| Linear, generalized linear, and nonlinear mixed models | lme4-package lme4 |
| Refit a fitted model with all available optimizers | allFit |
| Arabidopsis clipping/fertilization data | Arabidopsis |
| Model-based (Semi-)Parametric Bootstrap for Mixed Models | bootMer |
| Breakage Angle of Chocolate Cakes | cake |
| Contagious bovine pleuropneumonia | cbpp |
| Extended Convergence Checking | checkConv |
| Compute Confidence Intervals for Parameters of a [ng]lmer Fit | confint.merMod confint.thpr |
| Assessing Convergence for Fitted Models | convergence |
| Extract the deviance component list | devcomp |
| Deviance Function in Terms of Standard Deviations/Correlations | devfun2 |
| Drop all possible single fixed-effect terms from a mixed effect model | drop1.merMod |
| Dummy variables (experimental) | dummy |
| Yield of dyestuff by batch | Dyestuff Dyestuff2 |
| Expand terms with ''||'' notation into separate ''|'' terms | expandDoubleVerts || |
| Attempt to convert grouping variables to factors | factorize |
| Determine random-effects expressions from a formula | findbars |
| Extract fixed-effects estimates | fixed.effects fixef fixef.merMod |
| add information to data based on a fitted model | fortify fortify.merMod getData getData.merMod |
| Extract or Get Generalized Components from a Fitted Mixed Effects Model | getL getL,merMod-method getME getME.merMod |
| Univariate Gauss-Hermite quadrature rule | GHrule |
| Fitting Generalized Linear Mixed-Effects Models | glmer |
| Fitting Negative Binomial GLMMs | glmer.nb negative.binomial |
| Handle for 'glmerLaplace' | glmerLaplaceHandle |
| Generator object for the 'glmFamily' class | glmFamily |
| Class '"glmFamily"' - a reference class for 'family' | glmFamily-class |
| Class '"golden"' and Generator for Golden Search Optimizer Class | golden golden-class |
| Sparse Gaussian / Gauss-Hermite Quadrature grid | GQdk GQN |
| Data on red grouse ticks from Elston et al. 2001 | grouseticks grouseticks_agg |
| Diagonal elements of the hat matrix | hatvalues.merMod |
| Influence Diagnostics for Mixed-Effects Models | cooks.distance.influence.merMod cooks.distance.merMod dfbeta.influence.merMod dfbetas.influence.merMod influence.merMod |
| University Lecture/Instructor Evaluations by Students at ETH | InstEval |
| Is f1 nested within f2? | isNested |
| Check characteristics of models | isGLMM isGLMM.merMod isLMM isLMM.merMod isNLMM isNLMM.merMod isREML isREML.merMod |
| Test Fitted Model for (Near) Singularity | isSingular |
| Detect testing level for lme4 examples and tests | lme4_testlevel |
| Fit Linear Mixed-Effects Models | lmer |
| Control of Mixed Model Fitting | .makeCC glmerControl lmerControl nlmerControl |
| Fit List of lm or glm Objects with a Common Model | lmList plot.lmList |
| Class "lmList4" of 'lm' Objects on Common Model | lmList4-class show,lmList4-method |
| Generator objects for the response classes | glmResp lmerResp lmResp nlsResp |
| Reference Classes for Response Modules, '"(lm|glm|nls|lmer)Resp"' | glmResp-class lmerResp-class lmResp-class nlsResp-class |
| Class "merMod" of Fitted Mixed-Effect Models | anova.merMod as.function.merMod coef.merMod deviance.merMod df.residual.merMod extractAIC.merMod family.merMod fitted.merMod formula.merMod glmerMod-class lmerMod-class logLik.merMod merMod merMod-class model.frame.merMod model.matrix.merMod ngrps.merMod nlmerMod-class nobs nobs.merMod print.merMod print.summary.merMod REMLcrit show,merMod-method show.merMod show.summary.merMod summary.merMod summary.summary.merMod terms.merMod update.merMod vcov.merMod vcov.summary.merMod weights.merMod |
| Generator object for the 'merPredD' class | merPredD |
| Class '"merPredD"' - a Dense Predictor Reference Class | merPredD-class |
| Create a 'merMod' Object | mkMerMod |
| Create an lmerResp, glmResp or nlsResp instance | mkRespMod |
| Make Random Effect Terms: Create Z, Lambda, Lind, etc. | mkNewReTrms mkReTrms |
| Make templates suitable for guiding mixed model simulations | mkDataTemplate mkParsTemplate |
| Make Variance and Correlation Matrices from 'theta' | mkVarCorr |
| Modular Functions for Mixed Model Fits | glFormula lFormula mkGlmerDevfun mkLmerDevfun modular optimizeGlmer optimizeLmer updateGlmerDevfun |
| Self-naming list function | namedList |
| Nelder-Mead Optimization of Parameters, Possibly (Box) Constrained | Nelder_Mead |
| Class '"NelderMead"' of Nelder-Mead optimizers and its Generator | NelderMead NelderMead-class |
| Number of Levels of a Factor or a "merMod" Model | ngrps |
| Manipulate a Nonlinear Model Formula | nlformula |
| Fitting Nonlinear Mixed-Effects Models | nlmer |
| Wrappers for additional optimizers | nlminbwrap nloptwrap |
| Omit terms separated by vertical bars in a formula | nobars |
| Paste strength by batch and cask | Pastes |
| Variation in penicillin testing | Penicillin |
| Diagnostic Plots for 'merMod' Fits | plot.merMod qqmath.merMod |
| Mixed-Effects Profile Plots (Regular / Density / Pairs) | densityplot.thpr splom.thpr xyplot.thpr |
| Predictions from a model at new data values | predict.merMod |
| Profile method for merMod objects | as.data.frame.thpr log.thpr logProf profile-methods profile.merMod varianceProf |
| Print and Summary Method Utilities for Mixed Effects | .prt.aictab .prt.call .prt.family .prt.grps .prt.methTit .prt.resids .prt.VC .prt.warn formatVC llikAIC methTitle |
| Getting p-values for fitted models | mcmcsamp pvalues |
| Extract the modes of the random effects | as.data.frame.ranef.mer dotplot.ranef.mer qqmath.ranef.mer ranef ranef.merMod |
| Refit a (merMod) Model with a Different Response | refit refit.merMod |
| Refit a Model by Maximum Likelihood Criterion | refitML refitML.merMod |
| PCA of random-effects covariance matrix | rePCA |
| Generator object for the rePos (random-effects positions) class | rePos |
| Class '"rePos"' | rePos-class |
| residuals of merMod objects | residuals.glmResp residuals.lmResp residuals.merMod |
| Extract Residual Standard Deviation 'Sigma' | sigma sigma.merMod |
| A 'simulate' Method for 'formula' objects that dispatches based on the Left-Hand Side | simulate.formula |
| Simulate Responses From 'merMod' Object | .simulateFun simulate.merMod |
| Reaction times in a sleep deprivation study | sleepstudy |
| "Sub[stitute] Bars" | subbars |
| Troubleshooting | troubleshooting |
| Extract Variance and Correlation Components | as.data.frame.VarCorr.merMod print.VarCorr.merMod VarCorr VarCorr.merMod |
| Convert between representations of (co-)variance structures | cov2sdcor Cv_to_Sv Cv_to_Vv mlist2vec sdcor2cov Sv_to_Cv vcconv vec2mlist vec2STlist Vv_to_Cv |
| Verbal Aggression item responses | VerbAgg |
