lme4 v1.1-12


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