lme4 v1.0-6

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

Date 2014-02-02
Contact LME4 Authors
LinkingTo Rcpp, RcppEigen
LazyData yes
License GPL (>= 2)
URL https://github.com/lme4/lme4/ http://lme4.r-forge.r-project.org/
BuildVignettes yes
Packaged 2014-02-02 16:13:00 UTC; ripley
NeedsCompilation yes
Repository CRAN
Date/Publication 2014-02-02 19:03:23

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