lme4 v1.1-9

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