# Linear Mixed-Effects Models using 'Eigen' and S4

## Documentation for package ‘lme4’ version 2.0-1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G H I L M N O P Q R S T U V W X misc

lme4-package | Linear, generalized linear, and nonlinear mixed models

## -- A --

allFit | Refit a fitted model with all available optimizers to check convergence
anova.merMod | Class "merMod" of Fitted Mixed-Effect Models
anyStructured | Test if a 'merMod' Object Has Current Representation
Arabidopsis | Arabidopsis clipping/fertilization data
as.data.frame.ranef.mer | Extract the modes of the random effects
as.data.frame.thpr | Profile method for merMod objects
as.data.frame.VarCorr.merMod | Extract Variance and Correlation Components of Covariance
as.function.merMod | Class "merMod" of Fitted Mixed-Effect Models

## -- B --

bootMer | Model-based (Semi-)Parametric Bootstrap for Mixed Models

## -- C --

cake | Breakage Angle of Chocolate Cakes
cbpp | Contagious bovine pleuropneumonia
cbpp2 | Contagious bovine pleuropneumonia
checkConv | Extended Convergence Checking
coef.merMod | Class "merMod" of Fitted Mixed-Effect Models
confint.merMod | Compute Confidence Intervals for Parameters of a [ng]lmer Fit
confint.thpr | Compute Confidence Intervals for Parameters of a [ng]lmer Fit
convergence | Assessing Convergence for Fitted Models
cooks.distance.influence.merMod | Influence Diagnostics for Mixed-Effects Models
cooks.distance.merMod | Influence Diagnostics for Mixed-Effects Models
cov2sdcor | Convert between representations of (co-)variance structures
culcitalogreg | Coral-eating seastar Culcita novaeguineae data (binary predation version)
culcitalvolume | Coral-eating seastar Culcita novaeguineae data (volume loss version)
Cv_to_Sv | Convert between representations of (co-)variance structures
Cv_to_Vv | Convert between representations of (co-)variance structures

## -- D --

densityplot.thpr | Mixed-Effects Profile Plots (Regular / Density / Pairs)
devcomp | Extract the deviance component list
devfun2 | Deviance Function in Terms of Standard Deviations/Correlations
deviance.merMod | Class "merMod" of Fitted Mixed-Effect Models
df.residual.merMod | Class "merMod" of Fitted Mixed-Effect Models
dfbeta.influence.merMod | Influence Diagnostics for Mixed-Effects Models
dfbetas.influence.merMod | Influence Diagnostics for Mixed-Effects Models
diagnostic.plots | Diagnostic Plots for 'merMod' Fits
diagnosticPlots | Diagnostic Plots for 'merMod' Fits
diagnostics | Diagnostic Plots for 'merMod' Fits
diagnostic_plots | Diagnostic Plots for 'merMod' Fits
dotplot.ranef.mer | Extract the modes of the random effects
drop1.merMod | Drop all possible single fixed-effect terms from a mixed effect model
dummy | Dummy variables (experimental)
Dyestuff | Yield of dyestuff by batch
Dyestuff2 | Yield of dyestuff by batch

## -- E --

expandDoubleVerts | (deprecated) formula-processing functions
extractAIC.merMod | Class "merMod" of Fitted Mixed-Effect Models

## -- F --

factorize | Attempt to convert grouping variables to factors
family.merMod | Class "merMod" of Fitted Mixed-Effect Models
findbars | (deprecated) formula-processing functions
fitted.merMod | Class "merMod" of Fitted Mixed-Effect Models
fixed.effects | Extract fixed-effects estimates
fixef | Extract fixed-effects estimates
fixef.merMod | Extract fixed-effects estimates
forceNewMerMod | Test if a 'merMod' Object Has Current Representation
formatVC | Print and Summary Method Utilities for Mixed Effects
formula.merMod | Class "merMod" of Fitted Mixed-Effect Models
fortify | add information to data based on a fitted model
fortify.merMod | add information to data based on a fitted model

## -- G --

getData | add information to data based on a fitted model
getData.merMod | add information to data based on a fitted model
getDoublevertDefault | Retrieve default double-vertical-bar-expansion method
getL | Extract or Get Generalized Components from a Fitted Mixed Effects Model
getL-method | Extract or Get Generalized Components from a Fitted Mixed Effects Model
getME | Extract or Get Generalized Components from a Fitted Mixed Effects Model
getME.merMod | Extract or Get Generalized Components from a Fitted Mixed Effects Model
getReCovs | Extract Fitted Covariance Structures
getSingTol | Test Fitted Model for (Near) Singularity
GHrule | Univariate Gauss-Hermite quadrature rule
glFormula | Modular Functions for Mixed Model Fits
glmer | Fitting Generalized Linear Mixed-Effects Models
glmer.nb | Fitting Negative Binomial GLMMs
glmerControl | Control of Mixed Model Fitting
glmerLaplaceHandle | Handle for 'glmerLaplace'
glmerMod-class | Class "merMod" of Fitted Mixed-Effect Models
glmFamily | Generator object for the 'glmFamily' class
glmFamily-class | Class '"glmFamily"' - a reference class for 'family'
glmResp | Generator objects for the response classes
glmResp-class | Reference Classes for Response Modules, '"(lm|glm|nls|lmer)Resp"'
golden | Class '"golden"' and Generator for Golden Search Optimizer Class
golden-class | Class '"golden"' and Generator for Golden Search Optimizer Class
gopherdat2 | Gopher tortoises shell remains
GQdk | Sparse Gaussian / Gauss-Hermite Quadrature grid
GQN | Sparse Gaussian / Gauss-Hermite Quadrature grid
grouseticks | Data on red grouse ticks from Elston et al. 2001
grouseticks_agg | Data on red grouse ticks from Elston et al. 2001

## -- H --

hatvalues.merMod | Diagonal elements of the hat matrix

## -- I --

influence.merMod | Influence Diagnostics for Mixed-Effects Models
InstEval | University Lecture/Instructor Evaluations by Students at ETH
isGLMM | Check characteristics of models
isGLMM.merMod | Check characteristics of models
isLMM | Check characteristics of models
isLMM.merMod | Check characteristics of models
isNested | (deprecated) formula-processing functions
isNewMerMod | Test if a 'merMod' Object Has Current Representation
isNLMM | Check characteristics of models
isNLMM.merMod | Check characteristics of models
isREML | Check characteristics of models
isREML.merMod | Check characteristics of models
isSingular | Test Fitted Model for (Near) Singularity
isSingular-method | Test Fitted Model for (Near) Singularity
isSingular-methods | Test Fitted Model for (Near) Singularity

## -- L --

lFormula | Modular Functions for Mixed Model Fits
llikAIC | Print and Summary Method Utilities for Mixed Effects
lme4 | Linear, generalized linear, and nonlinear mixed models
lme4_testlevel | Detect testing level for lme4 examples and tests
lmer | Fit Linear Mixed-Effects Models
lmerControl | Control of Mixed Model Fitting
lmerMod-class | Class "merMod" of Fitted Mixed-Effect Models
lmerResp | Generator objects for the response classes
lmerResp-class | Reference Classes for Response Modules, '"(lm|glm|nls|lmer)Resp"'
lmList | Fit List of lm or glm 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, '"(lm|glm|nls|lmer)Resp"'
log.thpr | Profile method for merMod objects
logLik.merMod | Class "merMod" of Fitted Mixed-Effect Models
logProf | Profile method for merMod objects

## -- M --

mcmcsamp | Getting p-values for fitted models
merMod | Class "merMod" of Fitted Mixed-Effect Models
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
methTitle | Print and Summary Method Utilities for Mixed Effects
mkDataTemplate | Make templates suitable for guiding mixed model simulations
mkGlmerDevfun | Modular Functions for Mixed Model Fits
mkLmerDevfun | Modular Functions for Mixed Model Fits
mkMerMod | Create a 'merMod' Object
mkNewReTrms | Make new random effect terms for prediction
mkParsTemplate | Make templates suitable for guiding mixed model simulations
mkRespMod | Create an lmerResp, glmResp or nlsResp instance
mkReTrms | (deprecated) formula-processing functions
mkVarCorr | Make Variance and Correlation Components of Covariance
mlist2vec | Convert between representations of (co-)variance structures
model.frame.merMod | Class "merMod" of Fitted Mixed-Effect Models
model.matrix.merMod | Class "merMod" of Fitted Mixed-Effect Models
modular | Modular Functions for Mixed Model Fits

## -- N --

namedList | Self-naming list function
negative.binomial | Fitting Negative Binomial GLMMs
NelderMead | Class '"NelderMead"' of Nelder-Mead optimizers and its Generator
NelderMead-class | Class '"NelderMead"' of Nelder-Mead optimizers and its Generator
Nelder_Mead | Nelder-Mead Optimization of Parameters, Possibly (Box) Constrained
ngrps | Number of Levels of a Factor or a "merMod" Model
ngrps.merMod | Class "merMod" of Fitted Mixed-Effect Models
nlformula | Manipulate a Nonlinear Model Formula
nlmer | Fitting Nonlinear Mixed-Effects Models
nlmerControl | Control of Mixed Model Fitting
nlmerMod-class | Class "merMod" of Fitted Mixed-Effect Models
nlminbwrap | Wrappers for additional optimizers
nloptwrap | Wrappers for additional optimizers
nlsResp | Generator objects for the response classes
nlsResp-class | Reference Classes for Response Modules, '"(lm|glm|nls|lmer)Resp"'
nobars | (deprecated) formula-processing functions
nobs | Class "merMod" of Fitted Mixed-Effect Models
nobs.merMod | Class "merMod" of Fitted Mixed-Effect Models

## -- O --

optimizeGlmer | Modular Functions for Mixed Model Fits
optimizeLmer | Modular Functions for Mixed Model Fits

## -- P --

Pastes | Paste strength by batch and cask
Penicillin | Variation in penicillin testing
plot.lmList | Fit List of lm or glm Objects with a Common Model
plot.merMod | Diagnostic Plots for 'merMod' Fits
predict.merMod | Predictions from a model at new data values
print.merMod | Class "merMod" of Fitted Mixed-Effect Models
print.summary.merMod | Summary for a [ng]lmer Fit
print.VarCorr.merMod | Extract Variance and Correlation Components of Covariance
profile-methods | Profile method for merMod objects
profile.merMod | Profile method for merMod objects
pvalues | Getting p-values for fitted models

## -- Q --

qqmath.merMod | Diagnostic Plots for 'merMod' Fits
qqmath.ranef.mer | Extract the modes of the random effects
qqplot | Diagnostic Plots for 'merMod' Fits

## -- R --

ranef | Extract the modes of the random effects
ranef.merMod | Extract the modes of the random effects
refit | Refit a (merMod) Model with a Different Response
refit.merMod | Refit a (merMod) Model with a Different Response
refitML | Refit a Model by Maximum Likelihood Criterion
refitML.merMod | Refit a Model by Maximum Likelihood Criterion
REMLcrit | Class "merMod" of Fitted Mixed-Effect Models
reOnly | (deprecated) formula-processing functions
rePCA | PCA of random-effects covariance matrix
rePos | Generator object for the rePos (random-effects positions) class
rePos-class | Class '"rePos"'
residuals.glmResp | residuals of merMod objects
residuals.lmResp | residuals of merMod objects
residuals.merMod | residuals of merMod objects

## -- S --

salamander | Mountain dusky salamander mating
schizophrenia | National Institute of Mental Health Schizophrenia Collaborative Study
sdcor2cov | Convert between representations of (co-)variance structures
show-method | Class "lmList4" of 'lm' Objects on Common Model
show-method | Class "merMod" of Fitted Mixed-Effect Models
show.merMod | Class "merMod" of Fitted Mixed-Effect Models
show.summary.merMod | Summary for a [ng]lmer Fit
sigma | Extract Residual Standard Deviation 'Sigma'
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 | Simulate Responses From 'merMod' Object
sleepstudy | Reaction times in a sleep deprivation study
splom.thpr | Mixed-Effects Profile Plots (Regular / Density / Pairs)
subbars | (deprecated) formula-processing functions
summary | Summary for a [ng]lmer Fit
summary.merMod | Summary for a [ng]lmer Fit
Sv_to_Cv | Convert between representations of (co-)variance structures

## -- T --

terms.merMod | Class "merMod" of Fitted Mixed-Effect Models
toenail | Toenail onychomycosis data from dermatophyte infections
troubleshooting | Troubleshooting

## -- U --

update.merMod | Class "merMod" of Fitted Mixed-Effect Models
updateGlmerDevfun | Modular Functions for Mixed Model Fits

## -- V --

VarCorr | Extract Variance and Correlation Components of Covariance
VarCorr.merMod | Extract Variance and Correlation Components of Covariance
varianceProf | Profile method for merMod objects
vcconv | Convert between representations of (co-)variance structures
vcov.merMod | Covariance matrix of estimated parameters
vcov.summary.merMod | Covariance matrix of estimated parameters
vec2mlist | Convert between representations of (co-)variance structures
vec2STlist | Convert between representations of (co-)variance structures
VerbAgg | Verbal Aggression item responses
Vv_to_Cv | Convert between representations of (co-)variance structures

## -- W --

weights.merMod | Class "merMod" of Fitted Mixed-Effect Models

## -- X --

xyplot.thpr | Mixed-Effects Profile Plots (Regular / Density / Pairs)

## -- misc --

.makeCC | Control of Mixed Model Fitting
.prt.aictab | Print and Summary Method Utilities for Mixed Effects
.prt.call | Print and Summary Method Utilities for Mixed Effects
.prt.family | Print and Summary Method Utilities for Mixed Effects
.prt.grps | Print and Summary Method Utilities for Mixed Effects
.prt.methTit | Print and Summary Method Utilities for Mixed Effects
.prt.resids | Print and Summary Method Utilities for Mixed Effects
.prt.VC | Print and Summary Method Utilities for Mixed Effects
.prt.warn | Print and Summary Method Utilities for Mixed Effects
.simulateFun | Simulate Responses From 'merMod' Object