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lme4 (version 1.1-31)

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

544,654

Version

1.1-31

License

GPL (>= 2)

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Maintainer

Ben Bolker

Last Published

November 1st, 2022

Functions in lme4 (1.1-31)

Pastes

Paste strength by batch and cask
Dyestuff

Yield of dyestuff by batch
Arabidopsis

Arabidopsis clipping/fertilization data
NelderMead-class

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

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

Variation in penicillin testing
confint.merMod

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

Breakage Angle of Chocolate Cakes
GHrule

Univariate Gauss-Hermite quadrature rule
VarCorr

Extract Variance and Correlation Components
GQdk

Sparse Gaussian / Gauss-Hermite Quadrature grid
glmerLaplaceHandle

Handle for glmerLaplace
golden-class

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

Contagious bovine pleuropneumonia
VerbAgg

Verbal Aggression item responses
expandDoubleVerts

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

Refit a fitted model with all available optimizers
glmer

Fitting Generalized Linear Mixed-Effects Models
lmerControl

Control of Mixed Model Fitting
lmer

Fit Linear Mixed-Effects Models
convergence

Assessing Convergence for Fitted Models
factorize

Attempt to convert grouping variables to factors
checkConv

Extended Convergence Checking
modular

Modular Functions for Mixed Model Fits
grouseticks

Data on red grouse ticks from Elston et al. 2001
drop1.merMod

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

Generator object for the merPredD class
lmList

Fit List of lm or glm Objects with a Common Model
hatvalues.merMod

Diagonal elements of the hat matrix
lmList4-class

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

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

Extract the modes of the random effects
glmFamily-class

pvalues

Getting p-values for fitted models
fixef

Extract fixed-effects estimates
findbars

Determine random-effects expressions from a formula
mkMerMod

Create a 'merMod' Object
glmFamily

Generator object for the glmFamily class
devcomp

Extract the deviance component list
rePos

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

Dummy variables (experimental)
influence.merMod

Influence Diagnostics for Mixed-Effects Models
devfun2

Deviance Function in Terms of Standard Deviations/Correlations
isNested

Is f1 nested within f2?
isREML

Check characteristics of models
isSingular

Test Fitted Model for (Near) Singularity
refit

Refit a (merMod) Model with a Different Response
lme4-package

Linear, generalized linear, and nonlinear mixed models
glmer.nb

Fitting Negative Binomial GLMMs
lme4_testlevel

Detect testing level for lme4 examples and tests
lmResp-class

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

Predictions from a model at new data values
mkReTrms

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

Generator objects for the response classes
nloptwrap

Wrappers for additional optimizers
mkRespMod

Create an lmerResp, glmResp or nlsResp instance
nlformula

Manipulate a Nonlinear Model Formula
profile-methods

Profile method for merMod objects
subbars

"Sub[stitute] Bars"
nlmer

Fitting Nonlinear Mixed-Effects Models
vcconv

Convert between representations of (co-)variance structures
troubleshooting

Troubleshooting
rePCA

PCA of random-effects covariance matrix
fortify

add information to data based on a fitted model
rePos-class

Class "rePos"
refitML

Refit a Model by Maximum Likelihood Criterion
simulate.merMod

Simulate Responses From merMod Object
residuals.merMod

residuals of merMod objects
sigma

Extract Residual Standard Deviation 'Sigma'
nobars

Omit terms separated by vertical bars in a formula
sleepstudy

Reaction times in a sleep deprivation study
prt-utilities

Print and Summary Method Utilities for Mixed Effects
getME

Extract or Get Generalized Components from a Fitted Mixed Effects Model
merPredD-class

Class "merPredD" - a Dense Predictor Reference Class
merMod-class

Class "merMod" of Fitted Mixed-Effect Models
mkSimulateTemplate

Make templates suitable for guiding mixed model simulations
mkVarCorr

Make Variance and Correlation Matrices from theta
simulate.formula

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

Diagnostic Plots for 'merMod' Fits
plots.thpr

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

University Lecture/Instructor Evaluations by Students at ETH
NelderMead

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