lme4 v1.1-19

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