<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Dear all,<div class=""><br class=""></div><div class="">This is currently being fixed and a new version of lmerTest is on its way to CRAN, cf. <a href="https://cran.r-project.org/package=lmerTest" class="">https://cran.r-project.org/package=lmerTest</a></div><div class=""><br class=""></div><div class="">The latest version of lme4 was released to CRAN without our knowledge and that version caused lmerTest to fail its tests on most platforms (mostly because the new default optimiser is much less accurate than the old default optimiser, cf. <a href="https://github.com/lme4/lme4/issues/501" class="">https://github.com/lme4/lme4/issues/501</a>). After being notified of the problems we have updated lmerTest as soon as possible. </div><div class=""><br class=""></div><div class="">BR</div><div class="">Rune<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On 11 Feb 2019, at 07.39, Per B. Brockhoff <<a href="mailto:perbb@dtu.dk" class="">perbb@dtu.dk</a>> wrote:</div><div class=""><div dir="auto" class=""><div class=""><br class="">
<div dir="ltr" class="">Sendt fra min iPhone</div>
<div dir="ltr" class=""><br class="">
Start på videresendt besked:<br class="">
<br class="">
</div>
<blockquote type="cite" class="">
<div dir="ltr" class=""><b class="">Fra:</b> Andreas Tille <<a href="mailto:tille@debian.org" class="">tille@debian.org</a>><br class="">
<b class="">Dato:</b> 10. februar 2019 kl. 16.07.12 CET<br class="">
<b class="">Til:</b> Paul Gevers <<a href="mailto:elbrus@debian.org" class="">elbrus@debian.org</a>>, <<a href="mailto:921938@bugs.debian.org" class="">921938@bugs.debian.org</a>>, "Per Bruun Brockhoff" <<a href="mailto:perbb@dtu.dk" class="">perbb@dtu.dk</a>><br class="">
<b class="">Emne:</b> <b class="">Vedr.: Bug#921938: lme4 breaks r-cran-lmertest autopkgtest</b><br class="">
<br class="">
</div>
</blockquote>
<blockquote type="cite" class="">
<div dir="ltr" class=""><span class="">Hi again,</span><br class="">
<span class=""></span><br class="">
<span class="">may be you get all the relevant information directly from CRAN:</span><br class="">
<span class=""></span><br class="">
<span class=""> <a href="https://cloud.r-project.org/web/checks/check_results_lmerTest.html" class="">https://cloud.r-project.org/web/checks/check_results_lmerTest.html</a></span><br class="">
<span class=""></span><br class="">
<span class="">Kind regards</span><br class="">
<span class=""></span><br class="">
<span class=""> Andreas.</span><br class="">
<span class=""></span><br class="">
<span class="">On Sun, Feb 10, 2019 at 03:44:55PM +0100, Andreas Tille wrote:</span><br class="">
<blockquote type="cite" class=""><span class="">Control: tags -1 help upstream</span><br class="">
</blockquote>
<blockquote type="cite" class=""><span class="">Control: forwarded -1 Per Bruun Brockhoff <<a href="mailto:perbb@dtu.dk" class="">perbb@dtu.dk</a>></span><br class="">
</blockquote>
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
<blockquote type="cite" class=""><span class="">Hi Per,</span><br class="">
</blockquote>
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
<blockquote type="cite" class=""><span class="">the Debian packaged version of lmerTest seems to show issues with the</span><br class="">
</blockquote>
<blockquote type="cite" class=""><span class="">latest version of lme4. From your insight into lmerTest can you give</span><br class="">
</blockquote>
<blockquote type="cite" class=""><span class="">some hint about possible reasons for this incompatibility?</span><br class="">
</blockquote>
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
<blockquote type="cite" class=""><span class="">Kind regards</span><br class="">
</blockquote>
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
<blockquote type="cite" class=""><span class=""> Andreas.</span><br class="">
</blockquote>
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
<blockquote type="cite" class=""><span class="">PS: Please let me know whether you need further information.</span><br class="">
</blockquote>
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
<blockquote type="cite" class=""><span class="">On Sun, Feb 10, 2019 at 01:35:53PM +0100, Paul Gevers wrote:</span><br class="">
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Source: lme4, r-cran-lmertest</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Control: found -1 lme4/1.1-20-1</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Control: found -1 r-cran-lmertest/3.0-1-2</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Severity: important</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">X-Debbugs-CC: <a href="mailto:debian-ci@lists.debian.org" class="">
debian-ci@lists.debian.org</a></span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">User: <a href="mailto:debian-ci@lists.debian.org" class="">debian-ci@lists.debian.org</a></span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Usertags: breaks needs-update</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Dear maintainers,</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">With a recent upload of lme4 the autopkgtest of r-cran-lmertest fails in</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">testing when that autopkgtest is run with the binary packages of lme4</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">from unstable. It passes when run with only packages from testing. In</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">tabular form:</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> pass fail</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">lme4 from testing 1.1-20-1</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">r-cran-lmertest from testing 3.0-1-2</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">all others from testing from testing</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">I copied some of the output at the bottom of this report.</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Currently this regression is blocking the migration of lme4 to testing</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">[1]. Due to the nature of this issue, I filed this bug report against</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">both packages. Can you please investigate the situation and reassign the</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">bug to the right package? If needed, please change the bug's severity.</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">More information about this bug and the reason for filing it can be found on</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""><a href="https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation" class="">https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation</a></span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Paul</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">[1] <a href="https://qa.debian.org/excuses.php?package=lme4" class="">
https://qa.debian.org/excuses.php?package=lme4</a></span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""><a href="https://ci.debian.net/data/autopkgtest/testing/amd64/r/r-cran-lmertest/1896879/log.gz" class="">https://ci.debian.net/data/autopkgtest/testing/amd64/r/r-cran-lmertest/1896879/log.gz</a></span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">autopkgtest [04:42:34]: test run-unit-test: [-----------------------</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">BEGIN TEST test_a_utils.R</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">R version 3.5.2 (2018-12-20) -- "Eggshell Igloo"</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Copyright (C) 2018 The R Foundation for Statistical Computing</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Platform: x86_64-pc-linux-gnu (64-bit)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">R is free software and comes with ABSOLUTELY NO WARRANTY.</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">You are welcome to redistribute it under certain conditions.</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Type 'license()' or 'licence()' for distribution details.</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">R is a collaborative project with many contributors.</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Type 'contributors()' for more information and</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">'citation()' on how to cite R or R packages in publications.</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Type 'demo()' for some demos, 'help()' for on-line help, or</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">'help.start()' for an HTML browser interface to help.</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Type 'q()' to quit R.</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""># test_a_utils.R</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">library(lmerTest)</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Loading required package: lme4</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Loading required package: Matrix</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Attaching package: 'lmerTest'</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">The following object is masked from 'package:lme4':</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> lmer</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">The following object is masked from 'package:stats':</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> step</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""># test safeDeparse() - equivalence and differences to deparse():</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">deparse_args <- formals(deparse)</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">safeDeparse_args <- formals(lmerTest:::safeDeparse)</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">stopifnot(</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ all.equal(names(deparse_args), names(safeDeparse_args)),</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ all.equal(deparse_args[!names(deparse_args) %in% c("control",</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">"width.cutoff")],</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ safeDeparse_args[!names(safeDeparse_args) %in%</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">c("control", "width.cutoff")]),</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ all.equal(deparse_args[["width.cutoff"]], 60L),</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ all(eval(safeDeparse_args[["control"]]) %in%</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">eval(deparse_args[["control"]])),</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ all.equal(safeDeparse_args[["width.cutoff"]], 500L)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ )</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">BEGIN TEST test_anova.R</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">R version 3.5.2 (2018-12-20) -- "Eggshell Igloo"</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Copyright (C) 2018 The R Foundation for Statistical Computing</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Platform: x86_64-pc-linux-gnu (64-bit)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">R is free software and comes with ABSOLUTELY NO WARRANTY.</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">You are welcome to redistribute it under certain conditions.</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Type 'license()' or 'licence()' for distribution details.</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">R is a collaborative project with many contributors.</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Type 'contributors()' for more information and</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">'citation()' on how to cite R or R packages in publications.</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Type 'demo()' for some demos, 'help()' for on-line help, or</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">'help.start()' for an HTML browser interface to help.</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Type 'q()' to quit R.</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""># test_anova.R</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">library(lmerTest)</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Loading required package: lme4</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Loading required package: Matrix</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Attaching package: 'lmerTest'</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">The following object is masked from 'package:lme4':</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> lmer</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">The following object is masked from 'package:stats':</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> step</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""># WRE says "using if(requireNamespace("pkgname")) is preferred, if</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">possible."</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""># even in tests:</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">assertError <- function(expr, ...)</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ if(requireNamespace("tools")) tools::assertError(expr, ...) else</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">invisible()</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">assertWarning <- function(expr, ...)</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ if(requireNamespace("tools")) tools::assertWarning(expr, ...) else</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">invisible()</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""># Kenward-Roger only available with pbkrtest and only then validated</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">in R >= 3.3.3</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""># (faulty results for R < 3.3.3 may be due to unstated dependencies in</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">pbkrtest)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">has_pbkrtest <- requireNamespace("pbkrtest", quietly = TRUE) &&</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">getRversion() >= "3.3.3"</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">data("sleepstudy", package="lme4")</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">TOL <- 1e-4</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">####################################</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">## Basic anova tests</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">####################################</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">m <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy)</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">####### ddf argument:</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">(an1 <- anova(m)) # Also testing print method.</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Type III Analysis of Variance Table with Satterthwaite's method</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Sum Sq Mean Sq NumDF DenDF F value Pr(>F)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Days 30024 30024 1 16.995 45.843 3.273e-06 ***</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">---</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">(an2 <- anova(m, ddf="Satterthwaite"))</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Type III Analysis of Variance Table with Satterthwaite's method</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Sum Sq Mean Sq NumDF DenDF F value Pr(>F)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Days 30024 30024 1 16.995 45.843 3.273e-06 ***</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">---</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">(an2b <- anova(m, ddf="Satterthwaite", type=3))</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Type III Analysis of Variance Table with Satterthwaite's method</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Sum Sq Mean Sq NumDF DenDF F value Pr(>F)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Days 30024 30024 1 16.995 45.843 3.273e-06 ***</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">---</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">(an2c <- anova(m, ddf="Satterthwaite", type=2))</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Type II Analysis of Variance Table with Satterthwaite's method</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Sum Sq Mean Sq NumDF DenDF F value Pr(>F)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Days 30024 30024 1 16.995 45.843 3.273e-06 ***</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">---</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">stopifnot(isTRUE(</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ all.equal(an1, an2, tolerance=TOL)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ ))</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">(an3 <- anova(m, ddf="Sat")) ## Abbreviated argument</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Type III Analysis of Variance Table with Satterthwaite's method</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Sum Sq Mean Sq NumDF DenDF F value Pr(>F)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Days 30024 30024 1 16.995 45.843 3.273e-06 ***</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">---</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">stopifnot(isTRUE(</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ all.equal(an1, an3, tolerance=TOL)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ ))</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">if(has_pbkrtest) {</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ (anova(m, ddf="Kenward-Roger"))</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ (anova(m, ddf="Kenward-Roger", type=3))</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ }</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Type III Analysis of Variance Table with Kenward-Roger's method</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Sum Sq Mean Sq NumDF DenDF F value Pr(>F)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Days 30024 30024 1 17 45.843 3.268e-06 ***</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">---</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">(an1 <- anova(m, ddf="lme4"))</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Analysis of Variance Table</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Df Sum Sq Mean Sq F value</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Days 1 30024 30024 45.843</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">(an2 <- anova(m, ddf="lme4", type=3)) # 'type' is ignored with ddf="lme4"</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Analysis of Variance Table</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Df Sum Sq Mean Sq F value</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Days 1 30024 30024 45.843</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">stopifnot(isTRUE(</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ all.equal(an1, an2, tolerance=TOL)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ ))</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">res <- assertError(anova(m, ddf="KR")) ## Error on incorrect arg.</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">stopifnot(</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ grepl("'arg' should be one of ", unlist(res[[1]])$message)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ )</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">## lme4 method:</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">an1 <- anova(m, ddf="lme4")</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">an2 <- anova(as(m, "lmerMod"))</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">stopifnot(isTRUE(</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ all.equal(an1, an2, tolerance=TOL)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ ))</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">###### type argument:</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">(an1 <- anova(m, type="1")) # valid type arg.</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Type I Analysis of Variance Table with Satterthwaite's method</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Sum Sq Mean Sq NumDF DenDF F value Pr(>F)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Days 30024 30024 1 16.995 45.843 3.273e-06 ***</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">---</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">(an2 <- anova(m, type="I")) # same</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Type I Analysis of Variance Table with Satterthwaite's method</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Sum Sq Mean Sq NumDF DenDF F value Pr(>F)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Days 30024 30024 1 16.995 45.843 3.273e-06 ***</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">---</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">stopifnot(isTRUE(</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ all.equal(an1, an2, tolerance=TOL)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ ))</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">(an3 <- anova(m, type=1)) # Not strictly valid, but accepted</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Type I Analysis of Variance Table with Satterthwaite's method</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Sum Sq Mean Sq NumDF DenDF F value Pr(>F)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Days 30024 30024 1 16.995 45.843 3.273e-06 ***</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">---</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">stopifnot(isTRUE(</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ all.equal(an1, an3, tolerance=TOL)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ ))</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">(an1 <- anova(m, type="2")) # valid type arg.</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Type II Analysis of Variance Table with Satterthwaite's method</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Sum Sq Mean Sq NumDF DenDF F value Pr(>F)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Days 30024 30024 1 16.995 45.843 3.273e-06 ***</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">---</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">(an2 <- anova(m, type="II")) # same</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Type II Analysis of Variance Table with Satterthwaite's method</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Sum Sq Mean Sq NumDF DenDF F value Pr(>F)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Days 30024 30024 1 16.995 45.843 3.273e-06 ***</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">---</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">stopifnot(isTRUE(</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ all.equal(an1, an2, tolerance=TOL)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ ))</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">(an3 <- anova(m, type=3)) # Not strictly valid, but accepted</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Type III Analysis of Variance Table with Satterthwaite's method</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Sum Sq Mean Sq NumDF DenDF F value Pr(>F)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Days 30024 30024 1 16.995 45.843 3.273e-06 ***</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">---</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">stopifnot(isTRUE(</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ all.equal(an1, an3, check.attributes=FALSE, tolerance=TOL)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ ))</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">(an1 <- anova(m, type="3")) # valid type arg.</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Type III Analysis of Variance Table with Satterthwaite's method</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Sum Sq Mean Sq NumDF DenDF F value Pr(>F)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Days 30024 30024 1 16.995 45.843 3.273e-06 ***</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">---</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">(an2 <- anova(m, type="III")) # same</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Type III Analysis of Variance Table with Satterthwaite's method</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Sum Sq Mean Sq NumDF DenDF F value Pr(>F)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Days 30024 30024 1 16.995 45.843 3.273e-06 ***</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">---</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">stopifnot(isTRUE(</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ all.equal(an1, an2, tolerance=TOL)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ ))</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">(an3 <- anova(m, type=3)) # Not strictly valid, but accepted</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Type III Analysis of Variance Table with Satterthwaite's method</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Sum Sq Mean Sq NumDF DenDF F value Pr(>F)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Days 30024 30024 1 16.995 45.843 3.273e-06 ***</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">---</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">stopifnot(isTRUE(</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ all.equal(an1, an3, tolerance=TOL)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ ))</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">assertError(anova(m, type=0)) # Not valid arg.</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">assertError(anova(m, type="i")) # Not valid arg.</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">####### Model comparison:</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">fm <- lm(Reaction ~ Days, sleepstudy)</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">(an <- anova(m, fm))</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">refitting model(s) with ML (instead of REML)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Data: sleepstudy</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Models:</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">fm: Reaction ~ Days</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">m: Reaction ~ Days + (Days | Subject)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Df AIC BIC logLik deviance Chisq Chi Df Pr(>Chisq)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">fm 3 1906.3 1915.9 -950.15 1900.3</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">m 6 1763.9 1783.1 -875.97 1751.9 148.35 3 < 2.2e-16 ***</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">---</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">stopifnot(</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ nrow(an) == 2L,</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ rownames(an)[2] == "m"</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ )</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">m2 <- lmer(Reaction ~ Days + I(Days^2) + (Days | Subject), sleepstudy)</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">(an <- anova(m, m2, refit=FALSE))</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Data: sleepstudy</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Models:</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">m: Reaction ~ Days + (Days | Subject)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">m2: Reaction ~ Days + I(Days^2) + (Days | Subject)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Df AIC BIC logLik deviance Chisq Chi Df Pr(>Chisq)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">m 6 1755.6 1774.8 -871.81 1743.6</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">m2 7 1756.8 1779.2 -871.41 1742.8 0.8127 1 0.3673</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">stopifnot(</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ nrow(an) == 2L,</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ rownames(an)[1] == "m"</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ )</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">####################################</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">## Example with factor fixef:</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">####################################</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">## 'temp' is continuous, 'temperature' an ordered factor with 6 levels</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">data("cake", package="lme4")</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">m <- lmer(angle ~ recipe * temp + (1|recipe:replicate), cake)</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">(an <- anova(m))</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Type III Analysis of Variance Table with Satterthwaite's method</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Sum Sq Mean Sq NumDF DenDF F value Pr(>F)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">recipe 4.00 2.00 2 254.02 0.0957 0.9088</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">temp 1966.71 1966.71 1 222.00 94.1632 <2e-16 ***</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">recipe:temp 1.74 0.87 2 222.00 0.0417 0.9592</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">---</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">(an_lme4 <- anova(m, ddf="lme4"))</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Analysis of Variance Table</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Df Sum Sq Mean Sq F value</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">recipe 2 10.39 5.20 0.2488</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">temp 1 1966.71 1966.71 94.1632</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">recipe:temp 2 1.74 0.87 0.0417</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">if(has_pbkrtest) {</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ (an_KR <- anova(m, ddf="Kenward-Roger"))</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ # res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")],</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ # an_lme4[, c("Sum Sq", "Mean Sq", "F value")])</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ # stopifnot(isTRUE(res))</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")],</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ an_KR[, c("Sum Sq", "Mean Sq", "F value")],</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">tolerance=TOL)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ stopifnot(isTRUE(res))</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ }</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">stopifnot(all.equal(c(2, 1, 2), an$NumDF, tol=1e-6),</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ all.equal(c(254.0157612, 222, 222), an$DenDF, tol=TOL))</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">an3 <- anova(m, type=3)</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">an2 <- anova(m, type=2)</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">an1 <- anova(m, type=1)</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">## Data is balanced, so Type II and III should be identical:</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">## One variable is continuous, so Type I and II/III are different:</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">stopifnot(</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ isTRUE(all.equal(an3, an2, check.attributes=FALSE, tolerance=TOL)),</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ !isTRUE(all.equal(an1, an2, check.attributes=FALSE, tolerance=1e-8))</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ )</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""># Using an ordered factor:</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">m <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake)</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">(an1 <- anova(m, type=1))</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Type I Analysis of Variance Table with Satterthwaite's method</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Sum Sq Mean Sq NumDF DenDF F value Pr(>F)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">recipe 10.19 5.09 2 42 0.2488 0.7809</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">temperature 2100.30 420.06 5 210 20.5199 <2e-16 ***</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">recipe:temperature 205.98 20.60 10 210 1.0062 0.4393</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">---</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">(an2 <- anova(m, type=2))</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Type II Analysis of Variance Table with Satterthwaite's method</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Sum Sq Mean Sq NumDF DenDF F value Pr(>F)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">recipe 10.19 5.09 2 42 0.2488 0.7809</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">temperature 2100.30 420.06 5 210 20.5199 <2e-16 ***</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">recipe:temperature 205.98 20.60 10 210 1.0062 0.4393</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">---</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""># Type 3 is also available with ordered factors:</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">(an3 <- anova(m, type=3))</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Type III Analysis of Variance Table with Satterthwaite's method</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Sum Sq Mean Sq NumDF DenDF F value Pr(>F)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">recipe 10.19 5.09 2 42 0.2488 0.7809</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">temperature 2100.30 420.06 5 210 20.5199 <2e-16 ***</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">recipe:temperature 205.98 20.60 10 210 1.0062 0.4393</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">---</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">## Balanced data and only factors: Type I, II and III should be the same:</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">stopifnot(</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ isTRUE(all.equal(an1, an2, check.attributes=FALSE, tolerance=TOL)),</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ isTRUE(all.equal(an1, an3, check.attributes=FALSE, tolerance=TOL))</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ )</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">(an <- anova(m, type=1))</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Type I Analysis of Variance Table with Satterthwaite's method</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Sum Sq Mean Sq NumDF DenDF F value Pr(>F)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">recipe 10.19 5.09 2 42 0.2488 0.7809</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">temperature 2100.30 420.06 5 210 20.5199 <2e-16 ***</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">recipe:temperature 205.98 20.60 10 210 1.0062 0.4393</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">---</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">(an_lme4 <- anova(m, type=1, ddf="lme4"))</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Analysis of Variance Table</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Df Sum Sq Mean Sq F value</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">recipe 2 10.19 5.09 0.2488</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">temperature 5 2100.30 420.06 20.5199</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">recipe:temperature 10 205.98 20.60 1.0062</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")],</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ an_lme4[, c("Sum Sq", "Mean Sq", "F value")],</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">tolerance=TOL)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">stopifnot(isTRUE(res))</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">if(has_pbkrtest) {</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ (an_KR <- anova(m, type=1, ddf="Kenward-Roger"))</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")],</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ an_KR[, c("Sum Sq", "Mean Sq", "F value")],</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">tolerance=TOL)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ stopifnot(isTRUE(res))</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ }</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">stopifnot(all.equal(c(2, 5, 10), an$NumDF, tolerance=TOL),</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ all.equal(c(42, 210, 210), an$DenDF, tolerance=TOL))</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">########</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">## Make case with balanced unordered factors:</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">cake2 <- cake</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">cake2$temperature <- factor(cake2$temperature, ordered = FALSE)</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""># str(cake2)</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">stopifnot(</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ !is.ordered(cake2$temperature)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ )</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">m <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake2)</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">(an1 <- anova(m, type=1))</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Type I Analysis of Variance Table with Satterthwaite's method</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Sum Sq Mean Sq NumDF DenDF F value Pr(>F)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">recipe 10.19 5.09 2 42 0.2488 0.7809</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">temperature 2100.30 420.06 5 210 20.5199 <2e-16 ***</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">recipe:temperature 205.98 20.60 10 210 1.0062 0.4393</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">---</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">(an2 <- anova(m, type=2))</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Type II Analysis of Variance Table with Satterthwaite's method</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Sum Sq Mean Sq NumDF DenDF F value Pr(>F)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">recipe 10.19 5.09 2 42 0.2488 0.7809</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">temperature 2100.30 420.06 5 210 20.5199 <2e-16 ***</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">recipe:temperature 205.98 20.60 10 210 1.0062 0.4393</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">---</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">(an3 <- anova(m, type=3))</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Type III Analysis of Variance Table with Satterthwaite's method</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Sum Sq Mean Sq NumDF DenDF F value Pr(>F)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">recipe 10.19 5.09 2 42 0.2488 0.7809</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">temperature 2100.30 420.06 5 210 20.5199 <2e-16 ***</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">recipe:temperature 205.98 20.60 10 210 1.0062 0.4393</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">---</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">## Balanced data and only factors: Type I, II, and III should be the same:</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">stopifnot(</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ isTRUE(all.equal(an1, an2, check.attributes=FALSE, tolerance=TOL)),</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ isTRUE(all.equal(an3, an2, check.attributes=FALSE, tolerance=TOL))</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ )</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">########</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""># No intercept:</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">m <- lmer(angle ~ 0 + recipe * temp + (1|recipe:replicate), cake)</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">(an <- anova(m, type=1))</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Type I Analysis of Variance Table with Satterthwaite's method</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Sum Sq Mean Sq NumDF DenDF F value Pr(>F)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">recipe 21442.9 7147.6 3 42 342.2200 <2e-16 ***</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">temp 1966.7 1966.7 1 222 94.1632 <2e-16 ***</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">recipe:temp 1.7 0.9 2 222 0.0417 0.9592</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">---</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">(an2 <- anova(m, type=2))</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Type II Analysis of Variance Table with Satterthwaite's method</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Sum Sq Mean Sq NumDF DenDF F value Pr(>F)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">recipe 4.48 1.49 3 254.02 0.0714 0.9752</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">temp 1966.71 1966.71 1 222.00 94.1632 <2e-16 ***</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">recipe:temp 1.74 0.87 2 222.00 0.0417 0.9592</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">---</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">(an2 <- anova(m, type=3))</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Type III Analysis of Variance Table with Satterthwaite's method</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Sum Sq Mean Sq NumDF DenDF F value Pr(>F)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">recipe 4.48 1.49 3 254.02 0.0714 0.9752</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">temp 1966.71 1966.71 1 222.00 94.1632 <2e-16 ***</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">recipe:temp 1.74 0.87 2 222.00 0.0417 0.9592</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">---</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">if(has_pbkrtest)</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ (an_KR <- anova(m, ddf="Kenward-Roger"))</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Type III Analysis of Variance Table with Kenward-Roger's method</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Sum Sq Mean Sq NumDF DenDF F value Pr(>F)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">recipe 4.48 1.49 3 254.02 0.0714 0.9752</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">temp 1966.71 1966.71 1 222.00 94.1632 <2e-16 ***</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">recipe:temp 1.74 0.87 2 222.00 0.0417 0.9592</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">---</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">(an_lme4 <- anova(m, ddf="lme4"))</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Analysis of Variance Table</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Df Sum Sq Mean Sq F value</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">recipe 3 21442.9 7147.6 342.2200</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">temp 1 1966.7 1966.7 94.1632</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">recipe:temp 2 1.7 0.9 0.0417</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")],</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ an_lme4[, c("Sum Sq", "Mean Sq", "F value")],</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">tolerance=TOL)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">stopifnot(isTRUE(res))</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""># ML-fit:</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">m <- lmer(angle ~ recipe * temp + (1|recipe:replicate), cake, REML=FALSE)</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">(an <- anova(m, type=1))</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Type I Analysis of Variance Table with Satterthwaite's method</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Sum Sq Mean Sq NumDF DenDF F value Pr(>F)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">recipe 10.99 5.49 2 45 0.2666 0.7672</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">temp 1966.71 1966.71 1 225 95.4357 <2e-16 ***</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">recipe:temp 1.74 0.87 2 225 0.0423 0.9586</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">---</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">if(has_pbkrtest)</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ assertError(an <- anova(m, ddf="Kenward-Roger")) # KR fits should be</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">REML</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">(an_lme4 <- anova(m, ddf="lme4"))</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Analysis of Variance Table</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Df Sum Sq Mean Sq F value</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">recipe 2 10.99 5.49 0.2666</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">temp 1 1966.71 1966.71 95.4357</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">recipe:temp 2 1.74 0.87 0.0423</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")],</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ an_lme4[, c("Sum Sq", "Mean Sq", "F value")],</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">tolerance=TOL)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">stopifnot(isTRUE(res))</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">####################################</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">## Using contr.sum:</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">####################################</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">m <- lmer(angle ~ recipe * temp + (1|recipe:replicate), cake,</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ contrasts = list('recipe' = "contr.sum"))</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">(an <- anova(m, type=1))</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Type I Analysis of Variance Table with Satterthwaite's method</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Sum Sq Mean Sq NumDF DenDF F value Pr(>F)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">recipe 10.39 5.20 2 42 0.2488 0.7809</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">temp 1966.71 1966.71 1 222 94.1632 <2e-16 ***</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">recipe:temp 1.74 0.87 2 222 0.0417 0.9592</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">---</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">(an2 <- anova(m, type=2))</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Type II Analysis of Variance Table with Satterthwaite's method</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Sum Sq Mean Sq NumDF DenDF F value Pr(>F)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">recipe 4.00 2.00 2 254.02 0.0957 0.9088</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">temp 1966.71 1966.71 1 222.00 94.1632 <2e-16 ***</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">recipe:temp 1.74 0.87 2 222.00 0.0417 0.9592</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">---</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">(an3 <- anova(m, type=3))</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Type III Analysis of Variance Table with Satterthwaite's method</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Sum Sq Mean Sq NumDF DenDF F value Pr(>F)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">recipe 4.00 2.00 2 254.02 0.0957 0.9088</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">temp 1966.71 1966.71 1 222.00 94.1632 <2e-16 ***</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">recipe:temp 1.74 0.87 2 222.00 0.0417 0.9592</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">---</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">stopifnot(</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ isTRUE(all.equal(an2, an3, check.attributes=FALSE, tolerance=TOL))</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ )</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">if(has_pbkrtest)</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ (an_KR <- anova(m, type=1, ddf="Kenward-Roger"))</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Type I Analysis of Variance Table with Kenward-Roger's method</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Sum Sq Mean Sq NumDF DenDF F value Pr(>F)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">recipe 10.39 5.20 2 42 0.2488 0.7809</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">temp 1966.71 1966.71 1 222 94.1632 <2e-16 ***</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">recipe:temp 1.74 0.87 2 222 0.0417 0.9592</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">---</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">(an_lme4 <- anova(m, ddf="lme4"))</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Analysis of Variance Table</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Df Sum Sq Mean Sq F value</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">recipe 2 10.39 5.20 0.2488</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">temp 1 1966.71 1966.71 94.1632</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">recipe:temp 2 1.74 0.87 0.0417</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")],</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ an_lme4[, c("Sum Sq", "Mean Sq", "F value")],</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">tolerance=TOL)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">stopifnot(isTRUE(res))</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">####################################</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">## Example with continuous fixef:</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">####################################</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""># Example with no fixef:</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">m <- lmer(Reaction ~ -1 + (Days | Subject), sleepstudy)</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""># m <- lmer(Reaction ~ 0 + (Days | Subject), sleepstudy) # alternative</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">stopifnot(length(fixef(m)) == 0L)</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">(an <- anova(m, type=1))</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Type I Analysis of Variance Table with Satterthwaite's method</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Sum Sq Mean Sq NumDF DenDF F value Pr(>F)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">(an_2 <- anova(m, type=2))</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Type II Analysis of Variance Table with Satterthwaite's method</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Sum Sq Mean Sq NumDF DenDF F value Pr(>F)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">(an_3 <- anova(m, type=3))</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Type III Analysis of Variance Table with Satterthwaite's method</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Sum Sq Mean Sq NumDF DenDF F value Pr(>F)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">stopifnot(nrow(an) == 0L,</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ nrow(an_2) == 0L,</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ nrow(an_3) == 0L)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""># anova(m, ddf="lme4") # Bug in lme4 it seems</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">if(has_pbkrtest) {</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ (an_KR <- anova(m, ddf="Kenward-Roger"))</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ stopifnot(</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ nrow(an_KR) == 0L</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ )</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ }</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""># Example with intercept only:</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">m <- lmer(Reaction ~ (Days | Subject), sleepstudy)</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""># m <- lmer(Reaction ~ 1 + (Days | Subject), sleepstudy) # alternative</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">stopifnot(length(fixef(m)) == 1L,</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ names(fixef(m)) == "(Intercept)")</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">(an <- anova(m))</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Type III Analysis of Variance Table with Satterthwaite's method</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Sum Sq Mean Sq NumDF DenDF F value Pr(>F)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">(an_2 <- anova(m, type=2))</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Type II Analysis of Variance Table with Satterthwaite's method</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Sum Sq Mean Sq NumDF DenDF F value Pr(>F)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">(an_3 <- anova(m, type=3))</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Type III Analysis of Variance Table with Satterthwaite's method</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Sum Sq Mean Sq NumDF DenDF F value Pr(>F)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">(an_lme4 <- anova(m, ddf="lme4"))</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Analysis of Variance Table</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Df Sum Sq Mean Sq F value</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">stopifnot(nrow(an) == 0L,</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ nrow(an_2) == 0L,</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ nrow(an_3) == 0L,</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ nrow(an_lme4) == 0L)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">if(has_pbkrtest) {</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ (an_KR <- anova(m, ddf="Kenward-Roger"))</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ stopifnot(</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ nrow(an_KR) == 0L</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ )</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ }</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""># Example with 1 fixef without intercept:</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">m <- lmer(Reaction ~ Days - 1 + (Days | Subject), sleepstudy)</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Warning message:</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Model failed to converge with max|grad| = 0.00416642 (tol = 0.002,</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">component 1)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""># m <- lmer(Reaction ~ 0 + Days + (Days | Subject), sleepstudy) #</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">alternative</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">stopifnot(length(fixef(m)) == 1L,</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ names(fixef(m)) == "Days")</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">(an <- anova(m))</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Type III Analysis of Variance Table with Satterthwaite's method</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Sum Sq Mean Sq NumDF DenDF F value Pr(>F)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Days 93779 93779 1 16.995 143.19 1.054e-09 ***</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">---</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">(an_2 <- anova(m, type=2))</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Type II Analysis of Variance Table with Satterthwaite's method</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Sum Sq Mean Sq NumDF DenDF F value Pr(>F)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Days 93779 93779 1 16.995 143.19 1.054e-09 ***</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">---</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">(an_3 <- anova(m, type=3))</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Type III Analysis of Variance Table with Satterthwaite's method</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Sum Sq Mean Sq NumDF DenDF F value Pr(>F)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Days 93779 93779 1 16.995 143.19 1.054e-09 ***</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">---</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">(an_lme4 <- anova(m, ddf="lme4"))</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Analysis of Variance Table</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""> Df Sum Sq Mean Sq F value</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Days 1 93779 93779 143.19</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">stopifnot(nrow(an) == 1L,</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ nrow(an_2) == 1L,</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ nrow(an_3) == 1L,</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ nrow(an_lme4) == 1L)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">if(has_pbkrtest) {</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ (an_KR <- anova(m, ddf="Kenward-Roger"))</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ stopifnot(</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ nrow(an_KR) == 1L</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ )</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ }</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")],</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ an_lme4[, c("Sum Sq", "Mean Sq", "F value")],</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">tolerance=TOL)</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">stopifnot(isTRUE(res))</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">stopifnot(isTRUE(all.equal(</span><br class="">
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ c(1, 17), unname(unlist(an[, c("NumDF", "DenDF")])), tolerance=TOL</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">+ )))</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Error: isTRUE(all.equal(c(1, 17), unname(unlist(an[, c("NumDF",</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">"DenDF")])), .... is not TRUE</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">Execution halted</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">autopkgtest [04:42:39]: test run-unit-test: -----------------------]</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">_______________________________________________</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class="">R-pkg-team mailing list</span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""><a href="mailto:R-pkg-team@alioth-lists.debian.net" class="">R-pkg-team@alioth-lists.debian.net</a></span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class="">
<blockquote type="cite" class=""><span class=""><a href="https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/r-pkg-team" class="">https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/r-pkg-team</a></span><br class="">
</blockquote>
</blockquote>
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
<blockquote type="cite" class=""><span class="">-- </span><br class="">
</blockquote>
<blockquote type="cite" class=""><span class=""><a href="http://fam-tille.de/" class="">http://fam-tille.de</a></span><br class="">
</blockquote>
<span class=""></span><br class="">
<span class="">-- </span><br class="">
<span class=""><a href="http://fam-tille.de/" class="">http://fam-tille.de</a></span><br class="">
</div>
</blockquote>
</div>
</div>
</div></blockquote></div><br class=""></div></body></html>