Linear Mixed-Effects Models using 'Eigen' and S4

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Documentation for package ‘lme4’ version 1.1-35.1

• 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
anova.merMod	Class "merMod" of Fitted Mixed-Effect Models
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
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
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
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
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	Expand terms with "||" notation into separate "|" terms
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	Determine random-effects expressions from a formula
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
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
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
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
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	Is f1 nested within f2?
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

-- 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 Random Effect Terms: Create Z, Lambda, Lind, etc.
mkParsTemplate	Make templates suitable for guiding mixed model simulations
mkRespMod	Create an lmerResp, glmResp or nlsResp instance
mkReTrms	Make Random Effect Terms: Create Z, Lambda, Lind, etc.
mkVarCorr	Make Variance and Correlation Matrices from 'theta'
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	Omit terms separated by vertical bars in a formula
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	Class "merMod" of Fitted Mixed-Effect Models
print.VarCorr.merMod	Extract Variance and Correlation Components
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

-- 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
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 --

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	Class "merMod" of Fitted Mixed-Effect Models
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	"Sub[stitute] Bars"
summary.merMod	Class "merMod" of Fitted Mixed-Effect Models
summary.summary.merMod	Class "merMod" of Fitted Mixed-Effect Models
Sv_to_Cv	Convert between representations of (co-)variance structures

-- T --

terms.merMod	Class "merMod" of Fitted Mixed-Effect Models
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
VarCorr.merMod	Extract Variance and Correlation Components
varianceProf	Profile method for merMod objects
vcconv	Convert between representations of (co-)variance structures
vcov.merMod	Class "merMod" of Fitted Mixed-Effect Models
vcov.summary.merMod	Class "merMod" of Fitted Mixed-Effect Models
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
||	Expand terms with "||" notation into separate "|" terms