Files in lme4/lme4

Linear Mixed-Effects Models using 'Eigen' and S4

.Rbuildignore

.github/.gitignore

.github/workflows/R-CMD-check-allOS.yaml

.github/workflows/R-CMD-check.yaml

.github/workflows/rhub.yaml

.gitignore

.travis.yml

ChangeLog

DESCRIPTION

LICENSE.note

Makefile

NAMESPACE

R/AllClass.R R/AllGeneric.R R/GHrule.R R/allFit.R R/bootMer.R R/checkConv.R R/deriv.R R/error_factory.R R/lmList.R R/lmer.R R/lmerControl.R R/mcmcsamp.R R/methods.R R/modular.R R/nbinom.R R/optimizer.R R/plot.R R/plots.R R/predict.R R/profile.R R/rePCA.R R/simulate.formula.R R/sparsegrid.R

R/sysdata.rda

R/utilities.R R/vcconv.R R/zzz.R README.md TODO.md

data/Arabidopsis.rda

data/Dyestuff.rda

data/Dyestuff2.rda

data/InstEval.rda

data/Pastes.rda

data/Penicillin.rda

data/VerbAgg.rda

data/cake.rda

data/cbpp.rda

data/grouseticks.rda

data/sleepstudy.rda

do-roxy

inst/CITATION

inst/NEWS.Rd

inst/testdata/Johnson.rda

inst/testdata/SO_sep25.RData

inst/testdata/Thailand.rda

inst/testdata/badprof.rds

inst/testdata/boo01L.RData

inst/testdata/colonizer_rand.rda

inst/testdata/confint_ex.rda

inst/testdata/crabs_randdata00.Rda

inst/testdata/crabs_randdata2.Rda

inst/testdata/culcita_dat.RData

inst/testdata/dat20101314.csv

inst/testdata/dataEx_Glmer.txt

inst/testdata/fakesim.RData

inst/testdata/gopherdat2.RData

inst/testdata/gotway_hessianfly.rda

inst/testdata/harmel_density.R

inst/testdata/harmel_profile.rds

inst/testdata/hotpower.csv

inst/testdata/koller-data.R inst/testdata/lme-tst-fits.R

inst/testdata/lme-tst-fits.rda

inst/testdata/lme-tst-funs.R

inst/testdata/lmerperf.rda

inst/testdata/mastitis.rda

inst/testdata/polytom2.RData

inst/testdata/polytom3.RData

inst/testdata/polytomous_test.RData

inst/testdata/polytomous_vcov_ex.RData

inst/testdata/prLogistic.RData

inst/testdata/radinger_dat.RData

inst/testdata/rankMatrix.rds

inst/testdata/respiratory.RData

inst/testdata/sbTobb.Rdata

inst/testdata/strip_env.R

inst/testdata/survdat_reduced.Rda

inst/testdata/tprfm1.RData

inst/testdata/trees513.R

inst/testdata/trees513.RData

man/Arabidopsis.Rd man/Dyestuff.Rd man/GHrule.Rd man/GQdk.Rd man/InstEval.Rd man/NelderMead-class.Rd man/Nelder_Mead.Rd man/Pastes.Rd man/Penicillin.Rd man/VarCorr.Rd man/VerbAgg.Rd man/allFit.Rd man/bootMer.Rd man/cake.Rd man/cbpp.Rd man/checkConv.Rd man/confint.merMod.Rd man/convergence.Rd man/devcomp.Rd man/devfun2.Rd man/drop1.merMod.Rd man/dummy.Rd man/expandDoubleVerts.Rd man/factorize.Rd man/findbars.Rd man/fixef.Rd man/fortify.Rd man/getME.Rd man/glmFamily-class.Rd man/glmFamily.Rd man/glmer.Rd man/glmer.nb.Rd man/glmerLaplaceHandle.Rd man/golden-class.Rd man/grouseticks.Rd man/hatvalues.merMod.Rd man/influence.merMod.Rd man/isNested.Rd man/isREML.Rd man/isSingular.Rd man/lmList.Rd man/lmList4-class.Rd man/lmResp-class.Rd man/lmResp.Rd man/lme4-package.Rd man/lme4_testlevel.Rd man/lmer.Rd man/lmerControl.Rd man/merMod-class.Rd man/merPredD-class.Rd man/merPredD.Rd man/mkMerMod.Rd man/mkReTrms.Rd man/mkRespMod.Rd man/mkSimulationTemplate.Rd man/mkVarCorr.Rd man/modular.Rd man/namedList.Rd man/ngrps.Rd man/nlformula.Rd man/nlmer.Rd man/nloptwrap.Rd man/nobars.Rd man/plot.merMod.Rd man/plots.thpr.Rd man/predict.merMod.Rd man/profile-methods.Rd man/pvalues.Rd man/ranef.Rd man/rePCA.Rd man/rePos-class.Rd man/rePos.Rd man/refit.Rd man/refitML.Rd man/residuals.merMod.Rd man/sigma.Rd man/simulate.formula.Rd man/simulate.merMod.Rd man/sleepstudy.Rd man/subbars.Rd man/troubleshooting.Rd man/utilities.Rd man/vcconv.Rd

misc/Done

misc/GH_425.R misc/GH_557.R misc/Pastes-nloptwrap.R misc/R_lapackstuff.md

misc/cache/__packages

misc/cache/buildpkg_ef639b7437c856b62a405d4bf7cec7fd.RData

misc/cache/buildpkg_ef639b7437c856b62a405d4bf7cec7fd.rdb

misc/cache/buildpkg_ef639b7437c856b62a405d4bf7cec7fd.rdx

misc/cache/getCRANtimes_c3686613f1274313805d459214acbb8f.RData

misc/cache/getCRANtimes_c3686613f1274313805d459214acbb8f.rdb

misc/cache/getCRANtimes_c3686613f1274313805d459214acbb8f.rdx

misc/cache/getmedpkg_aa71765d8aedb8d6cb8fbacc16830e3e.RData

misc/cache/getmedpkg_aa71765d8aedb8d6cb8fbacc16830e3e.rdb

misc/cache/getmedpkg_aa71765d8aedb8d6cb8fbacc16830e3e.rdx

misc/cache/medpkgtime_7eacf1a5017a90996110563c28afe8c7.RData

misc/cache/medpkgtime_7eacf1a5017a90996110563c28afe8c7.rdb

misc/cache/medpkgtime_7eacf1a5017a90996110563c28afe8c7.rdx

misc/cache/timecal_e786ac690ec60ab22cbc284cb1045812.RData

misc/cache/timecal_e786ac690ec60ab22cbc284cb1045812.rdb

misc/cache/timecal_e786ac690ec60ab22cbc284cb1045812.rdx

misc/cache/timecheck_81f5aa89c9c5d3344fccb5ddc7ddca45.RData

misc/cache/timecheck_81f5aa89c9c5d3344fccb5ddc7ddca45.rdb

misc/cache/timecheck_81f5aa89c9c5d3344fccb5ddc7ddca45.rdx

misc/cache/timeinstall_7fd5adba719d64adf8f19741517f6fda.RData

misc/cache/timeinstall_7fd5adba719d64adf8f19741517f6fda.rdb

misc/cache/timeinstall_7fd5adba719d64adf8f19741517f6fda.rdx

misc/cache/timetests_0eb1bec346e325d61021cc51aa702920.RData

misc/cache/timetests_0eb1bec346e325d61021cc51aa702920.rdb

misc/cache/timetests_0eb1bec346e325d61021cc51aa702920.rdx

misc/cooks_distance.R misc/cp_vignette.R misc/diagnose_summary.R misc/gammaClamp.R

misc/glmer_JSS/Makefile

misc/glmer_JSS/cbpp.csv

misc/glmer_JSS/cbpp2.csv

misc/glmer_JSS/glmer.Rnw

misc/glmer_JSS/glmer.bib

misc/glmer_JSS/glmer.pdf misc/glmer_JSS/glmer_bootbatch.R

misc/glmer_JSS/glmer_bootbatch.RData

misc/glmer_JSS/glmer_profbatch.R

misc/glmer_JSS/glmer_profbatch.RData

misc/glmer_JSS/jss.bst

misc/glmer_JSS/jss.cls

misc/glmer_JSS/jsslogo.jpg

misc/issues/211-dev-weights.R misc/issues/287-glmer.nb.R misc/issues/303-predict-miss-levels.R misc/issues/318-glmer.nb.R

misc/issues/Bachl_data.RData

misc/issues/Bachl_issue130.R misc/issues/Banta_conv.Rmd misc/issues/GH386.R misc/issues/GH_303.R misc/issues/GH_316.rmd misc/issues/OddSets.R

misc/issues/OddSets1.Rdata

misc/issues/VA.RData

misc/issues/VerbAgg.R misc/issues/Xrank_168.R misc/issues/condVar.R misc/issues/conv_dmartin.R misc/issues/conv_simfuns.R misc/issues/convdat.R

misc/issues/convergence.html

misc/issues/convergence.rmd

misc/issues/dialectNL.rda

misc/issues/dialectNL2.rda

misc/issues/dynload.R

misc/issues/fit+pr_AV3.rda

misc/issues/glmernb_foraging.R

misc/issues/glmernb_foraging_models.rda

misc/issues/glmernb_foraging_subset.csv

misc/issues/glmmvcov_v3.R

misc/issues/lme4_knitr_conv2.html

misc/issues/lme4_knitr_conv2.rmd misc/issues/lme4_order.Rmd misc/issues/nbinom_refit.R

misc/issues/offset_test.rds

misc/issues/penicillin_conv.R

misc/issues/penicillin_conv.RData

misc/issues/penicillin_conv.pdf misc/issues/polytom.R misc/issues/polytomous_2014mar.R

misc/issues/polytomous_test.RData

misc/issues/rank-32bit-stla-ex.R misc/issues/refit_vs_fit.R misc/issues/schizo.R misc/issues/wieling_batch1.R

misc/issues/wieling_batch1.RData

misc/issues/wieling_batch1.html

misc/issues/wieling_batch2.R misc/issues/wieling_batchfuns.R

misc/issues/wieling_results.csv

misc/lme4_GH691.R

misc/lme4_GH691_Dataone.csv

misc/lme4_GH691_test.csv

misc/lme4_GH727.Rmd

misc/lme4_GH727_rgl.png

misc/lme4_bigpred.R misc/lme4_times.R misc/logLikGLMM/logLikGLMM.R misc/notes/deviance.rmd misc/notes/eval_levels.rmd misc/notes/interface.md misc/notes/laplDiag.Rmd

misc/notes/laplDiag.html

misc/notes/laplDiag.md misc/notes/lme4_status.md

misc/notes/mixed_interface.html

misc/notes/mixed_interface.rmd misc/notes/options.md misc/notes/release_notes.md misc/notes/release_notes.rmd

misc/notes/toenail.csv

misc/oldcode/jml.R misc/oldcode/mlirt.R misc/pkgtests/README.md

misc/pkgtests/lme4_compat_report.html

misc/pkgtests/lme4_notes.csv

misc/pkgtests/pkgdepfuns.R misc/pkgtests/pkgdeptests.R

misc/pkgtests/runCheck

misc/pkgtests/setTestEnv

misc/pkgtests/unsetTestEnv

misc/profile.Rmd misc/ranefIndex.R

misc/test_timings.Rnw

misc/test_timings.pdf

src/Makevars

src/Makevars.win

src/external.cpp

src/glmFamily.cpp

src/glmFamily.h

src/lme4CholmodDecomposition.h

src/mcmcsamp.cpp

src/mcmcsamp.h

src/optimizer.cpp

src/optimizer.h

src/predModule.cpp

src/predModule.h

src/respModule.cpp

src/respModule.h

tests/AAAtest-all.R tests/HSAURtrees.R

tests/README

tests/README.md tests/REMLdev.R tests/ST.R tests/agridat_gotway.R tests/bootMer.R tests/boundary.R tests/confint.R tests/devCritFun.R tests/drop.R tests/drop1contrasts.R tests/dynload.R tests/elston.R tests/evalCall.R tests/extras.R tests/falsezero_dorie.R tests/fewlevels.R tests/getME.R tests/glmer-1.R tests/glmerControlPass.R tests/glmerWarn.R tests/glmmExt.R tests/glmmWeights.R tests/hatvalues.R tests/is.R tests/lmList-tst.R tests/lme4_nlme.R tests/lmer-0.R tests/lmer-1.R

tests/lmer-1.Rout.save

tests/lmer-conv.R tests/lmer2_ex.R tests/methods.R tests/minval.R tests/modFormula.R tests/nbinom.R tests/nlmer-conv.R tests/nlmer.R

tests/nlmer.Rout.save

tests/offset.R tests/optimizer.R tests/polytomous.R tests/prLogistic.R tests/predict_basis.R tests/predsim.R tests/priorWeights.R tests/priorWeightsModComp.R tests/profile-tst.R tests/refit.R tests/resids.R tests/respiratory.R tests/simulate.R tests/test-glmernbref.R tests/testOptControl.R tests/testcolonizer.R tests/testcrab.R tests/testthat/test-NAhandling.R tests/testthat/test-allFit.R tests/testthat/test-catch.R tests/testthat/test-doubleVertNotation.R tests/testthat/test-eval.R tests/testthat/test-factors.R tests/testthat/test-formulaEval.R tests/testthat/test-glmFamily.R tests/testthat/test-glmer.R tests/testthat/test-glmernb.R tests/testthat/test-glmernbref.R tests/testthat/test-glmmFail.R tests/testthat/test-lmList.R tests/testthat/test-lmer.R tests/testthat/test-lmerResp.R tests/testthat/test-methods.R tests/testthat/test-nbinom.R tests/testthat/test-nlmer.R tests/testthat/test-oldRZXfailure.R tests/testthat/test-predict.R tests/testthat/test-ranef.R tests/testthat/test-rank.R tests/testthat/test-resids.R tests/testthat/test-simulate_formula.R tests/testthat/test-start.R tests/testthat/test-stepHalving.R tests/testthat/test-summary.R

tests/testthat/test-summary_testlevel_1.rda

tests/testthat/test-utils.R tests/throw.R tests/varcorr.R tests/vcov-etc.R testsx/identZ.R

testsx/randcrabdata.RData

vignettes/PLSvGLS.Rnw

vignettes/Theory.Rnw

vignettes/blkarray.sty

vignettes/framed.sty

vignettes/jss.bst

vignettes/jss.cls

vignettes/lme4.bib

vignettes/lmer.Rnw

vignettes/lmer.bib

vignettes/lmerperf.Rmd

lme4/lme4 documentation built on May 4, 2024, 6:46 p.m.