# lme4 v1.1-10

0

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by Ben Bolker

## Linear Mixed-Effects Models using 'Eigen' and S4

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".

## Functions in lme4

Name | Description | |

getME | Extract or Get Generalized Components from a Fitted Mixed Effects Model | |

VerbAgg | Verbal Aggression item responses | |

findbars | Determine random-effects expressions from a formula | |

GQdk | Sparse Gaussian / Gauss-Hermite Quadrature grid | |

GHrule | Univariate Gauss-Hermite quadrature rule | |

cbpp | Contagious bovine pleuropneumonia | |

Pastes | Paste strength by batch and cask | |

convergence | Assessing Convergence for Fitted Models | |

glmFamily | Generator object for the glmFamily class | |

glmFamily-class | Class "glmFamily" - a reference class for family | |

cake | Breakage Angle of Chocolate Cakes | |

rePos-class | Class "rePos" | |

confint.merMod | Compute Confidence Intervals for Parameters of a [ng]lmer Fit | |

VarCorr | Extract Variance and Correlation Components | |

mkdevfun | Create Deviance Evaluation Function from Predictor and Response Module | |

fixef | Extract fixed-effects estimates | |

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

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

residuals.merMod | residuals of merMod objects | |

fortify | add information to data based on a fitted model | |

InstEval | University Lecture/Instructor Evaluations by Students at ETH | |

nlformula | Manipulate a Nonlinear Model Formula | |

lmList | Fit List of lm Objects with a Common Model | |

factorize | Attempt to convert grouping variables to factors | |

drop1.merMod | Drop all possible single fixed-effect terms from a mixed effect model | |

glmer.nb | Fitting GLMM's for Negative Binomial | |

glmer | Fitting Generalized Linear Mixed-Effects Models | |

sigma | Extract Residual Standard Deviation 'Sigma' | |

dummy | Dummy variables (experimental) | |

nobars | Omit terms separated by vertical bars in a formula | |

modular | Modular Functions for Mixed Model Fits | |

predict.merMod | Predictions from a model at new data values | |

golden-class | Class "golden" and Generator for Golden Search Optimizer Class | |

grouseticks | Data on red grouse ticks from Elston et al. 2001 | |

simulate.merMod | Simulate Responses From merMod Object | |

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

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

Penicillin | Variation in penicillin testing | |

pvalues | Getting p-values for fitted models | |

profile-methods | Profile method for merMod objects | |

subbars | "Sub[stitute] Bars" | |

isREML | Check characteristics of models | |

lme4-package | Linear, generalized linear, and nonlinear mixed models | |

lmer | Fit Linear Mixed-Effects Models | |

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

mkRespMod | Create an lmerResp, glmResp or nlsResp instance | |

plots.thpr | Mixed-Effects Profile Plots (Regular / Density / Pairs) | |

varianceProf | Transform Profile to the variance scale | |

mkVarCorr | Make Variance and Correlation Matrices from theta | |

Dyestuff | Yield of dyestuff by batch | |

lmerControl | Control of Mixed Model Fitting | |

merPredD | Generator object for the merPredD class | |

devcomp | Extract the deviance component list | |

hatvalues.merMod | Diagonal elements of the hat matrix | |

ranef | Extract the modes of the random effects | |

vcconv | Convert between representations of (co-)variance structures | |

sleepstudy | Reaction times in a sleep deprivation study | |

mkMerMod | Create a 'merMod' Object | |

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

isNested | Is f1 nested within f2? | |

glmerLaplaceHandle | Handle for glmerLaplace | |

troubleshooting | Troubleshooting | |

mkSimulateTemplate | Make templates suitable for guiding mixed model simulations | |

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

nloptwrap | Wrappers for additional optimizers | |

plot.merMod | diagnostic plots for merMod fits | |

nlmer | Fitting Nonlinear Mixed-Effects Models | |

prt-utilities | Print and Summary Method Utilities for Mixed Effects | |

lmList4-class | Class "lmList4" of 'lm' Objects on Common Model | |

refitML | Refit a Model by Maximum Likelihood Criterion | |

refit | Refit a (merMod) Model with a Different Response | |

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

merMod-class | Class "merMod" of Fitted Mixed-Effect Models | |

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

Arabidopsis | Arabidopsis clipping/fertilization data | |

lmResp | Generator objects for the response classes | |

plot.lmList4 | plots for lmList4 objects | |

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## Details

Contact | LME4 Authors |

LinkingTo | Rcpp (>= 0.10.5), RcppEigen |

VignetteBuilder | knitr |

LazyData | yes |

License | GPL (>= 2) |

URL | https://github.com/lme4/lme4/ http://lme4.r-forge.r-project.org/ |

BugReports | https://github.com/lme4/lme4/issues |

NeedsCompilation | yes |

Packaged | 2015-10-05 17:56:37 UTC; bolker |

Repository | CRAN |

Date/Publication | 2015-10-06 08:08:29 |

depends | base (>= 3.0.2) , Matrix (>= 1.1.1) , methods , R (>= 3.0.2) , stats |

suggests | boot , gamm4 , ggplot2 , HSAUR2 , knitr , MEMSS , mlmRev , numDeriv , optimx (>= 2013.8.6) , pbkrtest , PKPDmodels , testthat (>= 0.8.1) |

imports | graphics , grid , lattice , MASS , minqa (>= 1.1.15) , nlme , nloptr (>= 1.0.4) , parallel , splines , utils |

linkingto | Rcpp (>= 0.10.5) , RcppEigen |

Contributors | Steven Walker, Ben Bolker, Douglas Bates, Martin Maechler, Henrik Singmann, Rune Haubo Bojesen Christensen, Bin Dai, Gabor Grothendieck |

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