lme4 v1.1-14

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