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

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".

AuthorDouglas 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 publication2016-04-16 20:40:11
MaintainerBen Bolker <bbolker+lme4@gmail.com>
LicenseGPL (>= 2)
Version1.1-12
https://github.com/lme4/lme4/ http://lme4.r-forge.r-project.org/

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

Functions

|| Man page
anova.merMod Man page
Arabidopsis Man page
as.data.frame.thpr Man page
as.data.frame.VarCorr.merMod Man page
as.function.merMod Man page
bootMer Man page
cake Man page
cbpp Man page
coef.merMod Man page
confint.merMod Man page
convergence Man page
cov2sdcor Man page
Cv_to_Sv Man page
Cv_to_Vv Man page
densityplot.thpr Man page
devcomp Man page
deviance.merMod Man page
df.residual.merMod Man page
dotplot.ranef.mer Man page
drop1.merMod Man page
dummy Man page
Dyestuff Man page
Dyestuff2 Man page
expandDoubleVerts Man page
extractAIC.merMod Man page
factorize Man page
family.merMod Man page
findbars Man page
fitted.merMod Man page
fixed.effects Man page
fixef Man page
fixef.merMod Man page
formatVC Man page
formula.merMod Man page
fortify Man page
fortify.merMod Man page
getL Man page
getL,merMod-method Man page
getME Man page
getME.merMod Man page
GHrule Man page
glFormula Man page
glmer Man page
glmerControl Man page
glmerLaplaceHandle Man page
glmerMod-class Man page
glmer.nb Man page
glmFamily Man page
glmFamily-class Man page
glmResp Man page
glmResp-class Man page
golden Man page
golden-class Man page
GQdk Man page
GQN Man page
grouseticks Man page
grouseticks_agg Man page
hatvalues.merMod Man page
InstEval Man page
isGLMM Man page
isGLMM.merMod Man page
isLMM Man page
isLMM.merMod Man page
isNested Man page
isNLMM Man page
isNLMM.merMod Man page
isREML Man page
isREML.merMod Man page
lFormula Man page
llikAIC Man page
lme4 Man page
lme4-package Man page
lmer Man page
lmerControl Man page
lmerMod-class Man page
lmerResp Man page
lmerResp-class Man page
lmList Man page
lmList4-class Man page
lmResp Man page
lmResp-class Man page
logLik.merMod Man page
logProf Man page
log.thpr Man page
.makeCC Man page
mcmcsamp Man page
merMod Man page
merMod-class Man page
merPredD Man page
merPredD-class Man page
methTitle Man page
mkDataTemplate Man page
mkdevfun Man page
mkGlmerDevfun Man page
mkLmerDevfun Man page
mkMerMod Man page
mkParsTemplate Man page
mkRespMod Man page
mkReTrms Man page
mkVarCorr Man page
mlist2vec Man page
model.frame.merMod Man page
model.matrix.merMod Man page
modular Man page
negative.binomial Man page
NelderMead Man page
Nelder_Mead Man page
NelderMead-class Man page
ngrps Man page
ngrps.merMod Man page
nlformula Man page
nlmer Man page
nlmerControl Man page
nlmerMod-class Man page
nlminbwrap Man page
nloptwrap Man page
nlsResp Man page
nlsResp-class Man page
nobars Man page
nobs Man page
nobs.merMod Man page
optimizeGlmer Man page
optimizeLmer Man page
Pastes Man page
Penicillin Man page
plot.lmList Man page
plot.lmList4 Man page
plot.lmList4.confint Man page
plot.merMod Man page
predict.merMod Man page
print.merMod Man page
print.summary.merMod Man page
print.VarCorr.merMod Man page
profile.merMod Man page
profile-methods Man page
.prt.aictab Man page
.prt.call Man page
.prt.family Man page
.prt.grps Man page
.prt.methTit Man page
.prt.methTit Man page
.prt.resids Man page
.prt.VC Man page
.prt.warn Man page
pvalues Man page
qqmath.merMod Man page
qqmath.ranef.mer Man page
ranef Man page
ranef.merMod Man page
refit Man page
refit.merMod Man page
refitML Man page
refitML.merMod Man page
REMLcrit Man page
rePos Man page
rePos-class Man page
residuals.glmResp Man page
residuals.lmResp Man page
residuals.merMod Man page
sdcor2cov Man page
show,lmList4-method Man page
show.merMod Man page
show,merMod-method Man page
show.summary.merMod Man page
sigma Man page
sigma.merMod Man page
simulate.formula Man page
.simulateFun Man page
simulate.merMod Man page
sleepstudy Man page
splom.thpr Man page
subbars Man page
summary.merMod Man page
summary.summary.merMod Man page
Sv_to_Cv Man page
terms.merMod Man page
troubleshooting Man page
updateGlmerDevfun Man page
update.merMod Man page
VarCorr Man page
VarCorr.merMod Man page
varianceProf Man page
vcconv Man page
vcov.merMod Man page
vcov.summary.merMod Man page
vec2mlist Man page
vec2STlist Man page
VerbAgg Man page
Vv_to_Cv Man page
weights.merMod Man page
xyplot.thpr Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.