# lme4 v1.1-7

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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 | |

Pastes | Paste strength by batch and cask | |

lmResp-class | Classes "lmResp", "glmResp", "nlsResp" and "lmerResp" | |

devcomp | Extract the deviance component list | |

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

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

VerbAgg | Verbal Aggression item responses | |

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

lmResp | Generator objects for the response classes | |

nlmer | Fit Nonlinear Mixed-Effects Models | |

GHrule | Univariate Gauss-Hermite quadrature rule | |

varianceProf | Transform Profile to the variance scale | |

sigma | Extract residual standard error | |

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

glmer.nb | glmer() for Negative Binomial | |

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

dummy | Dummy variables (experimental) | |

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

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

simulate.merMod | Simulate responses from a merMod object | |

VarCorr | Extract Variance and Correlation Components | |

isNested | Is f1 nested within f2? | |

GQdk | Sparse Gaussian Quadrature grid | |

plot.merMod | diagnostic plots for merMod fits | |

cake | Breakage Angle of Chocolate Cakes | |

nloptwrap | Wrapper for nlOpt optimizers | |

subbars | "Sub[stitute] Bars" | |

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

lmerControl | Control of Mixed Model Fitting | |

lmer | Fit Linear Mixed-Effects Models | |

ranef | Extract the modes of the random effects | |

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

Penicillin | Variation in penicillin testing | |

glmFamily | Generator object for the glmFamily class | |

profile-methods | Profile method for merMod objects | |

isREML | Check characteristics of models | |

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

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

mkReTrms | Create Z, Lambda, Lind, etc. | |

golden | Generator object for the golden search optimizer class. | |

mkdevfun | Create a deviance evaluation function from a predictor and a response module | |

sleepstudy | Reaction times in a sleep deprivation study | |

Dyestuff | Yield of dyestuff by batch | |

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

cbpp | Contagious bovine pleuropneumonia | |

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

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

refit | Refit a model with a new response, by maximum likelihood criterion | |

ngrps | Number of levels | |

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

pvalues | Getting p-values for fitted models | |

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

golden-class | Class "golden" | |

merPredD-class | Class "merPredD" - a dense predictor reference class | |

merPredD | Generator object for the merPredD class | |

mkVarCorr | Make Variance and Correlation Matrices from theta | |

nlformula | Manipulate a Nonlinear Model Formula | |

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

rePos-class | Class "rePos" | |

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

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

glmer | Fit Generalized Linear Mixed-Effects Models | |

fixef | Extract fixed-effects estimates | |

GQN | Sparse Gauss-Hermite quadrature grids | |

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

residuals.merMod | residuals of merMod objects | |

modular | Modular functions for mixed model fits | |

mkMerMod | Create a merMod object | |

refitML | Refit a model by maximum likelihood criterion | |

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

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## Details

Contact | LME4 Authors |

LinkingTo | Rcpp, RcppEigen |

VignetteBuilder | knitr |

LazyData | yes |

License | GPL (>= 2) |

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

BuildVignettes | yes |

Packaged | 2014-07-19 17:33:54 UTC; hornik |

NeedsCompilation | yes |

Repository | CRAN |

Date/Publication | 2014-07-19 19:49:55 |

depends | base (>= 2.15.1) , Matrix (>= 1.1.1) , methods , R (>= 2.15.1) , Rcpp (>= 0.10.5) , stats |

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

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

linkingto | RcppEigen |

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

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