lme4 v1.1-16

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