lme4 v1.1-7

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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
Pastes Paste strength by batch and cask
lmResp-class Classes "lmResp", "glmResp", "nlsResp" and "lmerResp"
devcomp Extract the deviance component list
NelderMead-class Class "NelderMead" of Nelder-Mead optimizers and its Generator
findbars Determine random-effects expressions from a formula
VerbAgg Verbal Aggression item responses
expandDoubleVerts Expand terms with '||' notation into separate '|' terms
lmResp Generator objects for the response classes
nlmer Fit Nonlinear Mixed-Effects Models
GHrule Univariate Gauss-Hermite quadrature rule
varianceProf Transform Profile to the variance scale
sigma Extract residual standard error
getME Extract or Get Generalized Components from a Fitted Mixed Effects Model
glmer.nb glmer() for Negative Binomial
lmList List of lm Objects with a Common Model
dummy Dummy variables (experimental)
predict.merMod Predictions from a model at new data values
plots.thpr Mixed-Effects Profile Plots (Regular / Density / Pairs)
simulate.merMod Simulate responses from a merMod object
VarCorr Extract Variance and Correlation Components
isNested Is f1 nested within f2?
GQdk Sparse Gaussian Quadrature grid
plot.merMod diagnostic plots for merMod fits
cake Breakage Angle of Chocolate Cakes
nloptwrap Wrapper for nlOpt optimizers
subbars "Sub[stitute] Bars"
NelderMead Nelder-Mead Optimization of Parameters, Possibly (Box) Constrained
lmerControl Control of Mixed Model Fitting
lmer Fit Linear Mixed-Effects Models
ranef Extract the modes of the random effects
rePos Generator object for the rePos (random-effects positions) class
Penicillin Variation in penicillin testing
glmFamily Generator object for the glmFamily class
profile-methods Profile method for merMod objects
isREML Check characteristics of models
drop1.merMod Drop all possible single fixed-effect terms from a mixed effect model
confint.merMod Compute Confidence Intervals for Parameters of a [ng]lmer Fit
mkReTrms Create Z, Lambda, Lind, etc.
golden Generator object for the golden search optimizer class.
mkdevfun Create a deviance evaluation function from a predictor and a response module
sleepstudy Reaction times in a sleep deprivation study
Dyestuff Yield of dyestuff by batch
fortify add information to data based on a fitted model
cbpp Contagious bovine pleuropneumonia
lme4-package Linear, generalized linear, and nonlinear mixed models
grouseticks Data on red grouse ticks from Elston et al. 2001
refit Refit a model with a new response, by maximum likelihood criterion
ngrps Number of levels
mkRespMod Create an lmerResp, glmResp or nlsResp instance
pvalues Getting p-values for fitted models
InstEval University Lecture/Instructor Evaluations by Students at ETH
golden-class Class "golden"
merPredD-class Class "merPredD" - a dense predictor reference class
merPredD Generator object for the merPredD class
mkVarCorr Make Variance and Correlation Matrices from theta
nlformula Manipulate a Nonlinear Model Formula
merMod-class Class "merMod" of Fitted Mixed-Effect Models
rePos-class Class "rePos"
bootMer Model-based (Semi-)Parametric Bootstrap for Mixed Models
glmFamily-class Class "glmFamily" - a reference class for family
glmer Fit Generalized Linear Mixed-Effects Models
fixef Extract fixed-effects estimates
GQN Sparse Gauss-Hermite quadrature grids
lmList-class Class "lmList" of 'lm' Objects on Common Model
residuals.merMod residuals of merMod objects
modular Modular functions for mixed model fits
mkMerMod Create a merMod object
refitML Refit a model by maximum likelihood criterion
nobars Omit terms separated by vertical bars in a formula
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LinkingTo Rcpp, RcppEigen
VignetteBuilder knitr
LazyData yes
License GPL (>= 2)
URL https://github.com/lme4/lme4/ http://lme4.r-forge.r-project.org/
BuildVignettes yes
Packaged 2014-07-19 17:33:54 UTC; hornik
NeedsCompilation yes
Repository CRAN
Date/Publication 2014-07-19 19:49:55

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