lme4: Linear Mixed-Effects Models using 'Eigen' and S4

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Fit linear and generalized linear mixed-effects models. The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the 'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue".

Author
Douglas Bates [aut], Martin Maechler [aut], Ben Bolker [aut, cre], Steven Walker [aut], Rune Haubo Bojesen Christensen [ctb], Henrik Singmann [ctb], Bin Dai [ctb], Gabor Grothendieck [ctb], Peter Green [ctb]
Date of publication
2016-04-16 20:40:11
Maintainer
Ben Bolker <bbolker+lme4@gmail.com>
License
GPL (>= 2)
Version
1.1-12
URLs

View on CRAN

Man pages

Arabidopsis
Arabidopsis clipping/fertilization data
bootMer
Model-based (Semi-)Parametric Bootstrap for Mixed Models
cake
Breakage Angle of Chocolate Cakes
cbpp
Contagious bovine pleuropneumonia
confint.merMod
Compute Confidence Intervals for Parameters of a [ng]lmer Fit
convergence
Assessing Convergence for Fitted Models
devcomp
Extract the deviance component list
drop1.merMod
Drop all possible single fixed-effect terms from a mixed...
dummy
Dummy variables (experimental)
Dyestuff
Yield of dyestuff by batch
expandDoubleVerts
Expand terms with "||" notation into separate "|" terms
factorize
Attempt to convert grouping variables to factors
findbars
Determine random-effects expressions from a formula
fixef
Extract fixed-effects estimates
fortify
add information to data based on a fitted model
getME
Extract or Get Generalized Components from a Fitted Mixed...
GHrule
Univariate Gauss-Hermite quadrature rule
glmer
Fitting Generalized Linear Mixed-Effects Models
glmerLaplaceHandle
Handle for 'glmerLaplace'
glmer.nb
Fitting Negative Binomial GLMMs
glmFamily
Generator object for the 'glmFamily' class
glmFamily-class
Class '"glmFamily"' - a reference class for 'family'
golden-class
Class '"golden"' and Generator for Golden Search Optimizer...
GQdk
Sparse Gaussian / Gauss-Hermite Quadrature grid
grouseticks
Data on red grouse ticks from Elston et al. 2001
hatvalues.merMod
Diagonal elements of the hat matrix
InstEval
University Lecture/Instructor Evaluations by Students at ETH
isNested
Is f1 nested within f2?
isREML
Check characteristics of models
lme4-package
Linear, generalized linear, and nonlinear mixed models
lmer
Fit Linear Mixed-Effects Models
lmerControl
Control of Mixed Model Fitting
lmList
Fit List of lm Objects with a Common Model
lmList4-class
Class "lmList4" of 'lm' Objects on Common Model
lmResp
Generator objects for the response classes
lmResp-class
Reference Classes for Response Modules,...
merMod-class
Class "merMod" of Fitted Mixed-Effect Models
merPredD
Generator object for the 'merPredD' class
merPredD-class
Class '"merPredD"' - a Dense Predictor Reference Class
mkdevfun
Create Deviance Evaluation Function from Predictor and...
mkMerMod
Create a 'merMod' Object
mkRespMod
Create an lmerResp, glmResp or nlsResp instance
mkReTrms
Make Random Effect Terms: Create Z, Lambda, Lind, etc.
mkSimulationTemplate
Make templates suitable for guiding mixed model simulations
mkVarCorr
Make Variance and Correlation Matrices from 'theta'
modular
Modular Functions for Mixed Model Fits
Nelder_Mead
Nelder-Mead Optimization of Parameters, Possibly (Box)...
NelderMead-class
Class '"NelderMead"' of Nelder-Mead optimizers and its...
ngrps
Number of Levels of a Factor or a "merMod" Model
nlformula
Manipulate a Nonlinear Model Formula
nlmer
Fitting Nonlinear Mixed-Effects Models
nloptwrap
Wrappers for additional optimizers
nobars
Omit terms separated by vertical bars in a formula
Pastes
Paste strength by batch and cask
Penicillin
Variation in penicillin testing
plot.lmList4
plots for lmList4 objects
plot.merMod
diagnostic plots for merMod fits
plots.thpr
Mixed-Effects Profile Plots (Regular / Density / Pairs)
predict.merMod
Predictions from a model at new data values
profile-methods
Profile method for merMod objects
pvalues
Getting p-values for fitted models
ranef
Extract the modes of the random effects
refit
Refit a (merMod) Model with a Different Response
refitML
Refit a Model by Maximum Likelihood Criterion
rePos
Generator object for the rePos (random-effects positions)...
rePos-class
Class '"rePos"'
residuals.merMod
residuals of merMod objects
sigma
Extract Residual Standard Deviation 'Sigma'
simulate.merMod
Simulate Responses From 'merMod' Object
sleepstudy
Reaction times in a sleep deprivation study
subbars
"Sub[stitute] Bars"
troubleshooting
Troubleshooting
utilities
Print and Summary Method Utilities for Mixed Effects
VarCorr
Extract Variance and Correlation Components
varianceProf
Transform Profile to the variance scale
vcconv
Convert between representations of (co-)variance structures
VerbAgg
Verbal Aggression item responses

Files in this package

lme4
lme4/inst
lme4/inst/CITATION
lme4/inst/NEWS.Rd
lme4/inst/vignettedata
lme4/inst/vignettedata/calcium.txt
lme4/inst/vignettedata/mcmcsampdat.RData
lme4/inst/doc
lme4/inst/doc/Theory.Rnw
lme4/inst/doc/Theory.R
lme4/inst/doc/PLSvGLS.R
lme4/inst/doc/lmer.Rnw
lme4/inst/doc/lme4-extras.pdf
lme4/inst/doc/lmerperf.R
lme4/inst/doc/PLSvGLS.pdf
lme4/inst/doc/PLSvGLS.Rnw
lme4/inst/doc/Theory.pdf
lme4/inst/doc/profiling.txt
lme4/inst/doc/Doxyfile
lme4/inst/doc/lmerperf.html
lme4/inst/doc/lmerperf.Rmd
lme4/inst/doc/lmer.R
lme4/inst/doc/lmer.pdf
lme4/inst/testdata
lme4/inst/testdata/polytom2.RData
lme4/inst/testdata/badprof.rds
lme4/inst/testdata/confint_ex.rda
lme4/inst/testdata/dataEx_Glmer.txt
lme4/inst/testdata/colonizer_rand.rda
lme4/inst/testdata/sbTobb.Rdata
lme4/inst/testdata/respiratory.RData
lme4/inst/testdata/prLogistic.RData
lme4/inst/testdata/dat20101314.csv
lme4/inst/testdata/boo01L.RData
lme4/inst/testdata/Johnson.rda
lme4/inst/testdata/gopherdat2.RData
lme4/inst/testdata/koller-data.R
lme4/inst/testdata/polytom3.RData
lme4/inst/testdata/culcita_dat.RData
lme4/inst/testdata/mastitis.rda
lme4/inst/testdata/tprfm1.RData
lme4/inst/testdata/polytomous_test.RData
lme4/inst/testdata/badhess.RData
lme4/inst/testdata/lme-tst-funs.R
lme4/inst/testdata/hotpower.csv
lme4/inst/testdata/rankMatrix.rds
lme4/inst/testdata/lme-tst-fits.rda
lme4/inst/testdata/trees513.RData
lme4/inst/testdata/trees513.R
lme4/inst/testdata/Thailand.rda
lme4/inst/testdata/crabs_randdata00.Rda
lme4/inst/testdata/SO_sep25.RData
lme4/inst/testdata/gotway_hessianfly.rda
lme4/inst/testdata/lme-tst-fits.R
lme4/inst/testdata/polytomous_vcov_ex.RData
lme4/inst/testdata/crabs_randdata2.Rda
lme4/inst/testdata/lme-tst-fits.Rout
lme4/inst/testdata/survdat_reduced.Rda
lme4/inst/testdata/radinger_dat.RData
lme4/inst/utils
lme4/inst/utils/allFit.R
lme4/configure.ac
lme4/ToDo
lme4/tests
lme4/tests/refit.Rout
lme4/tests/offset.R
lme4/tests/offset.Rout
lme4/tests/varcorr.R
lme4/tests/boundary_plots.pdf
lme4/tests/Rplots.pdf
lme4/tests/lmer-1.R
lme4/tests/predsim.Rout
lme4/tests/getME.R
lme4/tests/ST.R
lme4/tests/utils.R
lme4/tests/resids.R
lme4/tests/glmerWarn.R
lme4/tests/falsezero_dorie.R
lme4/tests/lmer-conv.R
lme4/tests/vcov-etc.R
lme4/tests/nlmer.Rout.save
lme4/tests/drop.R
lme4/tests/fewlevels.R
lme4/tests/test_times.R
lme4/tests/predict_basis.Rout
lme4/tests/predict.Rout
lme4/tests/priorWeights.R
lme4/tests/prLogistic.R
lme4/tests/predict_basis.R
lme4/tests/refit_allequal.RData
lme4/tests/predict.R
lme4/tests/agridat_gotway.R
lme4/tests/test_timings.RData
lme4/tests/testcrab.R
lme4/tests/evalCall.R
lme4/tests/lmList-tst.R
lme4/tests/bootMer.Rout
lme4/tests/testOptControl.R
lme4/tests/drop1contrasts.R
lme4/tests/throw.R
lme4/tests/lmer2_ex.R
lme4/tests/methods.R
lme4/tests/README
lme4/tests/dynload.R
lme4/tests/glmmExt.R
lme4/tests/AAAtest-all.Rout
lme4/tests/confint.Rout
lme4/tests/priorWeightsModComp.R
lme4/tests/mkRout
lme4/tests/glmerControlPass.R
lme4/tests/glmmWeights.R
lme4/tests/testcolonizer.R
lme4/tests/is.R
lme4/tests/nbinom.R
lme4/tests/bootMer.R
lme4/tests/lme4_nlme.R
lme4/tests/AAAtest-all.R
lme4/tests/confint.R
lme4/tests/modFormula.R
lme4/tests/glmer-1.R
lme4/tests/condVar.R
lme4/tests/optimizer.R
lme4/tests/devCritFun.R
lme4/tests/nlmer.R
lme4/tests/lmer-0.R
lme4/tests/simulate.R
lme4/tests/REMLdev.R
lme4/tests/elston.R
lme4/tests/polytomous.R
lme4/tests/boundary.R
lme4/tests/lme-tst-fits.rda
lme4/tests/devfunQ.R
lme4/tests/hatvalues.R
lme4/tests/profile-tst.R
lme4/tests/nlmer-conv.R
lme4/tests/testthat
lme4/tests/testthat/test-resids.R
lme4/tests/testthat/test-utils.R
lme4/tests/testthat/Rplots.pdf
lme4/tests/testthat/test-doubleVertNotation.R
lme4/tests/testthat/napredict2.R
lme4/tests/testthat/refit_debug.rda
lme4/tests/testthat/test-factors.R
lme4/tests/testthat/test-oldRZXfailure.R
lme4/tests/testthat/test-glmer.R
lme4/tests/testthat/test-summary.R
lme4/tests/testthat/tmp.html
lme4/tests/testthat/test-lmList.R
lme4/tests/testthat/test-rank.R
lme4/tests/testthat/test-start.R
lme4/tests/testthat/wenseleers.rda
lme4/tests/testthat/test-formulaEval.R
lme4/tests/testthat/test-catch.R
lme4/tests/testthat/refit_debug_1.rda
lme4/tests/testthat/test-glmmFail.R
lme4/tests/testthat/test-glmFamily.R
lme4/tests/testthat/test-stepHalving.R
lme4/tests/testthat/test-lmer.R
lme4/tests/testthat/test-lmerResp.R
lme4/tests/testthat/good_offset.rds
lme4/tests/testthat/bad_offset.rds
lme4/tests/testthat/test-methods.R
lme4/tests/testthat/test-glmer.Rout
lme4/tests/testthat/test-nbinom_refit.R
lme4/tests/testthat/refit_debug_2.rda
lme4/tests/testthat/test-NAhandling.R
lme4/tests/testthat/test-glmernb.R
lme4/tests/timings.pdf
lme4/tests/respiratory.R
lme4/tests/HSAURtrees.R
lme4/tests/extras.R
lme4/tests/refit.R
lme4/tests/minval.R
lme4/tests/lmer-1.Rout.save
lme4/tests/predsim.R
lme4/src
lme4/src/Makevars
lme4/src/mcmcsamp.cpp
lme4/src/predModule.h
lme4/src/glmFamily.h
lme4/src/optimizer.cpp
lme4/src/lme4CholmodDecomposition.h
lme4/src/external.cpp
lme4/src/predModule.cpp
lme4/src/respModule.h
lme4/src/optimizer.h
lme4/src/glmFamily.cpp
lme4/src/Makevars.win
lme4/src/mcmcsamp.h
lme4/src/respModule.cpp
lme4/NAMESPACE
lme4/data
lme4/data/cake.rda
lme4/data/Arabidopsis.rda
lme4/data/InstEval.rda
lme4/data/cbpp.rda
lme4/data/Penicillin.rda
lme4/data/grouseticks.rda
lme4/data/Dyestuff.rda
lme4/data/Pastes.rda
lme4/data/VerbAgg.rda
lme4/data/sleepstudy.rda
lme4/data/Dyestuff2.rda
lme4/R
lme4/R/modular.R
lme4/R/vcconv.R
lme4/R/GHrule.R
lme4/R/checkConv.R
lme4/R/sparsegrid.R
lme4/R/plot.R
lme4/R/AllClass.R
lme4/R/predict.R
lme4/R/mcmcsamp.R
lme4/R/sysdata.rda
lme4/R/profile.R
lme4/R/utilities.R
lme4/R/hooks.R
lme4/R/nbinom.R
lme4/R/bootMer.R
lme4/R/optimizer.R
lme4/R/AllGeneric.R
lme4/R/deriv.R
lme4/R/lmer.R
lme4/R/lmList.R
lme4/R/lmerControl.R
lme4/vignettes
lme4/vignettes/Theory.Rnw
lme4/vignettes/lmer.Rnw
lme4/vignettes/lmer.bib
lme4/vignettes/blkarray.sty
lme4/vignettes/lmerperf.md
lme4/vignettes/PLSvGLS.Rnw
lme4/vignettes/lmerperf.Rmd
lme4/vignettes/lme4.bib
lme4/vignettes/lmer.R
lme4/MD5
lme4/build
lme4/build/vignette.rds
lme4/DESCRIPTION
lme4/ChangeLog
lme4/man
lme4/man/fortify.Rd
lme4/man/getME.Rd
lme4/man/lmList4-class.Rd
lme4/man/VarCorr.Rd
lme4/man/grouseticks.Rd
lme4/man/isNested.Rd
lme4/man/merPredD.Rd
lme4/man/confint.merMod.Rd
lme4/man/glmer.nb.Rd
lme4/man/predict.merMod.Rd
lme4/man/ngrps.Rd
lme4/man/NelderMead-class.Rd
lme4/man/simulate.merMod.Rd
lme4/man/lmResp.Rd
lme4/man/utilities.Rd
lme4/man/Arabidopsis.Rd
lme4/man/hatvalues.merMod.Rd
lme4/man/lmList.Rd
lme4/man/subbars.Rd
lme4/man/profile-methods.Rd
lme4/man/rePos-class.Rd
lme4/man/varianceProf.Rd
lme4/man/expandDoubleVerts.Rd
lme4/man/ranef.Rd
lme4/man/Nelder_Mead.Rd
lme4/man/GHrule.Rd
lme4/man/glmerLaplaceHandle.Rd
lme4/man/Dyestuff.Rd
lme4/man/merPredD-class.Rd
lme4/man/modular.Rd
lme4/man/lmResp-class.Rd
lme4/man/mkReTrms.Rd
lme4/man/glmFamily-class.Rd
lme4/man/pvalues.Rd
lme4/man/findbars.Rd
lme4/man/mkdevfun.Rd
lme4/man/vcconv.Rd
lme4/man/sleepstudy.Rd
lme4/man/lme4-package.Rd
lme4/man/plot.lmList4.Rd
lme4/man/glmer.Rd
lme4/man/residuals.merMod.Rd
lme4/man/GQdk.Rd
lme4/man/refitML.Rd
lme4/man/devcomp.Rd
lme4/man/golden-class.Rd
lme4/man/mkRespMod.Rd
lme4/man/drop1.merMod.Rd
lme4/man/InstEval.Rd
lme4/man/lmer.Rd
lme4/man/Pastes.Rd
lme4/man/merMod-class.Rd
lme4/man/nloptwrap.Rd
lme4/man/Penicillin.Rd
lme4/man/mkVarCorr.Rd
lme4/man/refit.Rd
lme4/man/nlmer.Rd
lme4/man/plots.thpr.Rd
lme4/man/rePos.Rd
lme4/man/glmFamily.Rd
lme4/man/nlformula.Rd
lme4/man/dummy.Rd
lme4/man/isREML.Rd
lme4/man/factorize.Rd
lme4/man/bootMer.Rd
lme4/man/convergence.Rd
lme4/man/fixef.Rd
lme4/man/lmerControl.Rd
lme4/man/mkMerMod.Rd
lme4/man/troubleshooting.Rd
lme4/man/mkSimulationTemplate.Rd
lme4/man/sigma.Rd
lme4/man/plot.merMod.Rd
lme4/man/VerbAgg.Rd
lme4/man/cbpp.Rd
lme4/man/nobars.Rd
lme4/man/cake.Rd