lme4 v1.1-23

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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
Dyestuff	Yield of dyestuff by batch
GHrule	Univariate Gauss-Hermite quadrature rule
GQdk	Sparse Gaussian / Gauss-Hermite Quadrature grid
NelderMead-class	Class "NelderMead" of Nelder-Mead optimizers and its Generator
VarCorr	Extract Variance and Correlation Components
Penicillin	Variation in penicillin testing
confint.merMod	Compute Confidence Intervals for Parameters of a [ng]lmer Fit
NelderMead	Nelder-Mead Optimization of Parameters, Possibly (Box) Constrained
Arabidopsis	Arabidopsis clipping/fertilization data
Pastes	Paste strength by batch and cask
checkConv	Extended Convergence Checking
cake	Breakage Angle of Chocolate Cakes
drop1.merMod	Drop all possible single fixed-effect terms from a mixed effect model
dummy	Dummy variables (experimental)
InstEval	University Lecture/Instructor Evaluations by Students at ETH
isNested	Is f1 nested within f2?
cbpp	Contagious bovine pleuropneumonia
isREML	Check characteristics of models
devcomp	Extract the deviance component list
convergence	Assessing Convergence for Fitted Models
bootMer	Model-based (Semi-)Parametric Bootstrap for Mixed Models
lme4-package	Linear, generalized linear, and nonlinear mixed models
glmFamily-class	Class "glmFamily" - a reference class for family
merPredD	Generator object for the merPredD class
findbars	Determine random-effects expressions from a formula
influence.merMod	Influence Diagnostics for Mixed-Effects Models
factorize	Attempt to convert grouping variables to factors
merPredD-class	Class "merPredD" - a Dense Predictor Reference Class
isSingular	Test Fitted Model for (Near) Singularity
expandDoubleVerts	Expand terms with '\|\|' notation into separate '\|' terms
hatvalues.merMod	Diagonal elements of the hat matrix
fortify	add information to data based on a fitted model
VerbAgg	Verbal Aggression item responses
devfun2	Deviance Function in Terms of Standard Deviations/Correlations
ngrps	Number of Levels of a Factor or a "merMod" Model
glmFamily	Generator object for the glmFamily class
nlmer	Fitting Nonlinear Mixed-Effects Models
grouseticks	Data on red grouse ticks from Elston et al. 2001
allFit	Refit a fitted model with all available optimizers
lmer	Fit Linear Mixed-Effects Models
nlformula	Manipulate a Nonlinear Model Formula
glmerLaplaceHandle	Handle for glmerLaplace
mkMerMod	Create a 'merMod' Object
nloptwrap	Wrappers for additional optimizers
lmResp-class	Reference Classes for Response Modules, "(lm\|glm\|nls\|lmer)Resp"
nobars	Omit terms separated by vertical bars in a formula
plot.merMod	Diagnostic Plots for 'merMod' Fits
rePos-class	Class "rePos"
getME	Extract or Get Generalized Components from a Fitted Mixed Effects Model
mkVarCorr	Make Variance and Correlation Matrices from theta
golden-class	Class "golden" and Generator for Golden Search Optimizer Class
lmList	Fit List of lm or glm Objects with a Common Model
residuals.merMod	residuals of merMod objects
sigma	Extract Residual Standard Deviation 'Sigma'
refit	Refit a (merMod) Model with a Different Response
lmResp	Generator objects for the response classes
lmList4-class	Class "lmList4" of 'lm' Objects on Common Model
plots.thpr	Mixed-Effects Profile Plots (Regular / Density / Pairs)
predict.merMod	Predictions from a model at new data values
rePos	Generator object for the rePos (random-effects positions) class
pvalues	Getting p-values for fitted models
simulate.merMod	Simulate Responses From merMod Object
fixef	Extract fixed-effects estimates
mkReTrms	Make Random Effect Terms: Create Z, Lambda, Lind, etc.
modular	Modular Functions for Mixed Model Fits
lmerControl	Control of Mixed Model Fitting
troubleshooting	Troubleshooting
refitML	Refit a Model by Maximum Likelihood Criterion
subbars	"Sub[stitute] Bars"
profile-methods	Profile method for merMod objects
sleepstudy	Reaction times in a sleep deprivation study
glmer	Fitting Generalized Linear Mixed-Effects Models
glmer.nb	Fitting Negative Binomial GLMMs
merMod-class	Class "merMod" of Fitted Mixed-Effect Models
mkRespMod	Create an lmerResp, glmResp or nlsResp instance
ranef	Extract the modes of the random effects
rePCA	PCA of random-effects covariance matrix
mkSimulateTemplate	Make templates suitable for guiding mixed model simulations
prt-utilities	Print and Summary Method Utilities for Mixed Effects
vcconv	Convert between representations of (co-)variance structures
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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/
BugReports	https://github.com/lme4/lme4/issues
Encoding	UTF-8
NeedsCompilation	yes
Packaged	2020-04-06 00:39:09 UTC; bolker
Repository	CRAN
Date/Publication	2020-04-07 10:00:21 UTC

imports	boot , graphics , grid , lattice , MASS , minqa (>= 1.1.15) , nlme (>= 3.1-123) , nloptr (>= 1.0.4) , parallel , splines , statmod , utils
suggests	car , dfoptim , gamm4 , ggplot2 , HSAUR2 , knitr , MEMSS , mlmRev , numDeriv , optimx (>= 2013.8.6) , pbkrtest , PKPDmodels , rmarkdown , testthat (>= 0.8.1)
depends	Matrix (>= 1.2-1) , methods , R (>= 3.2.0) , stats
linkingto	Rcpp (>= 0.10.5) , RcppEigen
Contributors	Steven Walker, Douglas Bates, John Fox, Henrik Singmann, Rune Haubo Bojesen Christensen, Bin Dai, Fabian Scheipl, Gabor Grothendieck, Peter Green, Martin Maechler