] 805s Get:50 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-render0 arm64 1.17.0-2ubuntu1 [16.4 kB] 805s Get:51 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-shm0 arm64 1.17.0-2ubuntu1 [5938 B] 805s Get:52 http://ftpmaster.internal/ubuntu resolute/main arm64 libxrender1 arm64 1:0.9.12-1 [19.5 kB] 805s Get:53 http://ftpmaster.internal/ubuntu resolute/main arm64 libcairo2 arm64 1.18.4-3 [556 kB] 806s Get:54 http://ftpmaster.internal/ubuntu resolute/main arm64 libdatrie1 arm64 0.2.14-1 [19.6 kB] 806s Get:55 http://ftpmaster.internal/ubuntu resolute/main arm64 libdeflate0 arm64 1.23-2build1 [46.8 kB] 806s Get:56 http://ftpmaster.internal/ubuntu resolute/main arm64 libdeflate-dev arm64 1.23-2build1 [54.3 kB] 806s Get:57 http://ftpmaster.internal/ubuntu resolute/main arm64 libgraphite2-3 arm64 1.3.14-11ubuntu1 [72.1 kB] 806s Get:58 http://ftpmaster.internal/ubuntu resolute/main arm64 libharfbuzz0b arm64 12.3.2-1 [510 kB] 806s Get:59 http://ftpmaster.internal/ubuntu resolute/main arm64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 806s Get:60 http://ftpmaster.internal/ubuntu resolute/main arm64 libice6 arm64 2:1.1.1-1build1 [43.0 kB] 806s Get:61 http://ftpmaster.internal/ubuntu resolute/main arm64 libicu-dev arm64 78.2-1ubuntu1 [12.5 MB] 841s Get:62 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg-turbo8 arm64 2.1.5-4ubuntu3 [161 kB] 841s Get:63 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg-turbo8-dev arm64 2.1.5-4ubuntu3 [301 kB] 841s Get:64 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 841s Get:65 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg8-dev arm64 8c-2ubuntu11 [1484 B] 841s Get:66 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg-dev arm64 8c-2ubuntu11 [1482 B] 841s Get:67 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-bootstrap all 3.4.1+dfsg-6 [129 kB] 841s Get:68 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-highlight.js all 10.7.3+dfsg-2 [144 kB] 841s Get:69 http://ftpmaster.internal/ubuntu resolute/main arm64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 841s Get:70 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-jquery-datatables all 1.11.5+dfsg-2build1 [145 kB] 841s Get:71 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack3 arm64 3.12.1-7ubuntu1 [2299 kB] 847s Get:72 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack-dev arm64 3.12.1-7ubuntu1 [4456 kB] 855s Get:73 http://ftpmaster.internal/ubuntu resolute/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu2 [174 kB] 855s Get:74 http://ftpmaster.internal/ubuntu resolute/main arm64 libncurses-dev arm64 6.6+20251231-1 [391 kB] 855s Get:75 http://ftpmaster.internal/ubuntu resolute/main arm64 libthai-data all 0.1.30-1 [155 kB] 855s Get:76 http://ftpmaster.internal/ubuntu resolute/main arm64 libthai0 arm64 0.1.30-1 [18.3 kB] 855s Get:77 http://ftpmaster.internal/ubuntu resolute/main arm64 libpango-1.0-0 arm64 1.57.0-1 [238 kB] 855s Get:78 http://ftpmaster.internal/ubuntu resolute/main arm64 libpangoft2-1.0-0 arm64 1.57.0-1 [51.5 kB] 855s Get:79 http://ftpmaster.internal/ubuntu resolute/main arm64 libpangocairo-1.0-0 arm64 1.57.0-1 [27.9 kB] 855s Get:80 http://ftpmaster.internal/ubuntu resolute/main arm64 libpaper2 arm64 2.2.5-0.3build1 [17.3 kB] 855s Get:81 http://ftpmaster.internal/ubuntu resolute/main arm64 libpaper-utils arm64 2.2.5-0.3build1 [15.4 kB] 855s Get:82 http://ftpmaster.internal/ubuntu resolute/main arm64 libpcre2-16-0 arm64 10.46-1 [225 kB] 855s Get:83 http://ftpmaster.internal/ubuntu resolute/main arm64 libpcre2-32-0 arm64 10.46-1 [213 kB] 855s Get:84 http://ftpmaster.internal/ubuntu resolute/main arm64 libpcre2-posix3 arm64 10.46-1 [7300 B] 855s Get:85 http://ftpmaster.internal/ubuntu resolute/main arm64 libpcre2-dev arm64 10.46-1 [772 kB] 857s Get:86 http://ftpmaster.internal/ubuntu resolute/main arm64 libpkgconf3 arm64 1.8.1-4build1 [33.7 kB] 857s Get:87 http://ftpmaster.internal/ubuntu resolute/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1ubuntu2 [899 kB] 860s Get:88 http://ftpmaster.internal/ubuntu resolute/main arm64 libpng-dev arm64 1.6.54-1 [268 kB] 860s Get:89 http://ftpmaster.internal/ubuntu resolute/main arm64 libreadline-dev arm64 8.3-3 [199 kB] 860s Get:90 http://ftpmaster.internal/ubuntu resolute/main arm64 libsharpyuv0 arm64 1.5.0-0.1build1 [16.7 kB] 860s Get:91 http://ftpmaster.internal/ubuntu resolute/main arm64 libsm6 arm64 2:1.2.6-1build1 [16.8 kB] 860s Get:92 http://ftpmaster.internal/ubuntu resolute/main arm64 libtcl8.6 arm64 8.6.17+dfsg-1build1 [983 kB] 863s Get:93 http://ftpmaster.internal/ubuntu resolute/main arm64 libjbig0 arm64 2.1-6.1ubuntu3 [29.2 kB] 863s Get:94 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebp7 arm64 1.5.0-0.1build1 [205 kB] 863s Get:95 http://ftpmaster.internal/ubuntu resolute/main arm64 libtiff6 arm64 4.7.0-3ubuntu3 [196 kB] 863s Get:96 http://ftpmaster.internal/ubuntu resolute/main arm64 libxft2 arm64 2.3.6-1build2 [43.2 kB] 863s Get:97 http://ftpmaster.internal/ubuntu resolute/main arm64 libxss1 arm64 1:1.2.3-1build4 [7102 B] 863s Get:98 http://ftpmaster.internal/ubuntu resolute/main arm64 libtk8.6 arm64 8.6.17-1 [811 kB] 866s Get:99 http://ftpmaster.internal/ubuntu resolute/main arm64 libxt6t64 arm64 1:1.2.1-1.3 [168 kB] 866s Get:100 http://ftpmaster.internal/ubuntu resolute/main arm64 libzstd-dev arm64 1.5.7+dfsg-3 [349 kB] 866s Get:101 http://ftpmaster.internal/ubuntu resolute/universe arm64 node-normalize.css all 8.0.1-5.1 [10.4 kB] 866s Get:102 http://ftpmaster.internal/ubuntu resolute/main arm64 zip arm64 3.0-15ubuntu3 [170 kB] 866s Get:103 http://ftpmaster.internal/ubuntu resolute/main arm64 unzip arm64 6.0-29ubuntu1 [176 kB] 866s Get:104 http://ftpmaster.internal/ubuntu resolute/main arm64 xdg-utils all 1.2.1-2ubuntu2 [66.1 kB] 866s Get:105 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-base-core arm64 4.5.2-1ubuntu2 [28.6 MB] 922s Get:106 http://ftpmaster.internal/ubuntu resolute/main arm64 liblzma-dev arm64 5.8.2-2 [180 kB] 922s Get:107 http://ftpmaster.internal/ubuntu resolute/main arm64 pkgconf-bin arm64 1.8.1-4build1 [21.7 kB] 922s Get:108 http://ftpmaster.internal/ubuntu resolute/main arm64 pkgconf arm64 1.8.1-4build1 [16.8 kB] 922s Get:109 http://ftpmaster.internal/ubuntu resolute/main arm64 libtirpc-dev arm64 1.3.6+ds-1 [202 kB] 922s Get:110 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-base-dev all 4.5.2-1ubuntu2 [1880 B] 922s Get:111 http://ftpmaster.internal/ubuntu resolute/universe arm64 pkg-r-autopkgtest all 20250812 [6158 B] 922s Get:112 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-backports arm64 1.5.0-2 [121 kB] 922s Get:113 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-boot all 1.3-32-1 [636 kB] 923s Get:114 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-cli arm64 3.6.4-1 [1374 kB] 925s Get:115 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-generics all 0.1.4-1 [84.0 kB] 925s Get:116 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-glue arm64 1.8.0-1 [163 kB] 926s Get:117 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rlang arm64 1.1.5-3 [1706 kB] 928s Get:118 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-lifecycle all 1.0.5+dfsg-1 [120 kB] 928s Get:119 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-magrittr arm64 2.0.3-1 [154 kB] 928s Get:120 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-utf8 arm64 1.2.4-1 [140 kB] 928s Get:121 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-vctrs arm64 0.6.5-1 [1327 kB] 930s Get:122 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-pillar all 1.11.1+dfsg-1 [456 kB] 930s Get:123 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-r6 all 2.6.1-1 [101 kB] 931s Get:124 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-fansi arm64 1.0.6-2 [627 kB] 931s Get:125 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-pkgconfig all 2.0.3-2build2 [20.4 kB] 931s Get:126 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-tibble arm64 3.2.1+dfsg-3 [420 kB] 931s Get:127 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-withr all 3.0.2+dfsg-1 [214 kB] 931s Get:128 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-tidyselect arm64 1.2.1+dfsg-1 [222 kB] 931s Get:129 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-dplyr arm64 1.1.4-4 [1534 kB] 934s Get:130 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-purrr arm64 1.0.4-1 [552 kB] 934s Get:131 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-stringi arm64 1.8.4-1build2 [901 kB] 936s Get:132 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-stringr all 1.5.1-1 [290 kB] 936s Get:133 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-cpp11 all 0.5.3-1 [242 kB] 936s Get:134 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-tidyr arm64 1.3.1-1 [1154 kB] 937s Get:135 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-broom all 1.0.12+dfsg-1 [1708 kB] 940s Get:136 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-colorspace arm64 2.1-1+dfsg-1 [1563 kB] 943s Get:137 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-gtable all 0.3.6+dfsg-1 [199 kB] 943s Get:138 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-isoband arm64 0.2.7-1 [1481 kB] 945s Get:139 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-s7 arm64 0.2.0-1 [329 kB] 945s Get:140 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-farver arm64 2.1.2-1 [1344 kB] 948s Get:141 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-labeling all 0.4.3-1 [62.1 kB] 948s Get:142 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rcolorbrewer all 1.1-3-1build2 [54.0 kB] 948s Get:143 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-viridislite all 0.4.3-1 [1088 kB] 950s Get:144 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-scales all 1.4.0-1 [725 kB] 951s Get:145 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 r-cran-ggplot2 all 4.0.2+dfsg-1 [4941 kB] 959s Get:146 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-cowplot all 1.1.3+dfsg-1 [614 kB] 961s Get:147 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-curl arm64 7.0.0+dfsg-1 [202 kB] 961s Get:148 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-deriv all 4.2.0-1 [154 kB] 961s Get:149 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-fracdiff arm64 1.5-3-1 [108 kB] 961s Get:150 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-lattice arm64 0.22-7-1 [1365 kB] 962s Get:151 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-zoo arm64 1.8-15-1 [1025 kB] 964s Get:152 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-lmtest arm64 0.9.40-1build1 [400 kB] 964s Get:153 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-nnet arm64 7.3-20-1 [113 kB] 964s Get:154 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-littler arm64 0.3.22-1 [85.1 kB] 964s Get:155 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 964s Get:156 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rcpp arm64 1.1.0-1 [2011 kB] 967s Get:157 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-timedate arm64 4052.112-1 [1298 kB] 969s Get:158 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-quadprog arm64 1.5-8-1build2 [31.9 kB] 969s Get:159 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-xts arm64 0.14.1-1 [1189 kB] 971s Get:160 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-ttr arm64 0.24.4-1 [509 kB] 971s Get:161 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-jsonlite arm64 1.9.1+dfsg-1 [445 kB] 971s Get:162 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-quantmod all 0.4.28-1 [1037 kB] 972s Get:163 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-tseries arm64 0.10-59-3 [381 kB] 972s Get:164 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-nlme arm64 3.1.168-1 [2310 kB] 976s Get:165 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-urca arm64 1.3-4-1build1 [1050 kB] 977s Get:166 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rcpparmadillo arm64 15.2.3-1-1 [916 kB] 979s Get:167 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-forecast arm64 8.23.0-1 [1564 kB] 982s Get:168 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-mass arm64 7.3-65-1 [1109 kB] 983s Get:169 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-matrix arm64 1.7-4-1 [4146 kB] 990s Get:170 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-modelr all 0.1.11-1 [195 kB] 990s Get:171 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-microbenchmark arm64 1.5.0-1 [67.5 kB] 990s Get:172 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-doby all 4.7.1-3 [4741 kB] 998s Get:173 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-evaluate all 1.0.5-1 [117 kB] 998s Get:174 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-xfun arm64 0.55+dfsg-1 [587 kB] 999s Get:175 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-highr all 0.11+dfsg-1 [38.5 kB] 999s Get:176 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-yaml arm64 2.3.10-1 [108 kB] 999s Get:177 http://ftpmaster.internal/ubuntu resolute/main arm64 libjs-mathjax all 2.7.9+dfsg-1build1 [6017 kB] 1008s Get:178 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-knitr all 1.51+dfsg-1 [847 kB] 1010s Get:179 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-minqa arm64 1.2.8-1 [112 kB] 1010s Get:180 http://ftpmaster.internal/ubuntu resolute/universe arm64 libnlopt0 arm64 2.7.1-7ubuntu1 [177 kB] 1010s Get:181 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-nloptr arm64 2.2.1-2 [250 kB] 1010s Get:182 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rbibutils arm64 2.3-1 [1016 kB] 1011s Get:183 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rdpack all 2.6.3-1 [636 kB] 1012s Get:184 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-reformulas all 0.4.4-1 [151 kB] 1012s Get:185 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rcppeigen arm64 0.3.4.0.2-1 [1422 kB] 1014s Get:186 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-statmod arm64 1.5.0-1 [294 kB] 1014s Get:187 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-lme4 arm64 1.1-38-1 [4177 kB] 1020s Get:188 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-numderiv all 2016.8-1.1-3build1 [116 kB] 1020s Get:189 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-lmertest all 3.2-0-1 [535 kB] 1021s Get:190 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-pbkrtest all 0.5.5-1 [217 kB] 1022s Preconfiguring packages ... 1022s Fetched 215 MB in 6min 27s (554 kB/s) 1022s Selecting previously unselected package libc-dev-bin. 1022s (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 ... 136600 files and directories currently installed.) 1022s Preparing to unpack .../000-libc-dev-bin_2.42-2ubuntu4_arm64.deb ... 1022s Unpacking libc-dev-bin (2.42-2ubuntu4) ... 1022s Selecting previously unselected package linux-libc-dev:arm64. 1022s Preparing to unpack .../001-linux-libc-dev_6.19.0-3.3_arm64.deb ... 1022s Unpacking linux-libc-dev:arm64 (6.19.0-3.3) ... 1022s Selecting previously unselected package libcrypt-dev:arm64. 1022s Preparing to unpack .../002-libcrypt-dev_1%3a4.5.1-1_arm64.deb ... 1022s Unpacking libcrypt-dev:arm64 (1:4.5.1-1) ... 1022s Selecting previously unselected package rpcsvc-proto. 1022s Preparing to unpack .../003-rpcsvc-proto_1.4.3-1build1_arm64.deb ... 1022s Unpacking rpcsvc-proto (1.4.3-1build1) ... 1022s Selecting previously unselected package libc6-dev:arm64. 1022s Preparing to unpack .../004-libc6-dev_2.42-2ubuntu4_arm64.deb ... 1022s Unpacking libc6-dev:arm64 (2.42-2ubuntu4) ... 1022s Selecting previously unselected package libisl23:arm64. 1022s Preparing to unpack .../005-libisl23_0.27-1build1_arm64.deb ... 1022s Unpacking libisl23:arm64 (0.27-1build1) ... 1022s Selecting previously unselected package libmpc3:arm64. 1022s Preparing to unpack .../006-libmpc3_1.3.1-2_arm64.deb ... 1022s Unpacking libmpc3:arm64 (1.3.1-2) ... 1022s Selecting previously unselected package cpp-15-aarch64-linux-gnu. 1022s Preparing to unpack .../007-cpp-15-aarch64-linux-gnu_15.2.0-12ubuntu1_arm64.deb ... 1022s Unpacking cpp-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 1023s Selecting previously unselected package cpp-15. 1023s Preparing to unpack .../008-cpp-15_15.2.0-12ubuntu1_arm64.deb ... 1023s Unpacking cpp-15 (15.2.0-12ubuntu1) ... 1023s Selecting previously unselected package cpp-aarch64-linux-gnu. 1023s Preparing to unpack .../009-cpp-aarch64-linux-gnu_4%3a15.2.0-4ubuntu1_arm64.deb ... 1023s Unpacking cpp-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 1023s Selecting previously unselected package cpp. 1023s Preparing to unpack .../010-cpp_4%3a15.2.0-4ubuntu1_arm64.deb ... 1023s Unpacking cpp (4:15.2.0-4ubuntu1) ... 1023s Selecting previously unselected package libcc1-0:arm64. 1023s Preparing to unpack .../011-libcc1-0_15.2.0-12ubuntu1_arm64.deb ... 1023s Unpacking libcc1-0:arm64 (15.2.0-12ubuntu1) ... 1023s Selecting previously unselected package libgomp1:arm64. 1023s Preparing to unpack .../012-libgomp1_15.2.0-12ubuntu1_arm64.deb ... 1023s Unpacking libgomp1:arm64 (15.2.0-12ubuntu1) ... 1023s Selecting previously unselected package libitm1:arm64. 1023s Preparing to unpack .../013-libitm1_15.2.0-12ubuntu1_arm64.deb ... 1023s Unpacking libitm1:arm64 (15.2.0-12ubuntu1) ... 1023s Selecting previously unselected package libasan8:arm64. 1023s Preparing to unpack .../014-libasan8_15.2.0-12ubuntu1_arm64.deb ... 1023s Unpacking libasan8:arm64 (15.2.0-12ubuntu1) ... 1023s Selecting previously unselected package liblsan0:arm64. 1023s Preparing to unpack .../015-liblsan0_15.2.0-12ubuntu1_arm64.deb ... 1023s Unpacking liblsan0:arm64 (15.2.0-12ubuntu1) ... 1023s Selecting previously unselected package libtsan2:arm64. 1023s Preparing to unpack .../016-libtsan2_15.2.0-12ubuntu1_arm64.deb ... 1023s Unpacking libtsan2:arm64 (15.2.0-12ubuntu1) ... 1023s Selecting previously unselected package libubsan1:arm64. 1023s Preparing to unpack .../017-libubsan1_15.2.0-12ubuntu1_arm64.deb ... 1023s Unpacking libubsan1:arm64 (15.2.0-12ubuntu1) ... 1023s Selecting previously unselected package libhwasan0:arm64. 1023s Preparing to unpack .../018-libhwasan0_15.2.0-12ubuntu1_arm64.deb ... 1023s Unpacking libhwasan0:arm64 (15.2.0-12ubuntu1) ... 1023s Selecting previously unselected package libgcc-15-dev:arm64. 1023s Preparing to unpack .../019-libgcc-15-dev_15.2.0-12ubuntu1_arm64.deb ... 1023s Unpacking libgcc-15-dev:arm64 (15.2.0-12ubuntu1) ... 1023s Selecting previously unselected package gcc-15-aarch64-linux-gnu. 1023s Preparing to unpack .../020-gcc-15-aarch64-linux-gnu_15.2.0-12ubuntu1_arm64.deb ... 1023s Unpacking gcc-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 1024s Selecting previously unselected package gcc-15. 1024s Preparing to unpack .../021-gcc-15_15.2.0-12ubuntu1_arm64.deb ... 1024s Unpacking gcc-15 (15.2.0-12ubuntu1) ... 1024s Selecting previously unselected package gcc-aarch64-linux-gnu. 1024s Preparing to unpack .../022-gcc-aarch64-linux-gnu_4%3a15.2.0-4ubuntu1_arm64.deb ... 1024s Unpacking gcc-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 1024s Selecting previously unselected package gcc. 1024s Preparing to unpack .../023-gcc_4%3a15.2.0-4ubuntu1_arm64.deb ... 1024s Unpacking gcc (4:15.2.0-4ubuntu1) ... 1024s Selecting previously unselected package libstdc++-15-dev:arm64. 1024s Preparing to unpack .../024-libstdc++-15-dev_15.2.0-12ubuntu1_arm64.deb ... 1024s Unpacking libstdc++-15-dev:arm64 (15.2.0-12ubuntu1) ... 1024s Selecting previously unselected package g++-15-aarch64-linux-gnu. 1024s Preparing to unpack .../025-g++-15-aarch64-linux-gnu_15.2.0-12ubuntu1_arm64.deb ... 1024s Unpacking g++-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 1024s Selecting previously unselected package g++-15. 1024s Preparing to unpack .../026-g++-15_15.2.0-12ubuntu1_arm64.deb ... 1024s Unpacking g++-15 (15.2.0-12ubuntu1) ... 1025s Selecting previously unselected package g++-aarch64-linux-gnu. 1025s Preparing to unpack .../027-g++-aarch64-linux-gnu_4%3a15.2.0-4ubuntu1_arm64.deb ... 1025s Unpacking g++-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 1025s Selecting previously unselected package g++. 1025s Preparing to unpack .../028-g++_4%3a15.2.0-4ubuntu1_arm64.deb ... 1025s Unpacking g++ (4:15.2.0-4ubuntu1) ... 1025s Selecting previously unselected package build-essential. 1025s Preparing to unpack .../029-build-essential_12.12ubuntu2_arm64.deb ... 1025s Unpacking build-essential (12.12ubuntu2) ... 1025s Selecting previously unselected package dctrl-tools. 1025s Preparing to unpack .../030-dctrl-tools_2.24-3build4_arm64.deb ... 1025s Unpacking dctrl-tools (2.24-3build4) ... 1025s Selecting previously unselected package fonts-dejavu-mono. 1025s Preparing to unpack .../031-fonts-dejavu-mono_2.37-8build1_all.deb ... 1025s Unpacking fonts-dejavu-mono (2.37-8build1) ... 1025s Selecting previously unselected package fonts-dejavu-core. 1025s Preparing to unpack .../032-fonts-dejavu-core_2.37-8build1_all.deb ... 1025s Unpacking fonts-dejavu-core (2.37-8build1) ... 1025s Selecting previously unselected package fontconfig-config. 1025s Preparing to unpack .../033-fontconfig-config_2.17.1-3ubuntu1_arm64.deb ... 1025s Unpacking fontconfig-config (2.17.1-3ubuntu1) ... 1025s Selecting previously unselected package libfontconfig1:arm64. 1025s Preparing to unpack .../034-libfontconfig1_2.17.1-3ubuntu1_arm64.deb ... 1025s Unpacking libfontconfig1:arm64 (2.17.1-3ubuntu1) ... 1025s Selecting previously unselected package fontconfig. 1025s Preparing to unpack .../035-fontconfig_2.17.1-3ubuntu1_arm64.deb ... 1025s Unpacking fontconfig (2.17.1-3ubuntu1) ... 1025s Selecting previously unselected package fonts-glyphicons-halflings. 1025s Preparing to unpack .../036-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-6_all.deb ... 1025s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-6) ... 1025s Selecting previously unselected package fonts-mathjax. 1025s Preparing to unpack .../037-fonts-mathjax_2.7.9+dfsg-1build1_all.deb ... 1025s Unpacking fonts-mathjax (2.7.9+dfsg-1build1) ... 1026s Selecting previously unselected package libgfortran5:arm64. 1026s Preparing to unpack .../038-libgfortran5_15.2.0-12ubuntu1_arm64.deb ... 1026s Unpacking libgfortran5:arm64 (15.2.0-12ubuntu1) ... 1026s Selecting previously unselected package libgfortran-15-dev:arm64. 1026s Preparing to unpack .../039-libgfortran-15-dev_15.2.0-12ubuntu1_arm64.deb ... 1026s Unpacking libgfortran-15-dev:arm64 (15.2.0-12ubuntu1) ... 1026s Selecting previously unselected package gfortran-15-aarch64-linux-gnu. 1026s Preparing to unpack .../040-gfortran-15-aarch64-linux-gnu_15.2.0-12ubuntu1_arm64.deb ... 1026s Unpacking gfortran-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 1026s Selecting previously unselected package gfortran-15. 1026s Preparing to unpack .../041-gfortran-15_15.2.0-12ubuntu1_arm64.deb ... 1026s Unpacking gfortran-15 (15.2.0-12ubuntu1) ... 1026s Selecting previously unselected package gfortran-aarch64-linux-gnu. 1026s Preparing to unpack .../042-gfortran-aarch64-linux-gnu_4%3a15.2.0-4ubuntu1_arm64.deb ... 1026s Unpacking gfortran-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 1026s Selecting previously unselected package gfortran. 1026s Preparing to unpack .../043-gfortran_4%3a15.2.0-4ubuntu1_arm64.deb ... 1026s Unpacking gfortran (4:15.2.0-4ubuntu1) ... 1026s Selecting previously unselected package icu-devtools. 1026s Preparing to unpack .../044-icu-devtools_78.2-1ubuntu1_arm64.deb ... 1026s Unpacking icu-devtools (78.2-1ubuntu1) ... 1026s Selecting previously unselected package libblas3:arm64. 1026s Preparing to unpack .../045-libblas3_3.12.1-7ubuntu1_arm64.deb ... 1026s Unpacking libblas3:arm64 (3.12.1-7ubuntu1) ... 1026s Selecting previously unselected package libblas-dev:arm64. 1026s Preparing to unpack .../046-libblas-dev_3.12.1-7ubuntu1_arm64.deb ... 1026s Unpacking libblas-dev:arm64 (3.12.1-7ubuntu1) ... 1026s Selecting previously unselected package libbz2-dev:arm64. 1026s Preparing to unpack .../047-libbz2-dev_1.0.8-6build2_arm64.deb ... 1026s Unpacking libbz2-dev:arm64 (1.0.8-6build2) ... 1026s Selecting previously unselected package libpixman-1-0:arm64. 1026s Preparing to unpack .../048-libpixman-1-0_0.46.4-1_arm64.deb ... 1026s Unpacking libpixman-1-0:arm64 (0.46.4-1) ... 1026s Selecting previously unselected package libxcb-render0:arm64. 1026s Preparing to unpack .../049-libxcb-render0_1.17.0-2ubuntu1_arm64.deb ... 1026s Unpacking libxcb-render0:arm64 (1.17.0-2ubuntu1) ... 1026s Selecting previously unselected package libxcb-shm0:arm64. 1026s Preparing to unpack .../050-libxcb-shm0_1.17.0-2ubuntu1_arm64.deb ... 1026s Unpacking libxcb-shm0:arm64 (1.17.0-2ubuntu1) ... 1026s Selecting previously unselected package libxrender1:arm64. 1026s Preparing to unpack .../051-libxrender1_1%3a0.9.12-1_arm64.deb ... 1026s Unpacking libxrender1:arm64 (1:0.9.12-1) ... 1026s Selecting previously unselected package libcairo2:arm64. 1026s Preparing to unpack .../052-libcairo2_1.18.4-3_arm64.deb ... 1026s Unpacking libcairo2:arm64 (1.18.4-3) ... 1026s Selecting previously unselected package libdatrie1:arm64. 1027s Preparing to unpack .../053-libdatrie1_0.2.14-1_arm64.deb ... 1027s Unpacking libdatrie1:arm64 (0.2.14-1) ... 1027s Selecting previously unselected package libdeflate0:arm64. 1027s Preparing to unpack .../054-libdeflate0_1.23-2build1_arm64.deb ... 1027s Unpacking libdeflate0:arm64 (1.23-2build1) ... 1027s Selecting previously unselected package libdeflate-dev:arm64. 1027s Preparing to unpack .../055-libdeflate-dev_1.23-2build1_arm64.deb ... 1027s Unpacking libdeflate-dev:arm64 (1.23-2build1) ... 1027s Selecting previously unselected package libgraphite2-3:arm64. 1027s Preparing to unpack .../056-libgraphite2-3_1.3.14-11ubuntu1_arm64.deb ... 1027s Unpacking libgraphite2-3:arm64 (1.3.14-11ubuntu1) ... 1027s Selecting previously unselected package libharfbuzz0b:arm64. 1027s Preparing to unpack .../057-libharfbuzz0b_12.3.2-1_arm64.deb ... 1027s Unpacking libharfbuzz0b:arm64 (12.3.2-1) ... 1027s Selecting previously unselected package x11-common. 1027s Preparing to unpack .../058-x11-common_1%3a7.7+24ubuntu1_all.deb ... 1027s Unpacking x11-common (1:7.7+24ubuntu1) ... 1027s Selecting previously unselected package libice6:arm64. 1027s Preparing to unpack .../059-libice6_2%3a1.1.1-1build1_arm64.deb ... 1027s Unpacking libice6:arm64 (2:1.1.1-1build1) ... 1027s Selecting previously unselected package libicu-dev:arm64. 1027s Preparing to unpack .../060-libicu-dev_78.2-1ubuntu1_arm64.deb ... 1027s Unpacking libicu-dev:arm64 (78.2-1ubuntu1) ... 1027s Selecting previously unselected package libjpeg-turbo8:arm64. 1027s Preparing to unpack .../061-libjpeg-turbo8_2.1.5-4ubuntu3_arm64.deb ... 1027s Unpacking libjpeg-turbo8:arm64 (2.1.5-4ubuntu3) ... 1027s Selecting previously unselected package libjpeg-turbo8-dev:arm64. 1027s Preparing to unpack .../062-libjpeg-turbo8-dev_2.1.5-4ubuntu3_arm64.deb ... 1027s Unpacking libjpeg-turbo8-dev:arm64 (2.1.5-4ubuntu3) ... 1027s Selecting previously unselected package libjpeg8:arm64. 1027s Preparing to unpack .../063-libjpeg8_8c-2ubuntu11_arm64.deb ... 1027s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 1027s Selecting previously unselected package libjpeg8-dev:arm64. 1027s Preparing to unpack .../064-libjpeg8-dev_8c-2ubuntu11_arm64.deb ... 1027s Unpacking libjpeg8-dev:arm64 (8c-2ubuntu11) ... 1027s Selecting previously unselected package libjpeg-dev:arm64. 1027s Preparing to unpack .../065-libjpeg-dev_8c-2ubuntu11_arm64.deb ... 1027s Unpacking libjpeg-dev:arm64 (8c-2ubuntu11) ... 1027s Selecting previously unselected package libjs-bootstrap. 1027s Preparing to unpack .../066-libjs-bootstrap_3.4.1+dfsg-6_all.deb ... 1027s Unpacking libjs-bootstrap (3.4.1+dfsg-6) ... 1028s Selecting previously unselected package libjs-highlight.js. 1028s Preparing to unpack .../067-libjs-highlight.js_10.7.3+dfsg-2_all.deb ... 1028s Unpacking libjs-highlight.js (10.7.3+dfsg-2) ... 1028s Selecting previously unselected package libjs-jquery. 1028s Preparing to unpack .../068-libjs-jquery_3.7.1+dfsg+~3.5.33-1build1_all.deb ... 1028s Unpacking libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 1028s Selecting previously unselected package libjs-jquery-datatables. 1028s Preparing to unpack .../069-libjs-jquery-datatables_1.11.5+dfsg-2build1_all.deb ... 1028s Unpacking libjs-jquery-datatables (1.11.5+dfsg-2build1) ... 1028s Selecting previously unselected package liblapack3:arm64. 1028s Preparing to unpack .../070-liblapack3_3.12.1-7ubuntu1_arm64.deb ... 1028s Unpacking liblapack3:arm64 (3.12.1-7ubuntu1) ... 1028s Selecting previously unselected package liblapack-dev:arm64. 1028s Preparing to unpack .../071-liblapack-dev_3.12.1-7ubuntu1_arm64.deb ... 1028s Unpacking liblapack-dev:arm64 (3.12.1-7ubuntu1) ... 1028s Selecting previously unselected package liblerc4:arm64. 1028s Preparing to unpack .../072-liblerc4_4.0.0+ds-5ubuntu2_arm64.deb ... 1028s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu2) ... 1028s Selecting previously unselected package 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unselected package libzstd-dev:arm64. 1029s Preparing to unpack .../099-libzstd-dev_1.5.7+dfsg-3_arm64.deb ... 1029s Unpacking libzstd-dev:arm64 (1.5.7+dfsg-3) ... 1029s Selecting previously unselected package node-normalize.css. 1029s Preparing to unpack .../100-node-normalize.css_8.0.1-5.1_all.deb ... 1029s Unpacking node-normalize.css (8.0.1-5.1) ... 1029s Selecting previously unselected package zip. 1030s Preparing to unpack .../101-zip_3.0-15ubuntu3_arm64.deb ... 1030s Unpacking zip (3.0-15ubuntu3) ... 1030s Selecting previously unselected package unzip. 1030s Preparing to unpack .../102-unzip_6.0-29ubuntu1_arm64.deb ... 1030s Unpacking unzip (6.0-29ubuntu1) ... 1030s Selecting previously unselected package xdg-utils. 1030s Preparing to unpack .../103-xdg-utils_1.2.1-2ubuntu2_all.deb ... 1030s Unpacking xdg-utils (1.2.1-2ubuntu2) ... 1030s Selecting previously unselected package r-base-core. 1030s Preparing to unpack .../104-r-base-core_4.5.2-1ubuntu2_arm64.deb ... 1030s Unpacking r-base-core (4.5.2-1ubuntu2) ... 1030s Selecting previously unselected package liblzma-dev:arm64. 1030s Preparing to unpack .../105-liblzma-dev_5.8.2-2_arm64.deb ... 1030s Unpacking liblzma-dev:arm64 (5.8.2-2) ... 1030s Selecting previously unselected package pkgconf-bin. 1030s Preparing to unpack .../106-pkgconf-bin_1.8.1-4build1_arm64.deb ... 1030s Unpacking pkgconf-bin (1.8.1-4build1) ... 1030s Selecting previously unselected package pkgconf:arm64. 1030s Preparing to unpack .../107-pkgconf_1.8.1-4build1_arm64.deb ... 1030s Unpacking pkgconf:arm64 (1.8.1-4build1) ... 1030s Selecting previously unselected package libtirpc-dev:arm64. 1030s Preparing to unpack .../108-libtirpc-dev_1.3.6+ds-1_arm64.deb ... 1030s Unpacking libtirpc-dev:arm64 (1.3.6+ds-1) ... 1030s Selecting previously unselected package r-base-dev. 1030s Preparing to unpack .../109-r-base-dev_4.5.2-1ubuntu2_all.deb ... 1030s Unpacking r-base-dev (4.5.2-1ubuntu2) ... 1030s Selecting previously unselected package pkg-r-autopkgtest. 1030s Preparing to unpack .../110-pkg-r-autopkgtest_20250812_all.deb ... 1030s Unpacking pkg-r-autopkgtest (20250812) ... 1030s Selecting previously unselected package r-cran-backports. 1030s Preparing to unpack .../111-r-cran-backports_1.5.0-2_arm64.deb ... 1030s Unpacking r-cran-backports (1.5.0-2) ... 1030s Selecting previously unselected package r-cran-boot. 1030s Preparing to unpack .../112-r-cran-boot_1.3-32-1_all.deb ... 1030s Unpacking r-cran-boot (1.3-32-1) ... 1030s Selecting previously unselected package r-cran-cli. 1030s Preparing to unpack .../113-r-cran-cli_3.6.4-1_arm64.deb ... 1030s Unpacking r-cran-cli (3.6.4-1) ... 1030s Selecting previously unselected package r-cran-generics. 1031s Preparing to unpack .../114-r-cran-generics_0.1.4-1_all.deb ... 1031s Unpacking r-cran-generics (0.1.4-1) ... 1031s Selecting previously unselected package r-cran-glue. 1031s Preparing to unpack .../115-r-cran-glue_1.8.0-1_arm64.deb ... 1031s Unpacking r-cran-glue (1.8.0-1) ... 1031s Selecting previously unselected package r-cran-rlang. 1031s Preparing to unpack .../116-r-cran-rlang_1.1.5-3_arm64.deb ... 1031s Unpacking r-cran-rlang (1.1.5-3) ... 1031s Selecting previously unselected package r-cran-lifecycle. 1031s Preparing to unpack .../117-r-cran-lifecycle_1.0.5+dfsg-1_all.deb ... 1031s Unpacking r-cran-lifecycle (1.0.5+dfsg-1) ... 1031s Selecting previously unselected package r-cran-magrittr. 1031s Preparing to unpack .../118-r-cran-magrittr_2.0.3-1_arm64.deb ... 1031s Unpacking r-cran-magrittr (2.0.3-1) ... 1031s Selecting previously unselected package r-cran-utf8. 1031s Preparing to unpack .../119-r-cran-utf8_1.2.4-1_arm64.deb ... 1031s Unpacking r-cran-utf8 (1.2.4-1) ... 1031s Selecting previously unselected package r-cran-vctrs. 1031s Preparing to unpack .../120-r-cran-vctrs_0.6.5-1_arm64.deb ... 1031s Unpacking r-cran-vctrs (0.6.5-1) ... 1031s Selecting previously unselected package r-cran-pillar. 1031s Preparing to unpack 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Selecting previously unselected package r-cran-tidyselect. 1031s Preparing to unpack .../127-r-cran-tidyselect_1.2.1+dfsg-1_arm64.deb ... 1031s Unpacking r-cran-tidyselect (1.2.1+dfsg-1) ... 1031s Selecting previously unselected package r-cran-dplyr. 1031s Preparing to unpack .../128-r-cran-dplyr_1.1.4-4_arm64.deb ... 1031s Unpacking r-cran-dplyr (1.1.4-4) ... 1031s Selecting previously unselected package r-cran-purrr. 1031s Preparing to unpack .../129-r-cran-purrr_1.0.4-1_arm64.deb ... 1031s Unpacking r-cran-purrr (1.0.4-1) ... 1031s Selecting previously unselected package r-cran-stringi. 1031s Preparing to unpack .../130-r-cran-stringi_1.8.4-1build2_arm64.deb ... 1031s Unpacking r-cran-stringi (1.8.4-1build2) ... 1031s Selecting previously unselected package r-cran-stringr. 1031s Preparing to unpack .../131-r-cran-stringr_1.5.1-1_all.deb ... 1031s Unpacking r-cran-stringr (1.5.1-1) ... 1031s Selecting previously unselected package r-cran-cpp11. 1032s Preparing to unpack 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1032s Selecting previously unselected package r-cran-s7. 1032s Preparing to unpack .../138-r-cran-s7_0.2.0-1_arm64.deb ... 1032s Unpacking r-cran-s7 (0.2.0-1) ... 1032s Selecting previously unselected package r-cran-farver. 1032s Preparing to unpack .../139-r-cran-farver_2.1.2-1_arm64.deb ... 1032s Unpacking r-cran-farver (2.1.2-1) ... 1032s Selecting previously unselected package r-cran-labeling. 1032s Preparing to unpack .../140-r-cran-labeling_0.4.3-1_all.deb ... 1032s Unpacking r-cran-labeling (0.4.3-1) ... 1032s Selecting previously unselected package r-cran-rcolorbrewer. 1032s Preparing to unpack .../141-r-cran-rcolorbrewer_1.1-3-1build2_all.deb ... 1032s Unpacking r-cran-rcolorbrewer (1.1-3-1build2) ... 1032s Selecting previously unselected package r-cran-viridislite. 1032s Preparing to unpack .../142-r-cran-viridislite_0.4.3-1_all.deb ... 1032s Unpacking r-cran-viridislite (0.4.3-1) ... 1032s Selecting previously unselected package r-cran-scales. 1032s Preparing to unpack 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Selecting previously unselected package r-cran-lattice. 1033s Preparing to unpack .../149-r-cran-lattice_0.22-7-1_arm64.deb ... 1033s Unpacking r-cran-lattice (0.22-7-1) ... 1033s Selecting previously unselected package r-cran-zoo. 1033s Preparing to unpack .../150-r-cran-zoo_1.8-15-1_arm64.deb ... 1033s Unpacking r-cran-zoo (1.8-15-1) ... 1033s Selecting previously unselected package r-cran-lmtest. 1033s Preparing to unpack .../151-r-cran-lmtest_0.9.40-1build1_arm64.deb ... 1033s Unpacking r-cran-lmtest (0.9.40-1build1) ... 1033s Selecting previously unselected package r-cran-nnet. 1033s Preparing to unpack .../152-r-cran-nnet_7.3-20-1_arm64.deb ... 1033s Unpacking r-cran-nnet (7.3-20-1) ... 1033s Selecting previously unselected package r-cran-littler. 1033s Preparing to unpack .../153-r-cran-littler_0.3.22-1_arm64.deb ... 1033s Unpacking r-cran-littler (0.3.22-1) ... 1033s Selecting previously unselected package r-cran-pkgkitten. 1033s Preparing to unpack .../154-r-cran-pkgkitten_0.2.4-1_all.deb ... 1033s Unpacking r-cran-pkgkitten (0.2.4-1) ... 1033s Selecting previously unselected package r-cran-rcpp. 1033s Preparing to unpack .../155-r-cran-rcpp_1.1.0-1_arm64.deb ... 1033s Unpacking r-cran-rcpp (1.1.0-1) ... 1033s Selecting previously unselected package r-cran-timedate. 1033s Preparing to unpack .../156-r-cran-timedate_4052.112-1_arm64.deb ... 1033s Unpacking r-cran-timedate (4052.112-1) ... 1033s Selecting previously unselected package r-cran-quadprog. 1033s Preparing to unpack .../157-r-cran-quadprog_1.5-8-1build2_arm64.deb ... 1033s Unpacking r-cran-quadprog (1.5-8-1build2) ... 1033s Selecting previously unselected package r-cran-xts. 1033s Preparing to unpack .../158-r-cran-xts_0.14.1-1_arm64.deb ... 1033s Unpacking r-cran-xts (0.14.1-1) ... 1033s Selecting previously unselected package r-cran-ttr. 1033s Preparing to unpack .../159-r-cran-ttr_0.24.4-1_arm64.deb ... 1033s Unpacking r-cran-ttr (0.24.4-1) ... 1033s Selecting previously unselected package r-cran-jsonlite. 1033s Preparing to unpack .../160-r-cran-jsonlite_1.9.1+dfsg-1_arm64.deb ... 1033s Unpacking r-cran-jsonlite (1.9.1+dfsg-1) ... 1033s Selecting previously unselected package r-cran-quantmod. 1033s Preparing to unpack .../161-r-cran-quantmod_0.4.28-1_all.deb ... 1033s Unpacking r-cran-quantmod (0.4.28-1) ... 1033s Selecting previously unselected package r-cran-tseries. 1033s Preparing to unpack .../162-r-cran-tseries_0.10-59-3_arm64.deb ... 1033s Unpacking r-cran-tseries (0.10-59-3) ... 1033s Selecting previously unselected package r-cran-nlme. 1033s Preparing to unpack .../163-r-cran-nlme_3.1.168-1_arm64.deb ... 1033s Unpacking r-cran-nlme (3.1.168-1) ... 1034s Selecting previously unselected package r-cran-urca. 1034s Preparing to unpack .../164-r-cran-urca_1.3-4-1build1_arm64.deb ... 1034s Unpacking r-cran-urca (1.3-4-1build1) ... 1034s Selecting previously unselected package r-cran-rcpparmadillo. 1034s Preparing to unpack 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Setting up libjs-bootstrap (3.4.1+dfsg-6) ... 1036s Setting up libitm1:arm64 (15.2.0-12ubuntu1) ... 1036s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 1036s Setting up cpp-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 1036s Setting up libice6:arm64 (2:1.1.1-1build1) ... 1036s Setting up liblapack3:arm64 (3.12.1-7ubuntu1) ... 1036s 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 1036s Setting up libgcc-15-dev:arm64 (15.2.0-12ubuntu1) ... 1036s Setting up fontconfig-config (2.17.1-3ubuntu1) ... 1037s Setting up libpaper-utils (2.2.5-0.3build1) ... 1037s Setting up libgfortran-15-dev:arm64 (15.2.0-12ubuntu1) ... 1037s Setting up libjs-jquery-datatables (1.11.5+dfsg-2build1) ... 1037s Setting up pkgconf:arm64 (1.8.1-4build1) ... 1037s Setting up libthai0:arm64 (0.1.30-1) ... 1037s Setting up cpp-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 1037s Setting up 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(8c-2ubuntu11) ... 1039s Setting up gcc (4:15.2.0-4ubuntu1) ... 1039s Setting up r-base-core (4.5.2-1ubuntu2) ... 1039s Creating config file /etc/R/Renviron with new version 1039s Setting up r-cran-labeling (0.4.3-1) ... 1039s Setting up r-cran-lattice (0.22-7-1) ... 1039s Setting up r-cran-nlme (3.1.168-1) ... 1039s Setting up r-cran-farver (2.1.2-1) ... 1039s Setting up r-cran-viridislite (0.4.3-1) ... 1039s Setting up r-cran-statmod (1.5.0-1) ... 1039s Setting up g++-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 1039s Setting up r-cran-nnet (7.3-20-1) ... 1039s Setting up gfortran-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 1039s Setting up r-cran-r6 (2.6.1-1) ... 1039s Setting up r-cran-pkgkitten (0.2.4-1) ... 1039s Setting up r-cran-numderiv (2016.8-1.1-3build1) ... 1039s Setting up r-cran-magrittr (2.0.3-1) ... 1039s Setting up r-cran-microbenchmark (1.5.0-1) ... 1039s Setting up r-cran-quadprog (1.5-8-1build2) ... 1039s Setting up r-cran-littler (0.3.22-1) ... 1039s Setting up 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to provide /usr/bin/f95 (f95) in auto mode 1039s 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 1039s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 1039s 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 1039s Setting up r-cran-rbibutils (2.3-1) ... 1039s Setting up r-cran-lifecycle (1.0.5+dfsg-1) ... 1039s Setting up r-cran-jsonlite (1.9.1+dfsg-1) ... 1039s Setting up r-cran-pkgconfig (2.0.3-2build2) ... 1039s Setting up r-cran-utf8 (1.2.4-1) ... 1039s Setting up r-cran-colorspace (2.1-1+dfsg-1) ... 1039s Setting up r-cran-stringi (1.8.4-1build2) ... 1039s Setting up r-cran-s7 (0.2.0-1) ... 1039s Setting up r-cran-cpp11 (0.5.3-1) ... 1039s Setting up r-cran-rcolorbrewer (1.1-3-1build2) ... 1039s Setting up r-cran-isoband (0.2.7-1) ... 1039s Setting up r-cran-scales (1.4.0-1) ... 1039s Setting up r-cran-gtable (0.3.6+dfsg-1) ... 1039s Setting up r-cran-zoo (1.8-15-1) ... 1039s Setting up r-cran-matrix (1.7-4-1) ... 1039s Setting up r-cran-knitr (1.51+dfsg-1) ... 1039s Setting up g++ (4:15.2.0-4ubuntu1) ... 1039s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 1039s Setting up r-cran-lmtest (0.9.40-1build1) ... 1039s Setting up build-essential (12.12ubuntu2) ... 1039s Setting up r-cran-rcpparmadillo (15.2.3-1-1) ... 1039s Setting up r-cran-vctrs (0.6.5-1) ... 1039s Setting up r-cran-rcppeigen (0.3.4.0.2-1) ... 1039s Setting up r-cran-pillar (1.11.1+dfsg-1) ... 1039s Setting up r-cran-minqa (1.2.8-1) ... 1039s Setting up r-base-dev (4.5.2-1ubuntu2) ... 1039s Setting up r-cran-stringr (1.5.1-1) ... 1039s Setting up r-cran-ggplot2 (4.0.2+dfsg-1) ... 1039s Setting up r-cran-tibble (3.2.1+dfsg-3) ... 1039s Setting up r-cran-xts (0.14.1-1) ... 1039s Setting up r-cran-rdpack (2.6.3-1) ... 1039s Setting up r-cran-tidyselect (1.2.1+dfsg-1) ... 1039s Setting up r-cran-purrr (1.0.4-1) ... 1039s Setting up pkg-r-autopkgtest (20250812) ... 1039s Setting up r-cran-dplyr (1.1.4-4) ... 1039s Setting up r-cran-reformulas (0.4.4-1) ... 1039s Setting up r-cran-ttr (0.24.4-1) ... 1039s Setting up r-cran-cowplot (1.1.3+dfsg-1) ... 1039s Setting up r-cran-lme4 (1.1-38-1) ... 1039s Setting up r-cran-lmertest (3.2-0-1) ... 1039s Setting up r-cran-tidyr (1.3.1-1) ... 1039s Setting up r-cran-quantmod (0.4.28-1) ... 1039s Setting up r-cran-tseries (0.10-59-3) ... 1039s Setting up r-cran-broom (1.0.12+dfsg-1) ... 1039s Setting up r-cran-forecast (8.23.0-1) ... 1039s Setting up r-cran-modelr (0.1.11-1) ... 1039s Setting up r-cran-doby (4.7.1-3) ... 1039s Setting up r-cran-pbkrtest (0.5.5-1) ... 1039s Processing triggers for libc-bin (2.42-2ubuntu4) ... 1039s Processing triggers for man-db (2.13.1-1build1) ... 1040s Processing triggers for install-info (7.2-5) ... 1042s autopkgtest [00:09:06]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 1042s autopkgtest [00:09:06]: test pkg-r-autopkgtest: [----------------------- 1042s Test: Try to load the R library lmerTest 1042s 1042s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 1042s Copyright (C) 2025 The R Foundation for Statistical Computing 1042s Platform: aarch64-unknown-linux-gnu 1042s 1042s R is free software and comes with ABSOLUTELY NO WARRANTY. 1042s You are welcome to redistribute it under certain conditions. 1042s Type 'license()' or 'licence()' for distribution details. 1042s 1042s R is a collaborative project with many contributors. 1042s Type 'contributors()' for more information and 1042s 'citation()' on how to cite R or R packages in publications. 1042s 1042s Type 'demo()' for some demos, 'help()' for on-line help, or 1042s 'help.start()' for an HTML browser interface to help. 1042s Type 'q()' to quit R. 1042s 1042s > library('lmerTest') 1042s Loading required package: lme4 1042s Loading required package: Matrix 1044s 1044s Attaching package: ‘lmerTest’ 1044s 1044s The following object is masked from ‘package:lme4’: 1044s 1044s lmer 1044s 1044s The following object is masked from ‘package:stats’: 1044s 1044s step 1044s 1044s > 1045s autopkgtest [00:09:09]: test pkg-r-autopkgtest: -----------------------] 1045s pkg-r-autopkgtest PASS 1045s autopkgtest [00:09:09]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 1045s autopkgtest [00:09:09]: @@@@@@@@@@@@@@@@@@@@ summary 1045s run-unit-test PASS 1045s pkg-r-autopkgtest PASS