lme4 v1.1-11

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