Package: lme4 2.0-3

Ben Bolker

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".

Authors:Douglas Bates [aut], Martin Maechler [aut], Ben Bolker [cre, aut], Steven Walker [aut], Anna Ly [aut], Mikael Jagan [aut], Rune Haubo Bojesen Christensen [ctb], Henrik Singmann [ctb], Bin Dai [ctb], Fabian Scheipl [ctb], Gabor Grothendieck [ctb], Peter Green [ctb], John Fox [ctb], Alexander Bauer [ctb], Pavel N. Krivitsky [ctb, cph], Emi Tanaka [ctb], Ross D. Boylan [ctb], Henrik Bengtsson [ctb]

lme4_2.0-3.tar.gz
lme4_2.0-3.zip(r-4.7)lme4_2.0-3.zip(r-4.6)lme4_2.0-3.zip(r-4.5)
lme4_2.0-3.tgz(r-4.6-x86_64)lme4_2.0-3.tgz(r-4.6-arm64)lme4_2.0-3.tgz(r-4.5-x86_64)lme4_2.0-3.tgz(r-4.5-arm64)
lme4_2.0-3.tar.gz(r-4.7-arm64)lme4_2.0-3.tar.gz(r-4.7-x86_64)lme4_2.0-3.tar.gz(r-4.6-arm64)lme4_2.0-3.tar.gz(r-4.6-x86_64)
lme4_2.0-3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
lme4/json (API)

# Install 'lme4' in R:

install.packages('lme4', repos = c('https://lme4.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/lme4/lme4/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

Arabidopsis - Arabidopsis clipping/fertilization data
cake - Breakage Angle of Chocolate Cakes
cbpp - Contagious bovine pleuropneumonia
cbpp2 - Contagious bovine pleuropneumonia
culcitalogreg - Coral-eating seastar Culcita novaeguineae data
culcitalvolume - Coral-eating seastar Culcita novaeguineae data
Dyestuff - Yield of dyestuff by batch
Dyestuff2 - Yield of dyestuff by batch
gopherdat2 - Gopher tortoises shell remains
grouseticks - Data on red grouse ticks from Elston et al. 2001
grouseticks_agg - Data on red grouse ticks from Elston et al. 2001
InstEval - University Lecture/Instructor Evaluations by Students at ETH
Pastes - Paste strength by batch and cask
Penicillin - Variation in penicillin testing
salamander - Mountain dusky salamander mating
schizophrenia - National Institute of Mental Health Schizophrenia Collaborative Study
sleepstudy - Reaction times in a sleep deprivation study
toenail - Toenail onychomycosis data from dermatophyte infections
VerbAgg - Verbal Aggression item responses

On CRAN:

cpp

21.91 score 691 stars 1.8k packages 63k scripts 666k downloads 9.3k mentions 129 exports 12 dependencies

Last updated from:0d5aff2e30. Checks:13 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	372
linux-devel-x86_64	OK	403
source / vignettes	OK	460
linux-release-arm64	OK	379
linux-release-x86_64	OK	416
macos-release-arm64	OK	231
macos-release-x86_64	OK	530
macos-oldrel-arm64	OK	222
macos-oldrel-x86_64	OK	513
windows-devel	OK	345
windows-release	OK	328
windows-oldrel	OK	312
wasm-release	OK	196

Exports:.makeCC .prt.aictab .prt.call .prt.family .prt.grps .prt.methTit .prt.resids .prt.VC .prt.warn .simulateFun allFit anyStructured bootMer checkConv confint.merMod cov2sdcor Cv_to_Sv Cv_to_Vv devcomp devfun2 dotplot.ranef.mer dummy expandDoubleVerts factorize findbars fixef forceNewMerMod formatVC fortify.merMod getData getDoublevertDefault getL getLambda getLambdat.dp getLambdat.i getLower getME getPar getParLength getParNames getProfLower getProfPar getProfUpper getReCovs getSingTol getTheta getThetaIndex getThetaIndexLength getThetaLength getThetaNames getUpper getVC getVCNames GHrule glFormula glmer glmer.nb glmerControl glmerLaplaceHandle glmFamily glmResp golden GQdk GQN isGLMM isLMM isNested isNewMerMod isNLMM isREML isSingular lFormula llikAIC lme4_testlevel lmer lmerControl lmerResp lmList lmResp logProf merPredD methTitle mkDataTemplate mkGlmerDevfun mkLmerDevfun mkMerMod mkNewReTrms mkParsTemplate mkRespMod mkReTrms mkVarCorr mlist2vec namedList negative.binomial Nelder_Mead NelderMead ngrps nlformula nlmer nlmerControl nlminbwrap nloptwrap nlsResp nobars optimizeGlmer optimizeLmer ranef refit refitML REMLcrit reOnly rePCA rePos sdcor2cov setPar setProfPar setTheta setVC show simulate.formula subbars Sv_to_Cv updateGlmerDevfun VarCorr varianceProf vcov.merMod vec2mlist vec2STlist Vv_to_Cv

Dependencies:boot lattice MASS Matrix minqa nlme nloptr rbibutils Rcpp RcppEigen Rdpack reformulas

Fitting Generalized Linear Mixed-Effects Models using lme4

Rendered fromglmer.Rnwusingknitr::knitr

Last update: 2026-07-03
Started: 2026-05-21

Covariance Structures

Rendered fromcovariance_structures.Rmdusingknitr::rmarkdown

Last update: 2026-06-24
Started: 2026-01-03

Autoscaling in lme4

Autoscale Mechanism | References

Rendered fromautoscale.Rmdusingknitr::rmarkdown

Last update: 2025-10-14
Started: 2025-10-14

Fitting Linear Mixed-Effects Models using lme4

Rendered fromlmer.Rnwusingknitr::knitr

Last update: 2025-07-24
Started: 2014-06-18

lme4 performance tips

Rendered fromlmerperf.Rmdusingknitr::rmarkdown

Last update: 2022-11-15
Started: 2014-10-01

Computational Methods

Rendered fromTheory.Rnwusingknitr::knitr

Last update: 2022-03-15
Started: 2012-03-15

PLS vs GLS for LMMs

Rendered fromPLSvGLS.Rnwusingutils::Sweave

Last update: 2012-03-15
Started: 2012-03-15

Help page	Topics
Linear, generalized linear, and nonlinear mixed models	lme4-package lme4
Refit a fitted model with all available optimizers to check convergence	allFit
Arabidopsis clipping/fertilization data	Arabidopsis
Model-based (Semi-)Parametric Bootstrap for Mixed Models	bootMer
Breakage Angle of Chocolate Cakes	cake
Contagious bovine pleuropneumonia	cbpp cbpp2
Extended Convergence Checking	checkConv
Compute Confidence Intervals for Parameters of a [ng]lmer Fit	confint.merMod confint.thpr
Assessing Convergence for Fitted Models	convergence
Coral-eating seastar Culcita novaeguineae data (binary predation version)	culcitalogreg
Coral-eating seastar Culcita novaeguineae data (volume loss version)	culcitalvolume
Extract the deviance component list	devcomp
Deviance Function in Terms of Standard Deviations/Correlations	devfun2
Deviance of Fitted Mixed-Effect Models	deviance deviance.merMod
Drop all possible single fixed-effect terms from a mixed effect model	drop1.merMod
Dummy variables (experimental)	dummy
Yield of dyestuff by batch	Dyestuff Dyestuff2
Attempt to convert grouping variables to factors	factorize
Extract fixed-effects estimates	fixed.effects fixef fixef.merMod
add information to data based on a fitted model	fortify fortify.merMod getData getData.merMod
Retrieve default double-vertical-bar-expansion method	getDoublevertDefault
Extract or Get Generalized Components from a Fitted Mixed Effects Model	getL getL,merMod-method getME getME.merMod
Extract Fitted Covariance Structures	getReCovs
Univariate Gauss-Hermite quadrature rule	GHrule
Fitting Generalized Linear Mixed-Effects Models	glmer
Fitting Negative Binomial GLMMs	glmer.nb negative.binomial
Handle for 'glmerLaplace'	glmerLaplaceHandle
Generator object for the 'glmFamily' class	glmFamily
Class '"glmFamily"' - a reference class for 'family'	glmFamily-class
Class '"golden"' and Generator for Golden Search Optimizer Class	golden golden-class
Gopher tortoises shell remains	gopherdat2
Sparse Gaussian / Gauss-Hermite Quadrature grid	GQdk GQN
Data on red grouse ticks from Elston et al. 2001	grouseticks grouseticks_agg
Diagonal elements of the hat matrix	hatvalues.merMod
Influence Diagnostics for Mixed-Effects Models	cooks.distance.influence.merMod cooks.distance.merMod dfbeta.influence.merMod dfbetas.influence.merMod influence.merMod
University Lecture/Instructor Evaluations by Students at ETH	InstEval
Test if a 'merMod' Object Has Current Representation	anyStructured forceNewMerMod isNewMerMod
Check characteristics of models	isGLMM isGLMM.merMod isLMM isLMM.merMod isNLMM isNLMM.merMod isREML isREML.merMod
Test Fitted Model for (Near) Singularity	getSingTol isSingular isSingular,Covariance.ar1-method isSingular,Covariance.cs-method isSingular,Covariance.diag-method isSingular,Covariance.us-method isSingular,merMod-method isSingular-methods
Detect testing level for lme4 examples and tests	lme4_testlevel
Fit Linear Mixed-Effects Models	lmer
Control of Mixed Model Fitting	.makeCC glmerControl lmerControl nlmerControl
Fit List of lm or glm Objects with a Common Model	lmList plot.lmList
Class "lmList4" of 'lm' Objects on Common Model	lmList4-class show,lmList4-method
Generator objects for the response classes	glmResp lmerResp lmResp nlsResp
Reference Classes for Response Modules, '"(lm\|glm\|nls\|lmer)Resp"'	glmResp-class lmerResp-class lmResp-class nlsResp-class
Class "merMod" of Fitted Mixed-Effect Models	anova.merMod as.function.merMod coef.merMod df.residual.merMod extractAIC.merMod family.merMod fitted.merMod formula.merMod glmerMod-class lmerMod-class logLik.merMod merMod merMod-class model.frame.merMod model.matrix.merMod ngrps.merMod nlmerMod-class nobs nobs.merMod print.merMod REMLcrit show,merMod-method show.merMod terms.merMod update.merMod weights.merMod
Generator object for the 'merPredD' class	merPredD
Class '"merPredD"' - a Dense Predictor Reference Class	merPredD-class
Create a 'merMod' Object	mkMerMod
Make new random effect terms for prediction	mkNewReTrms
Create an lmerResp, glmResp or nlsResp instance	mkRespMod
Make templates suitable for guiding mixed model simulations	mkDataTemplate mkParsTemplate
Make Variance and Correlation Components of Covariance	mkVarCorr
Modular Functions for Mixed Model Fits	glFormula lFormula mkGlmerDevfun mkLmerDevfun modular optimizeGlmer optimizeLmer updateGlmerDevfun
Self-naming list function	namedList
Nelder-Mead Optimization of Parameters, Possibly (Box) Constrained	Nelder_Mead
Class '"NelderMead"' of Nelder-Mead optimizers and its Generator	NelderMead NelderMead-class
Number of Levels of a Factor or a "merMod" Model	ngrps
Manipulate a Nonlinear Model Formula	nlformula
Fitting Nonlinear Mixed-Effects Models	nlmer
Wrappers for additional optimizers	nlminbwrap nloptwrap
Paste strength by batch and cask	Pastes
Variation in penicillin testing	Penicillin
Diagnostic Plots for 'merMod' Fits	diagnostic.plots diagnosticPlots diagnostics diagnostic_plots plot.merMod qqmath.merMod qqplot
Mixed-Effects Profile Plots (Regular / Density / Pairs)	densityplot.thpr splom.thpr xyplot.thpr
Predictions from a model at new data values	predict.merMod
Profile method for merMod objects	as.data.frame.thpr log.thpr logProf profile-methods profile.merMod varianceProf
Print and Summary Method Utilities for Mixed Effects	.prt.aictab .prt.call .prt.family .prt.grps .prt.methTit .prt.resids .prt.VC .prt.warn formatVC llikAIC methTitle
Getting p-values for fitted models	mcmcsamp pvalues
Extract the modes of the random effects	as.data.frame.ranef.mer dotplot.ranef.mer qqmath.ranef.mer ranef ranef.merMod
Refit a (merMod) Model with a Different Response	refit refit.merMod
Refit a Model by Maximum Likelihood Criterion	refitML refitML.merMod
(deprecated) formula-processing functions	expandDoubleVerts findbars isNested mkReTrms nobars reOnly subbars
PCA of random-effects covariance matrix	rePCA
Generator object for the rePos (random-effects positions) class	rePos
Class '"rePos"'	rePos-class
residuals of merMod objects	residuals.glmResp residuals.lmResp residuals.merMod
Mountain dusky salamander mating	salamander
National Institute of Mental Health Schizophrenia Collaborative Study	schizophrenia
Extract Residual Standard Deviation 'Sigma'	sigma sigma.merMod
A 'simulate' Method for 'formula' objects that dispatches based on the Left-Hand Side	simulate.formula
Simulate Responses From 'merMod' Object	.simulateFun simulate.merMod
Reaction times in a sleep deprivation study	sleepstudy
Summary for a [ng]lmer Fit	print.summary.merMod show.summary.merMod summary summary.merMod
Toenail onychomycosis data from dermatophyte infections	toenail
Troubleshooting	troubleshooting
Extract Variance and Correlation Components of Covariance	as.data.frame.VarCorr.merMod print.VarCorr.merMod VarCorr VarCorr.merMod
Convert between representations of (co-)variance structures	cov2sdcor Cv_to_Sv Cv_to_Vv mlist2vec sdcor2cov Sv_to_Cv vcconv vec2mlist vec2STlist Vv_to_Cv
Covariance matrix of estimated parameters	vcov.merMod vcov.summary.merMod
Verbal Aggression item responses	VerbAgg

Package: lme4 2.0-3

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

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