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lme4 (version 1.1-14)

Linear Mixed-Effects Models using 'Eigen' and S4

Description

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".

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install.packages('lme4')

Monthly Downloads

376,257

Version

1.1-14

License

GPL (>= 2)

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Maintainer

Ben Bolker

Last Published

September 27th, 2017

Functions in lme4 (1.1-14)

Arabidopsis

Arabidopsis clipping/fertilization data
Dyestuff

Yield of dyestuff by batch
NelderMead

Nelder-Mead Optimization of Parameters, Possibly (Box) Constrained
Pastes

Paste strength by batch and cask
InstEval

University Lecture/Instructor Evaluations by Students at ETH
NelderMead-class

Class "NelderMead" of Nelder-Mead optimizers and its Generator
VerbAgg

Verbal Aggression item responses
bootMer

Model-based (Semi-)Parametric Bootstrap for Mixed Models
Penicillin

Variation in penicillin testing
VarCorr

Extract Variance and Correlation Components
drop1.merMod

Drop all possible single fixed-effect terms from a mixed effect model
dummy

Dummy variables (experimental)
glmFamily-class

glmFamily

Generator object for the '>glmFamily class
cake

Breakage Angle of Chocolate Cakes
cbpp

Contagious bovine pleuropneumonia
glmer

Fitting Generalized Linear Mixed-Effects Models
glmer.nb

Fitting Negative Binomial GLMMs
glmerLaplaceHandle

Handle for glmerLaplace
golden-class

Class "golden" and Generator for Golden Search Optimizer Class
checkConv

Extended Convergence Checking
confint.merMod

Compute Confidence Intervals for Parameters of a [ng]lmer Fit
fortify

add information to data based on a fitted model
getME

Extract or Get Generalized Components from a Fitted Mixed Effects Model
isNested

Is f1 nested within f2?
isREML

Check characteristics of models
merPredD-class

Class "merPredD" - a Dense Predictor Reference Class
merPredD

GHrule

Univariate Gauss-Hermite quadrature rule
GQdk

Sparse Gaussian / Gauss-Hermite Quadrature grid
findbars

Determine random-effects expressions from a formula
fixef

Extract fixed-effects estimates
lmList

Fit List of lm Objects with a Common Model
lmList4-class

Class "lmList4" of 'lm' Objects on Common Model
lme4-package

Linear, generalized linear, and nonlinear mixed models
lmer

Fit Linear Mixed-Effects Models
convergence

Assessing Convergence for Fitted Models
devcomp

Extract the deviance component list
expandDoubleVerts

Expand terms with '||' notation into separate '|' terms
factorize

Attempt to convert grouping variables to factors
nlformula

Manipulate a Nonlinear Model Formula
nlmer

Fitting Nonlinear Mixed-Effects Models
plots.thpr

Mixed-Effects Profile Plots (Regular / Density / Pairs)
mkVarCorr

Make Variance and Correlation Matrices from theta
mkdevfun

Create Deviance Evaluation Function from Predictor and Response Module
sigma

Extract Residual Standard Deviation 'Sigma'
simulate.merMod

lmerControl

Control of Mixed Model Fitting
merMod-class

Class "merMod" of Fitted Mixed-Effect Models
ranef

Extract the modes of the random effects
rePos-class

Class "rePos"
grouseticks

Data on red grouse ticks from Elston et al. 2001
hatvalues.merMod

Diagonal elements of the hat matrix
mkMerMod

Create a 'merMod' Object
lmResp-class

Reference Classes for Response Modules, "(lm|glm|nls|lmer)Resp"
lmResp

Generator objects for the response classes
mkRespMod

Create an lmerResp, glmResp or nlsResp instance
mkSimulateTemplate

Make templates suitable for guiding mixed model simulations
nloptwrap

Wrappers for additional optimizers
nobars

Omit terms separated by vertical bars in a formula
refitML

Refit a Model by Maximum Likelihood Criterion
residuals.merMod

residuals of merMod objects
vcconv

Convert between representations of (co-)variance structures
predict.merMod

Predictions from a model at new data values
modular

Modular Functions for Mixed Model Fits
ngrps

Number of Levels of a Factor or a "merMod" Model
profile-methods

Profile method for merMod objects
pvalues

Getting p-values for fitted models
troubleshooting

Troubleshooting
mkReTrms

Make Random Effect Terms: Create Z, Lambda, Lind, etc.
plot.lmList4

plots for lmList4 objects
plot.merMod

Diagnostic Plots for 'merMod' Fits
rePos

Generator object for the rePos (random-effects positions) class
refit

Refit a (merMod) Model with a Different Response
sleepstudy

Reaction times in a sleep deprivation study
subbars

"Sub[stitute] Bars"
prt-utilities

Print and Summary Method Utilities for Mixed Effects