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lme4 (version 1.1-35.4)

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

install.packages('lme4')

Monthly Downloads

578,990

Version

1.1-35.4

License

GPL (>= 2)

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Repository

https://github.com/lme4/lme4/

Maintainer

Ben Bolker

Last Published

June 19th, 2024

Functions in lme4 (1.1-35.4)

Refit a fitted model with all available optimizers

Assessing Convergence for Fitted Models

glmFamily-class

Class "glmFamily" - a reference class for family

expandDoubleVerts

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

Fitting Negative Binomial GLMMs

Extended Convergence Checking

Determine random-effects expressions from a formula

Dummy variables (experimental)

hatvalues.merMod

Diagonal elements of the hat matrix

add information to data based on a fitted model

Check characteristics of models

Data on red grouse ticks from Elston et al. 2001

influence.merMod

Influence Diagnostics for Mixed-Effects Models

Extract fixed-effects estimates

Fitting Generalized Linear Mixed-Effects Models

Test Fitted Model for (Near) Singularity

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

Generator object for the glmFamily class

Is f1 nested within f2?

Class "golden" and Generator for Golden Search Optimizer Class

Extract or Get Generalized Components from a Fitted Mixed Effects Model

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

glmerLaplaceHandle

Handle for glmerLaplace

Fit Linear Mixed-Effects Models

Attempt to convert grouping variables to factors

Control of Mixed Model Fitting

mkSimulateTemplate

Make templates suitable for guiding mixed model simulations

Fit List of lm or glm Objects with a Common Model

Class "merMod" of Fitted Mixed-Effect Models

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

Make Variance and Correlation Matrices from theta

Generator object for the merPredD class

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

Detect testing level for lme4 examples and tests

Generator objects for the response classes

Class "merPredD" - a Dense Predictor Reference Class

Linear, generalized linear, and nonlinear mixed models

Create an lmerResp, glmResp or nlsResp instance

Create a 'merMod' Object

Modular Functions for Mixed Model Fits

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

Diagnostic Plots for 'merMod' Fits

Omit terms separated by vertical bars in a formula

Self-naming list function

Fitting Nonlinear Mixed-Effects Models

Manipulate a Nonlinear Model Formula

Wrappers for additional optimizers

Predictions from a model at new data values

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

profile-methods

Profile method for merMod objects

Getting p-values for fitted models

Refit a Model by Maximum Likelihood Criterion

Refit a (merMod) Model with a Different Response

Extract the modes of the random effects

PCA of random-effects covariance matrix

residuals.merMod

residuals of merMod objects

Print and Summary Method Utilities for Mixed Effects

Reaction times in a sleep deprivation study

Extract Residual Standard Deviation 'Sigma'

troubleshooting

Troubleshooting

Convert between representations of (co-)variance structures

simulate.formula

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

"Sub[stitute] Bars"

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

simulate.merMod

Simulate Responses From merMod Object

Class "rePos"

Sparse Gaussian / Gauss-Hermite Quadrature grid

Paste strength by batch and cask

Univariate Gauss-Hermite quadrature rule

Extract the deviance component list

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

Arabidopsis clipping/fertilization data

Contagious bovine pleuropneumonia

Extract Variance and Correlation Components

Variation in penicillin testing

Deviance Function in Terms of Standard Deviations/Correlations

Yield of dyestuff by batch

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

Breakage Angle of Chocolate Cakes

Verbal Aggression item responses

University Lecture/Instructor Evaluations by Students at ETH

NelderMead-class

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

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