lme4 v1.1-21

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