lme4 v1.1-8

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