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lme4 (version 1.1-26)

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

424,716

Version

1.1-26

License

GPL (>= 2)

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Last Published

December 1st, 2020

Functions in lme4 (1.1-26)

VarCorr

Extract Variance and Correlation Components
GHrule

Univariate Gauss-Hermite quadrature rule
GQdk

Sparse Gaussian / Gauss-Hermite Quadrature grid
NelderMead-class

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

University Lecture/Instructor Evaluations by Students at ETH
Dyestuff

Yield of dyestuff by batch
NelderMead

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

Arabidopsis clipping/fertilization data
Pastes

Paste strength by batch and cask
Penicillin

Variation in penicillin testing
bootMer

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

Breakage Angle of Chocolate Cakes
cbpp

Contagious bovine pleuropneumonia
glmFamily-class

checkConv

Extended Convergence Checking
glmFamily

Generator object for the '>glmFamily class
factorize

Attempt to convert grouping variables to factors
expandDoubleVerts

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

Is f1 nested within f2?
findbars

Determine random-effects expressions from a formula
influence.merMod

Influence Diagnostics for Mixed-Effects Models
VerbAgg

Verbal Aggression item responses
fixef

Extract fixed-effects estimates
merMod-class

Class "merMod" of Fitted Mixed-Effect Models
allFit

Refit a fitted model with all available optimizers
glmer.nb

Fitting Negative Binomial GLMMs
merPredD-class

Class "merPredD" - a Dense Predictor Reference Class
glmer

Fitting Generalized Linear Mixed-Effects Models
devcomp

Extract the deviance component list
lmer

Fit Linear Mixed-Effects Models
lmResp-class

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

Number of Levels of a Factor or a "merMod" Model
isREML

Check characteristics of models
modular

Modular Functions for Mixed Model Fits
lmList

Fit List of lm or glm Objects with a Common Model
isSingular

Test Fitted Model for (Near) Singularity
lmList4-class

Class "lmList4" of 'lm' Objects on Common Model
mkSimulateTemplate

Make templates suitable for guiding mixed model simulations
mkVarCorr

Make Variance and Correlation Matrices from theta
plot.merMod

Diagnostic Plots for 'merMod' Fits
plots.thpr

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

"Sub[stitute] Bars"
nloptwrap

Wrappers for additional optimizers
lmerControl

Control of Mixed Model Fitting
mkReTrms

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

Generator objects for the response classes
simulate.merMod

prt-utilities

Print and Summary Method Utilities for Mixed Effects
sleepstudy

Reaction times in a sleep deprivation study
nobars

Omit terms separated by vertical bars in a formula
confint.merMod

Compute Confidence Intervals for Parameters of a [ng]lmer Fit
devfun2

Deviance Function in Terms of Standard Deviations/Correlations
mkRespMod

Create an lmerResp, glmResp or nlsResp instance
golden-class

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

Dummy variables (experimental)
lme4-package

Linear, generalized linear, and nonlinear mixed models
predict.merMod

Predictions from a model at new data values
glmerLaplaceHandle

Handle for glmerLaplace
drop1.merMod

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

add information to data based on a fitted model
getME

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

Assessing Convergence for Fitted Models
troubleshooting

Troubleshooting
lme4_testlevel

Detect testing level for lme4 examples and tests
sigma

Extract Residual Standard Deviation 'Sigma'
profile-methods

Profile method for merMod objects
vcconv

Convert between representations of (co-)variance structures
rePos-class

Class "rePos"
hatvalues.merMod

Diagonal elements of the hat matrix
mkMerMod

Create a 'merMod' Object
rePCA

PCA of random-effects covariance matrix
nlformula

Manipulate a Nonlinear Model Formula
rePos

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

Data on red grouse ticks from Elston et al. 2001
merPredD

refit

Refit a (merMod) Model with a Different Response
nlmer

Fitting Nonlinear Mixed-Effects Models
pvalues

Getting p-values for fitted models
refitML

Refit a Model by Maximum Likelihood Criterion
ranef

Extract the modes of the random effects
residuals.merMod

residuals of merMod objects
simulate.formula

A simulate Method for formula objects that dispatches based on the Left-Hand Side