Linear Mixed-Effects Models using 'Eigen' and S4


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Documentation for package ‘lme4’ version 1.1-35.2

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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