lme4 v1.1-18-1

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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
checkConv	Extended Convergence Checking
confint.merMod	Compute Confidence Intervals for Parameters of a [ng]lmer Fit
devfun2	Deviance function defined in terms of standard deviations/correlations
drop1.merMod	Drop all possible single fixed-effect terms from a mixed effect model
prt-utilities	Print and Summary Method Utilities for Mixed Effects
glmerLaplaceHandle	Handle for glmerLaplace
merPredD-class	Class "merPredD" - a Dense Predictor Reference Class
merMod-class	Class "merMod" of Fitted Mixed-Effect Models
glmer.nb	Fitting Negative Binomial GLMMs
rePos-class	Class "rePos"
convergence	Assessing Convergence for Fitted Models
VerbAgg	Verbal Aggression item responses
lme4-package	Linear, generalized linear, and nonlinear mixed models
glmFamily-class	Class "glmFamily" - a reference class for family
NelderMead-class	Class "NelderMead" of Nelder-Mead optimizers and its Generator
getME	Extract or Get Generalized Components from a Fitted Mixed Effects Model
mkSimulateTemplate	Make templates suitable for guiding mixed model simulations
bootMer	Model-based (Semi-)Parametric Bootstrap for Mixed Models
lmResp-class	Reference Classes for Response Modules, "(lm\|glm\|nls\|lmer)Resp"
cbpp	Contagious bovine pleuropneumonia
cake	Breakage Angle of Chocolate Cakes
devcomp	Extract the deviance component list
fixef	Extract fixed-effects estimates
factorize	Attempt to convert grouping variables to factors
mkReTrms	Make Random Effect Terms: Create Z, Lambda, Lind, etc.
findbars	Determine random-effects expressions from a formula
modular	Modular Functions for Mixed Model Fits
glmFamily	Generator object for the glmFamily class
rePos	Generator object for the rePos (random-effects positions) class
glmer	Fitting Generalized Linear Mixed-Effects Models
nobars	Omit terms separated by vertical bars in a formula
residuals.merMod	residuals of merMod objects
mkVarCorr	Make Variance and Correlation Matrices from theta
sigma	Extract Residual Standard Deviation 'Sigma'
hatvalues.merMod	Diagonal elements of the hat matrix
fortify	add information to data based on a fitted model
isREML	Check characteristics of models
lmResp	Generator objects for the response classes
lmer	Fit Linear Mixed-Effects Models
nloptwrap	Wrappers for additional optimizers
lmList	Fit List of lm or glm Objects with a Common Model
lmList4-class	Class "lmList4" of 'lm' Objects on Common Model
plot.merMod	Diagnostic Plots for 'merMod' Fits
dummy	Dummy variables (experimental)
merPredD	Generator object for the merPredD class
expandDoubleVerts	Expand terms with '\|\|' notation into separate '\|' terms
vcconv	Convert between representations of (co-)variance structures
isNested	Is f1 nested within f2?
golden-class	Class "golden" and Generator for Golden Search Optimizer Class
mkMerMod	Create a 'merMod' Object
predict.merMod	Predictions from a model at new data values
mkRespMod	Create an lmerResp, glmResp or nlsResp instance
plots.thpr	Mixed-Effects Profile Plots (Regular / Density / Pairs)
simulate.merMod	Simulate Responses From merMod Object
pvalues	Getting p-values for fitted models
ranef	Extract the modes of the random effects
profile-methods	Profile method for merMod objects
nlformula	Manipulate a Nonlinear Model Formula
grouseticks	Data on red grouse ticks from Elston et al. 2001
lmerControl	Control of Mixed Model Fitting
subbars	"Sub[stitute] Bars"
refitML	Refit a Model by Maximum Likelihood Criterion
ngrps	Number of Levels of a Factor or a "merMod" Model
nlmer	Fitting Nonlinear Mixed-Effects Models
troubleshooting	Troubleshooting
refit	Refit a (merMod) Model with a Different Response
sleepstudy	Reaction times in a sleep deprivation study
GQdk	Sparse Gaussian / Gauss-Hermite Quadrature grid
GHrule	Univariate Gauss-Hermite quadrature rule
NelderMead	Nelder-Mead Optimization of Parameters, Possibly (Box) Constrained
Penicillin	Variation in penicillin testing
VarCorr	Extract Variance and Correlation Components
Arabidopsis	Arabidopsis clipping/fertilization data
Dyestuff	Yield of dyestuff by batch
InstEval	University Lecture/Instructor Evaluations by Students at ETH
Pastes	Paste strength by batch and cask
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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
Encoding	UTF-8
NeedsCompilation	yes
Packaged	2018-08-17 01:42:32 UTC; bolker
Repository	CRAN
Date/Publication	2018-08-17 23:20:06 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 (>= 1.2-1) , methods , R (>= 3.2.0) , stats
linkingto	Rcpp (>= 0.10.5) , RcppEigen
Contributors	Steven Walker, Douglas Bates, Henrik Singmann, Rune Haubo Bojesen Christensen, Bin Dai, Fabian Scheipl, Gabor Grothendieck, Peter Green, Martin Maechler