lme4 v1.1-14

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by Ben Bolker View Source

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

Name
PLSvGLS.Rnw
Theory.Rnw
lme4.bib
lmer.Rnw
lmer.bib
lmerperf.Rmd
lmerperf.md
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Details

Contact	LME4 Authors
LinkingTo	Rcpp (>= 0.10.5), RcppEigen
VignetteBuilder	knitr
LazyData	yes
License	GPL (>= 2)
URL	https://github.com/lme4/lme4/ http://lme4.r-forge.r-project.org/
BugReports	https://github.com/lme4/lme4/issues
NeedsCompilation	yes
Packaged	2017-09-20 02:40:54 UTC; bolker
Repository	CRAN
Date/Publication	2017-09-27 08:28:13 UTC

suggests	boot , gamm4 , ggplot2 , HSAUR2 , knitr , MEMSS , mlmRev , numDeriv , optimx (>= 2013.8.6) , pbkrtest , PKPDmodels , testthat (>= 0.8.1)
imports	graphics , grid , lattice , MASS , minqa (>= 1.1.15) , nlme (>= 3.1-123) , nloptr (>= 1.0.4) , parallel , splines , utils
depends	Matrix (>= 1.1.1) , methods , R (>= 3.0.2) , stats
linkingto	Rcpp (>= 0.10.5) , RcppEigen
Contributors	Steven Walker, Douglas Bates, Henrik Singmann, Rune Haubo Bojesen Christensen, Bin Dai, Gabor Grothendieck, Peter Green, Martin Maechler