Package index • lme4

All functions
`Arabidopsis`	Arabidopsis clipping/fertilization data
`Dyestuff` `Dyestuff2`	Yield of dyestuff by batch
`GHrule()`	Univariate Gauss-Hermite quadrature rule
`GQdk()` `GQN`	Sparse Gaussian / Gauss-Hermite Quadrature grid
`InstEval`	University Lecture/Instructor Evaluations by Students at ETH
`NelderMead()`	Class `"NelderMead"` of Nelder-Mead optimizers and its Generator
`Nelder_Mead()`	Nelder-Mead Optimization of Parameters, Possibly (Box) Constrained
`Pastes`	Paste strength by batch and cask
`Penicillin`	Variation in penicillin testing
`VarCorr(<merMod>)` `as.data.frame(<VarCorr.merMod>)` `print(<VarCorr.merMod>)`	Extract Variance and Correlation Components
`VerbAgg`	Verbal Aggression item responses
`allFit()`	Refit a fitted model with all available optimizers
`bootMer()`	Model-based (Semi-)Parametric Bootstrap for Mixed Models
`cake`	Breakage Angle of Chocolate Cakes
`cbpp`	Contagious bovine pleuropneumonia
`checkConv()`	Extended Convergence Checking
`confint(<merMod>)` `confint(<thpr>)`	Compute Confidence Intervals for Parameters of a [ng]lmer Fit
`convergence`	Assessing Convergence for Fitted Models
`devcomp()`	Extract the deviance component list
`devfun2()`	Deviance Function in Terms of Standard Deviations/Correlations
`drop1(<merMod>)`	Drop all possible single fixed-effect terms from a mixed effect model
`dummy()`	Dummy variables (experimental)
`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(<merMod>)`	Extract fixed-effects estimates
`fortify.merMod()` `getData(<merMod>)`	add information to data based on a fitted model
`getME()`	Extract or Get Generalized Components from a Fitted Mixed Effects Model
`glmFamily-class`	Class `"glmFamily"` - a reference class for `family`
`glmFamily()`	Generator object for the `glmFamily` class
`glmer()`	Fitting Generalized Linear Mixed-Effects Models
`glmer.nb()`	Fitting Negative Binomial GLMMs
`glmerLaplaceHandle()`	Handle for `glmerLaplace`
`golden()`	Class `"golden"` and Generator for Golden Search Optimizer Class
`grouseticks`	Data on red grouse ticks from Elston et al. 2001
`hatvalues(<merMod>)`	Diagonal elements of the hat matrix
`influence(<merMod>)` `cooks.distance(<influence.merMod>)` `dfbeta(<influence.merMod>)` `dfbetas(<influence.merMod>)`	Influence Diagnostics for Mixed-Effects Models
`isNested()`	Is f1 nested within f2?
`isREML()` `isLMM()` `isNLMM()` `isGLMM()`	Check characteristics of models
`isSingular()`	Test Fitted Model for (Near) Singularity
`lmList()`	Fit List of lm or glm Objects with a Common Model
`lmList4-class` `show,lmList4-method`	Class "lmList4" of 'lm' Objects on Common Model
`glmResp-class` `lmerResp-class` `lmResp-class` `nlsResp-class`	Reference Classes for Response Modules, `"(lm\|glm\|nls\|lmer)Resp"`
`lmResp()`	Generator objects for the response classes
`lme4` `lme4-package`	Linear, generalized linear, and nonlinear mixed models
`lme4_testlevel()`	Detect testing level for lme4 examples and tests
`lmer()`	Fit Linear Mixed-Effects Models
`lmerControl()` `glmerControl()` `nlmerControl()` `.makeCC()`	Control of Mixed Model Fitting
`anova(<merMod>)` `as.function(<merMod>)` `coef(<merMod>)` `deviance(<merMod>)` `REMLcrit()` `extractAIC(<merMod>)` `family(<merMod>)` `formula(<merMod>)` `fitted(<merMod>)` `logLik(<merMod>)` `nobs(<merMod>)` `ngrps(<merMod>)` `terms(<merMod>)` `model.frame(<merMod>)` `model.matrix(<merMod>)` `print(<merMod>)` `summary(<merMod>)` `print(<summary.merMod>)` `update(<merMod>)` `weights(<merMod>)`	Class "merMod" of Fitted Mixed-Effect Models
`merPredD-class`	Class `"merPredD"` - a Dense Predictor Reference Class
`merPredD()`	Generator object for the `merPredD` class
`mkMerMod()`	Create a 'merMod' Object
`mkReTrms()` `mkNewReTrms()`	Make Random Effect Terms: Create Z, Lambda, Lind, etc.
`mkRespMod()`	Create an lmerResp, glmResp or nlsResp instance
`mkParsTemplate()` `mkDataTemplate()`	Make templates suitable for guiding mixed model simulations
`mkVarCorr()`	Make Variance and Correlation Matrices from `theta`
`lFormula()` `mkLmerDevfun()` `optimizeLmer()` `glFormula()` `mkGlmerDevfun()` `optimizeGlmer()` `updateGlmerDevfun()`	Modular Functions for Mixed Model Fits
`namedList()`	Self-naming list function
`ngrps()`	Number of Levels of a Factor or a "merMod" Model
`nlformula()`	Manipulate a Nonlinear Model Formula
`nlmer()`	Fitting Nonlinear Mixed-Effects Models
`nloptwrap()` `nlminbwrap()`	Wrappers for additional optimizers
`nobars()`	Omit terms separated by vertical bars in a formula
`plot(<merMod>)` `qqmath(<merMod>)`	Diagnostic Plots for 'merMod' Fits
`xyplot(<thpr>)` `densityplot(<thpr>)` `splom(<thpr>)`	Mixed-Effects Profile Plots (Regular / Density / Pairs)
`predict(<merMod>)`	Predictions from a model at new data values
`profile(<merMod>)` `as.data.frame(<thpr>)` `log(<thpr>)` `logProf()` `varianceProf()`	Profile method for merMod objects
`mcmcsamp` `pvalues`	Getting p-values for fitted models
`ranef(<merMod>)` `dotplot(<ranef.mer>)` `qqmath(<ranef.mer>)` `as.data.frame(<ranef.mer>)`	Extract the modes of the random effects
`rePCA()`	PCA of random-effects covariance matrix
`rePos-class`	Class `"rePos"`
`rePos()`	Generator object for the rePos (random-effects positions) class
`refit()`	Refit a (merMod) Model with a Different Response
`refitML()`	Refit a Model by Maximum Likelihood Criterion
`residuals(<merMod>)` `residuals(<lmResp>)` `residuals(<glmResp>)`	residuals of merMod objects
`sigma(<merMod>)`	Extract Residual Standard Deviation 'Sigma'
`simulate(<formula>)`	A `simulate` Method for `formula` objects that dispatches based on the Left-Hand Side
`simulate(<merMod>)` `.simulateFun()`	Simulate Responses From `merMod` Object
`sleepstudy`	Reaction times in a sleep deprivation study
`subbars()`	"Sub[stitute] Bars"
`troubleshooting`	Troubleshooting
`llikAIC()` `methTitle()` `.prt.methTit()` `.prt.family()` `.prt.resids()` `.prt.call()` `.prt.aictab()` `.prt.grps()` `.prt.warn()` `.prt.VC()` `formatVC()`	Print and Summary Method Utilities for Mixed Effects
`mlist2vec()` `vec2mlist()` `vec2STlist()` `sdcor2cov()` `cov2sdcor()` `Vv_to_Cv()` `Sv_to_Cv()` `Cv_to_Vv()` `Cv_to_Sv()`	Convert between representations of (co-)variance structures
`vcov(<merMod>)`	Covariance matrix of estimated parameters

Reference

All functions