lme4 v1.1-6


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by Ben Bolker

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
bootMer Model-based (Semi-)Parametric Bootstrap for Mixed Models
dummy Dummy variables (experimental)
confint.merMod Compute confidence intervals on the parameters of an lme4 fit
GQdk Sparse Gaussian Quadrature grid
Penicillin Variation in penicillin testing
devcomp Extract the deviance component list
getME Extract or Get Generalized Components from a Fitted Mixed Effects Model
GQN Sparse Gauss-Hermite quadrature grids
fixef Extract fixed-effects estimates
cake Breakage Angle of Chocolate Cakes
findbars Determine random-effects expressions from a formula
VerbAgg Verbal Aggression item responses
InstEval University Lecture/Instructor Evaluations by Students at ETH
lmerControl Control of Mixed Model Fitting
drop1.merMod Drop all possible single fixed-effect terms from a mixed effect model
ranef Extract the modes of the random effects
fortify add information to data based on a fitted model
Pastes Paste strength by batch and cask
pvalues Getting p-values for fitted models
expandDoubleVerts Expand terms with '||' notation into separate '|' terms
lmList-class Class "lmList" of 'lm' Objects on Common Model
merPredD Generator object for the merPredD class
golden Generator object for the golden search optimizer class.
plots.thpr Mixed-Effects Profile Plots (Regular / Density / Pairs)
mkRespMod Create an lmerResp, glmResp or nlsResp instance
varianceProf Transform to the variance scale
profile-methods Profile method for merMod objects
golden-class Class "golden"
NelderMead-class Class "NelderMead" of Nelder-Mead optimizers and its Generator
mkVarCorr Make Variance and Correlation Matrices from theta
Dyestuff Yield of dyestuff by batch
simulate.merMod Simulate responses from a merMod object
NelderMead Nelder-Mead Optimization of Parameters, Possibly (Box) Constrained
modular Modular functions for mixed model fits
cbpp Contagious bovine pleuropneumonia
mkMerMod Create a merMod object
sigma Extract residual standard error
nlformula Manipulate a nonlinear model formula.
grouseticks Data on red grouse ticks from Elston et al. 2001
nobars Omit terms separated by vertical bars in a formula
glmer Fit Generalized Linear Mixed-Effects Models
lmResp Generator objects for the response classes
ngrps Number of levels
lmResp-class Classes "lmResp", "glmResp", "nlsResp" and "lmerResp"
nlmer Fit Nonlinear Mixed-Effects Models
residuals.merMod residuals of merMod objects
subbars "Sub[stitute] Bars"
rePos Generator object for the rePos (random-effects positions) class
refitML Refit a model by maximum likelihood criterion
plot.merMod diagnostic plots for merMod fits
merPredD-class Class "merPredD" - a dense predictor reference class
glmFamily-class Class "glmFamily" - a reference class for family
lme4-package Linear, generalized linear, and nonlinear mixed models
merMod-class Class "merMod" of Fitted Mixed-Effect Models
isNested Is f1 nested within f2?
sleepstudy Reaction times in a sleep deprivation study
mkReTrms Create Z, Lambda, Lind, etc.
refit Refit a model with a new response, by maximum likelihood criterion
isREML Check characteristics of models
predict.merMod Predictions from a model at new data values
mkdevfun Create a deviance evaluation function from a predictor and a response module
GHrule Univariate Gauss-Hermite quadrature rule
glmFamily Generator object for the glmFamily class
glmer.nb glmer() for Negative Binomial
lmer Fit Linear Mixed-Effects Models
rePos-class Class "rePos"
lmList List of lm Objects with a Common Model
VarCorr Extract Variance and Correlation Components
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