lme4 v1.1-23

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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".

Functions in lme4

Name Description
Dyestuff Yield of dyestuff by batch
GHrule Univariate Gauss-Hermite quadrature rule
GQdk Sparse Gaussian / Gauss-Hermite Quadrature grid
NelderMead-class Class "NelderMead" of Nelder-Mead optimizers and its Generator
VarCorr Extract Variance and Correlation Components
Penicillin Variation in penicillin testing
confint.merMod Compute Confidence Intervals for Parameters of a [ng]lmer Fit
NelderMead Nelder-Mead Optimization of Parameters, Possibly (Box) Constrained
Arabidopsis Arabidopsis clipping/fertilization data
Pastes Paste strength by batch and cask
checkConv Extended Convergence Checking
cake Breakage Angle of Chocolate Cakes
drop1.merMod Drop all possible single fixed-effect terms from a mixed effect model
dummy Dummy variables (experimental)
InstEval University Lecture/Instructor Evaluations by Students at ETH
isNested Is f1 nested within f2?
cbpp Contagious bovine pleuropneumonia
isREML Check characteristics of models
devcomp Extract the deviance component list
convergence Assessing Convergence for Fitted Models
bootMer Model-based (Semi-)Parametric Bootstrap for Mixed Models
lme4-package Linear, generalized linear, and nonlinear mixed models
glmFamily-class Class "glmFamily" - a reference class for family
merPredD Generator object for the merPredD class
findbars Determine random-effects expressions from a formula
influence.merMod Influence Diagnostics for Mixed-Effects Models
factorize Attempt to convert grouping variables to factors
merPredD-class Class "merPredD" - a Dense Predictor Reference Class
isSingular Test Fitted Model for (Near) Singularity
expandDoubleVerts Expand terms with '||' notation into separate '|' terms
hatvalues.merMod Diagonal elements of the hat matrix
fortify add information to data based on a fitted model
VerbAgg Verbal Aggression item responses
devfun2 Deviance Function in Terms of Standard Deviations/Correlations
ngrps Number of Levels of a Factor or a "merMod" Model
glmFamily Generator object for the glmFamily class
nlmer Fitting Nonlinear Mixed-Effects Models
grouseticks Data on red grouse ticks from Elston et al. 2001
allFit Refit a fitted model with all available optimizers
lmer Fit Linear Mixed-Effects Models
nlformula Manipulate a Nonlinear Model Formula
glmerLaplaceHandle Handle for glmerLaplace
mkMerMod Create a 'merMod' Object
nloptwrap Wrappers for additional optimizers
lmResp-class Reference Classes for Response Modules, "(lm|glm|nls|lmer)Resp"
nobars Omit terms separated by vertical bars in a formula
plot.merMod Diagnostic Plots for 'merMod' Fits
rePos-class Class "rePos"
getME Extract or Get Generalized Components from a Fitted Mixed Effects Model
mkVarCorr Make Variance and Correlation Matrices from theta
golden-class Class "golden" and Generator for Golden Search Optimizer Class
lmList Fit List of lm or glm Objects with a Common Model
residuals.merMod residuals of merMod objects
sigma Extract Residual Standard Deviation 'Sigma'
refit Refit a (merMod) Model with a Different Response
lmResp Generator objects for the response classes
lmList4-class Class "lmList4" of 'lm' Objects on Common Model
plots.thpr Mixed-Effects Profile Plots (Regular / Density / Pairs)
predict.merMod Predictions from a model at new data values
rePos Generator object for the rePos (random-effects positions) class
pvalues Getting p-values for fitted models
simulate.merMod Simulate Responses From merMod Object
fixef Extract fixed-effects estimates
mkReTrms Make Random Effect Terms: Create Z, Lambda, Lind, etc.
modular Modular Functions for Mixed Model Fits
lmerControl Control of Mixed Model Fitting
troubleshooting Troubleshooting
refitML Refit a Model by Maximum Likelihood Criterion
subbars "Sub[stitute] Bars"
profile-methods Profile method for merMod objects
sleepstudy Reaction times in a sleep deprivation study
glmer Fitting Generalized Linear Mixed-Effects Models
glmer.nb Fitting Negative Binomial GLMMs
merMod-class Class "merMod" of Fitted Mixed-Effect Models
mkRespMod Create an lmerResp, glmResp or nlsResp instance
ranef Extract the modes of the random effects
rePCA PCA of random-effects covariance matrix
mkSimulateTemplate Make templates suitable for guiding mixed model simulations
prt-utilities Print and Summary Method Utilities for Mixed Effects
vcconv Convert between representations of (co-)variance structures
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Vignettes of lme4

Name
PLSvGLS.Rnw
Theory.Rnw
lme4.bib
lmer.Rnw
lmer.bib
lmerperf.Rmd
lmerperf.md
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