lme4 v1.1-10


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