Package: lme4 2.0-1

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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], 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], Mikael Jagan [aut], Ross D. Boylan [ctb], Anna Ly [aut]

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lme4.pdf |lme4.html✨
lme4/json (API)
NEWS

# 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
  • Dyestuff - Yield of dyestuff by batch
  • Dyestuff2 - Yield of dyestuff by batch
  • InstEval - University Lecture/Instructor Evaluations by Students at ETH
  • Pastes - Paste strength by batch and cask
  • Penicillin - Variation in penicillin testing
  • VerbAgg - Verbal Aggression item responses
  • 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
  • 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
  • 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

On CRAN:

Conda:

cpp

21.56 score 671 stars 1.7k packages 63k scripts 565k downloads 9.3k mentions 106 exports 13 dependencies

Last updated from:e817c15561. Checks:6 ERROR, 2 OK, 5 NOTE. Indexed: yes.

TargetResultTotal timeArtifact
linux-devel-arm64ERROR283
linux-devel-x86_64ERROR272
source / vignettesOK384
linux-release-arm64ERROR287
linux-release-x86_64NOTE404
macos-devel-arm64ERROR192
macos-devel-x86_64ERROR367
macos-release-arm64NOTE238
macos-release-x86_64NOTE433
windows-develERROR288
windows-releaseNOTE383
windows-oldrelNOTE341
wasm-releaseOK179

Exports:.makeCC.prt.aictab.prt.call.prt.family.prt.grps.prt.methTit.prt.resids.prt.VC.prt.warn.simulateFunallFitanyStructuredbootMercheckConvconfint.merModcov2sdcorCv_to_SvCv_to_Vvdevcompdevfun2dotplot.ranef.merdummyexpandDoubleVertsfactorizefindbarsfixefforceNewMerModformatVCfortify.merModgetDatagetDoublevertDefaultgetLgetMEgetReCovsgetSingTolGHruleglFormulaglmerglmer.nbglmerControlglmerLaplaceHandleglmFamilyglmRespgoldenGQdkGQNisGLMMisLMMisNestedisNewMerModisNLMMisREMLisSingularlFormulallikAIClme4_testlevellmerlmerControllmerResplmListlmResplogProfmerPredDmethTitlemkDataTemplatemkGlmerDevfunmkLmerDevfunmkMerModmkNewReTrmsmkParsTemplatemkRespModmkReTrmsmkVarCorrmlist2vecnamedListnegative.binomialNelder_MeadNelderMeadngrpsnlformulanlmernlmerControlnlminbwrapnloptwrapnlsRespnobarsoptimizeGlmeroptimizeLmerranefrefitrefitMLREMLcritrePCArePossdcor2covshowsimulate.formulasubbarsSv_to_CvupdateGlmerDevfunVarCorrvarianceProfvcov.merModvec2mlistvec2STlistVv_to_Cv

Dependencies:bootlatticeMASSMatrixminqanlmenloptrrbibutilsRcppRcppEigenRdpackreformulasrlang

Autoscaling in lme4

Rendered fromautoscale.Rmdusingknitr::rmarkdownon Feb 20 2026.

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

Computational Methods

Rendered fromTheory.Rnwusingknitr::knitron Feb 20 2026.

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

Covariance Structures

Rendered fromcovariance_structures.Rmdusingknitr::rmarkdownon Feb 20 2026.

Last update: 2026-01-23
Started: 2026-01-03

Fitting Linear Mixed-Effects Models using lme4

Rendered fromlmer.Rnwusingknitr::knitron Feb 20 2026.

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

lme4 performance tips

Rendered fromlmerperf.Rmdusingknitr::rmarkdownon Feb 20 2026.

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

PLS vs GLS for LMMs

Rendered fromPLSvGLS.Rnwusingutils::Sweaveon Feb 20 2026.

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

Readme and manuals

Help Manual

Help pageTopics
Linear, generalized linear, and nonlinear mixed modelslme4-package lme4
Refit a fitted model with all available optimizers to check convergenceallFit
Arabidopsis clipping/fertilization dataArabidopsis
Model-based (Semi-)Parametric Bootstrap for Mixed ModelsbootMer
Breakage Angle of Chocolate Cakescake
Contagious bovine pleuropneumoniacbpp cbpp2
Extended Convergence CheckingcheckConv
Compute Confidence Intervals for Parameters of a [ng]lmer Fitconfint.merMod confint.thpr
Assessing Convergence for Fitted Modelsconvergence
Coral-eating seastar Culcita novaeguineae data (binary predation version)culcitalogreg
Coral-eating seastar Culcita novaeguineae data (volume loss version)culcitalvolume
Extract the deviance component listdevcomp
Deviance Function in Terms of Standard Deviations/Correlationsdevfun2
Drop all possible single fixed-effect terms from a mixed effect modeldrop1.merMod
Dummy variables (experimental)dummy
Yield of dyestuff by batchDyestuff Dyestuff2
Attempt to convert grouping variables to factorsfactorize
Extract fixed-effects estimatesfixed.effects fixef fixef.merMod
add information to data based on a fitted modelfortify fortify.merMod getData getData.merMod
Retrieve default double-vertical-bar-expansion methodgetDoublevertDefault
Extract or Get Generalized Components from a Fitted Mixed Effects ModelgetL getL,merMod-method getME getME.merMod
Extract Fitted Covariance StructuresgetReCovs
Univariate Gauss-Hermite quadrature ruleGHrule
Fitting Generalized Linear Mixed-Effects Modelsglmer
Fitting Negative Binomial GLMMsglmer.nb negative.binomial
Handle for 'glmerLaplace'glmerLaplaceHandle
Generator object for the 'glmFamily' classglmFamily
Class '"glmFamily"' - a reference class for 'family'glmFamily-class
Class '"golden"' and Generator for Golden Search Optimizer Classgolden golden-class
Gopher tortoises shell remainsgopherdat2
Sparse Gaussian / Gauss-Hermite Quadrature gridGQdk GQN
Data on red grouse ticks from Elston et al. 2001grouseticks grouseticks_agg
Diagonal elements of the hat matrixhatvalues.merMod
Influence Diagnostics for Mixed-Effects Modelscooks.distance.influence.merMod cooks.distance.merMod dfbeta.influence.merMod dfbetas.influence.merMod influence.merMod
University Lecture/Instructor Evaluations by Students at ETHInstEval
Test if a 'merMod' Object Has Current RepresentationanyStructured forceNewMerMod isNewMerMod
Check characteristics of modelsisGLMM isGLMM.merMod isLMM isLMM.merMod isNLMM isNLMM.merMod isREML isREML.merMod
Test Fitted Model for (Near) SingularitygetSingTol 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 testslme4_testlevel
Fit Linear Mixed-Effects Modelslmer
Control of Mixed Model Fitting.makeCC glmerControl lmerControl nlmerControl
Fit List of lm or glm Objects with a Common ModellmList plot.lmList
Class "lmList4" of 'lm' Objects on Common ModellmList4-class show,lmList4-method
Generator objects for the response classesglmResp 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 Modelsanova.merMod as.function.merMod coef.merMod deviance.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' classmerPredD
Class '"merPredD"' - a Dense Predictor Reference ClassmerPredD-class
Create a 'merMod' ObjectmkMerMod
Make new random effect terms for predictionmkNewReTrms
Create an lmerResp, glmResp or nlsResp instancemkRespMod
Make templates suitable for guiding mixed model simulationsmkDataTemplate mkParsTemplate
Make Variance and Correlation Components of CovariancemkVarCorr
Modular Functions for Mixed Model FitsglFormula lFormula mkGlmerDevfun mkLmerDevfun modular optimizeGlmer optimizeLmer updateGlmerDevfun
Self-naming list functionnamedList
Nelder-Mead Optimization of Parameters, Possibly (Box) ConstrainedNelder_Mead
Class '"NelderMead"' of Nelder-Mead optimizers and its GeneratorNelderMead NelderMead-class
Number of Levels of a Factor or a "merMod" Modelngrps
Manipulate a Nonlinear Model Formulanlformula
Fitting Nonlinear Mixed-Effects Modelsnlmer
Wrappers for additional optimizersnlminbwrap nloptwrap
Paste strength by batch and caskPastes
Variation in penicillin testingPenicillin
Diagnostic Plots for 'merMod' Fitsdiagnostic.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 valuespredict.merMod
Profile method for merMod objectsas.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 modelsmcmcsamp pvalues
Extract the modes of the random effectsas.data.frame.ranef.mer dotplot.ranef.mer qqmath.ranef.mer ranef ranef.merMod
Refit a (merMod) Model with a Different Responserefit refit.merMod
Refit a Model by Maximum Likelihood CriterionrefitML refitML.merMod
(deprecated) formula-processing functionsexpandDoubleVerts findbars isNested mkReTrms nobars subbars
PCA of random-effects covariance matrixrePCA
Generator object for the rePos (random-effects positions) classrePos
Class '"rePos"'rePos-class
residuals of merMod objectsresiduals.glmResp residuals.lmResp residuals.merMod
Mountain dusky salamander matingsalamander
National Institute of Mental Health Schizophrenia Collaborative Studyschizophrenia
Extract Residual Standard Deviation 'Sigma'sigma sigma.merMod
A 'simulate' Method for 'formula' objects that dispatches based on the Left-Hand Sidesimulate.formula
Simulate Responses From 'merMod' Object.simulateFun simulate.merMod
Reaction times in a sleep deprivation studysleepstudy
Summary for a [ng]lmer Fitprint.summary.merMod show.summary.merMod summary summary.merMod
Toenail onychomycosis data from dermatophyte infectionstoenail
Troubleshootingtroubleshooting
Extract Variance and Correlation Components of Covarianceas.data.frame.VarCorr.merMod print.VarCorr.merMod VarCorr VarCorr.merMod
Convert between representations of (co-)variance structurescov2sdcor Cv_to_Sv Cv_to_Vv mlist2vec sdcor2cov Sv_to_Cv vcconv vec2mlist vec2STlist Vv_to_Cv
Covariance matrix of estimated parametersvcov.merMod vcov.summary.merMod
Verbal Aggression item responsesVerbAgg
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