lme4 v1.1-17

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