lme4 v1.1-18-1


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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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