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lme4 (version 1.1-30)

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

374,093

Version

1.1-30

License

GPL (>= 2)

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Maintainer

Ben Bolker

Last Published

July 8th, 2022

Functions in lme4 (1.1-30)

cbpp

Contagious bovine pleuropneumonia
checkConv

Extended Convergence Checking
devfun2

Deviance Function in Terms of Standard Deviations/Correlations
devcomp

Extract the deviance component list
fortify

add information to data based on a fitted model
getME

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

Extract fixed-effects estimates
findbars

Determine random-effects expressions from a formula
convergence

Assessing Convergence for Fitted Models
confint.merMod

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

Check characteristics of models
glmFamily-class

glmFamily

Generator object for the glmFamily class
expandDoubleVerts

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

Attempt to convert grouping variables to factors
hatvalues.merMod

Diagonal elements of the hat matrix
grouseticks

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

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

Sparse Gaussian / Gauss-Hermite Quadrature grid
cake

Breakage Angle of Chocolate Cakes
glmerLaplaceHandle

Handle for glmerLaplace
golden-class

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

Is f1 nested within f2?
lmResp-class

Reference Classes for Response Modules, "(lm|glm|nls|lmer)Resp"
influence.merMod

Influence Diagnostics for Mixed-Effects Models
lmResp

Generator objects for the response classes
merMod-class

Class "merMod" of Fitted Mixed-Effect Models
glmer

Fitting Generalized Linear Mixed-Effects Models
allFit

Refit a fitted model with all available optimizers
dummy

Dummy variables (experimental)
VerbAgg

Verbal Aggression item responses
drop1.merMod

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

Fit Linear Mixed-Effects Models
lmerControl

Control of Mixed Model Fitting
mkSimulateTemplate

Make templates suitable for guiding mixed model simulations
glmer.nb

Fitting Negative Binomial GLMMs
mkReTrms

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

Make Variance and Correlation Matrices from theta
merPredD-class

Class "merPredD" - a Dense Predictor Reference Class
refitML

Refit a Model by Maximum Likelihood Criterion
residuals.merMod

residuals of merMod objects
rePCA

PCA of random-effects covariance matrix
mkRespMod

Create an lmerResp, glmResp or nlsResp instance
plot.merMod

Diagnostic Plots for 'merMod' Fits
rePos-class

Class "rePos"
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
pvalues

Getting p-values for fitted models
ranef

Extract the modes of the random effects
lme4-package

Linear, generalized linear, and nonlinear mixed models
prt-utilities

Print and Summary Method Utilities for Mixed Effects
vcconv

Convert between representations of (co-)variance structures
rePos

Generator object for the rePos (random-effects positions) class
plots.thpr

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

Refit a (merMod) Model with a Different Response
mkMerMod

Create a 'merMod' Object
lme4_testlevel

Detect testing level for lme4 examples and tests
merPredD

Generator object for the merPredD class
nloptwrap

Wrappers for additional optimizers
simulate.merMod

Simulate Responses From merMod Object
nobars

Omit terms separated by vertical bars in a formula
sleepstudy

Reaction times in a sleep deprivation study
nlformula

Manipulate a Nonlinear Model Formula
subbars

"Sub[stitute] Bars"
predict.merMod

Predictions from a model at new data values
nlmer

Fitting Nonlinear Mixed-Effects Models
troubleshooting

Troubleshooting
profile-methods

Profile method for merMod objects
sigma

Extract Residual Standard Deviation 'Sigma'
simulate.formula

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

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

Modular Functions for Mixed Model Fits
Arabidopsis

Arabidopsis clipping/fertilization data
GHrule

Univariate Gauss-Hermite quadrature rule
Penicillin

Variation in penicillin testing
InstEval

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

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

Yield of dyestuff by batch
NelderMead

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

Paste strength by batch and cask
VarCorr

Extract Variance and Correlation Components