lme4 v1.0-4
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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" | |
| merPredD-class | Class "merPredD" - a dense predictor reference class | |
| bootMer | Model-based (Semi-)Parametric Bootstrap for Mixed Models | |
| mkVarCorr | Make Variance and Correlation Matrices from theta | |
| predict.merMod | Predictions from a model at new data values | |
| fortify | add information to data based on a fitted model | |
| cake | Breakage angle of chocolate cakes | |
| cbpp | Contagious bovine pleuropneumonia | |
| golden-class | Class "golden" | |
| glmFamily-class | Class "glmFamily" - a reference class for family | |
| VerbAgg | Verbal Aggression item responses | |
| grouseticks | Data on red grouse ticks from Elston et al. 2001 | |
| InstEval | University Lecture/Instructor Evaluations by Students at ETH | |
| glmFamily | Generator object for the glmFamily class | |
| pvalues | Getting p-values for fitted models | |
| mkReTrms | Create Z, Lambda, Lind, etc. | |
| NelderMead | Generator object for the Nelder-Mead optimizer class. | |
| isNested | Is f1 nested within f2? | |
| sigma | Extract residual standard error | |
| lmList-class | Class "lmList" of 'lm' Objects on Common Model | |
| NelderMead-class | Class "NelderMead" | |
| sleepstudy | Reaction times in a sleep deprivation study | |
| GQdk | Sparse Gaussian Quadrature grid | |
| densityplot.thpr | densityplot from a mixed-effects profile | |
| lmList | List of lm Objects with a Common Model | |
| subbars | "Sub[stitute] Bars" | |
| devcomp | Extract the deviance component list | |
| rePos | Generator object for the rePos (random-effects positions) class | |
| profile-methods | Profile method for merMod objects | |
| findbars | Determine random-effects expressions from a formula | |
| refitML | Refit a model by maximum likelihood criterion | |
| lmResp | Generator objects for the response classes | |
| golden | Generator object for the golden search optimizer class. | |
| glmer.nb | glmer() for Negative Binomial | |
| getME | Extract or Get Generalized Components from a Fitted Mixed Effects Model | |
| glmer | Fit Generalized Linear Mixed-Effects Models | |
| merMod-class | Class "merMod" of Fitted Mixed-Effect Models | |
| merPredD | Generator object for the merPredD class | |
| plot.merMod | diagnostic plots for merMod fits | |
| mkRespMod | Create an lmerResp, glmResp or nlsResp instance | |
| GHrule | Univariate Gauss-Hermite quadrature rule | |
| isREML | Check characteristics of models | |
| confint.merMod | Compute confidence intervals on the parameters of an lme4 fit | |
| GQN | Sparse Gauss-Hermite quadrature grids | |
| lmerControl | Control of Mixed Model Fitting | |
| refit | Refit a model by maximum likelihood criterion | |
| lme4-package | Linear, generalized linear, and nonlinear mixed models | |
| rePos-class | Class "rePos" | |
| nlformula | Manipulate a nonlinear model formula. | |
| residuals.merMod | residuals of merMod objects | |
| modular | Modular functions for mixed model fits | |
| mkMerMod | Create a merMod object | |
| varianceProf | Transform to the variance scale | |
| fixef | Extract fixed-effects estimates | |
| lmer | Fit Linear Mixed-Effects Models | |
| ranef | Extract the modes of the random effects | |
| Dyestuff | Yield of dyestuff by batch | |
| VarCorr | Extract Variance and Correlation Components | |
| mkdevfun | Create a deviance evaluation function from a predictor and a response module | |
| nlmer | Fit Nonlinear Mixed-Effects Models | |
| splom.thpr | Profile pairs plot | |
| Penicillin | Variation in penicillin testing | |
| nobars | Omit terms separated by vertical bars in a formula | |
| simulate.merMod | Simulate responses from a merMod object | |
| No Results! | ||
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Details
| Date | 2013-09-08 |
| Contact | LME4 Authors |
| LinkingTo | Rcpp, RcppEigen |
| LazyData | yes |
| License | GPL (>= 2) |
| URL | http://lme4.r-forge.r-project.org/ |
| Collate | 'AllClass.R' 'AllGeneric.R' 'GHrule.R' 'lmer.R' 'lmList.R' 'profile.R' 'sparsegrid.R' 'utilities.R' 'optimizer.R' 'predict.R' 'bootMer.R' 'nbinom.R' 'mcmcsamp.R' 'plot.R' 'vcconv.R' 'modular.R' 'hooks.r' 'lmerControl.R' |
| BuildVignettes | yes |
| Packaged | 2013-09-21 07:50:15 UTC; ripley |
| NeedsCompilation | yes |
| Repository | CRAN |
| Date/Publication | 2013-09-21 10:00:40 |
| depends | base (>= 2.14.0) , lattice , Matrix (>= 1.0) , methods , R (>= 2.14.0) , stats |
| suggests | boot , ggplot2 , MEMSS , mlmRev , optimx (>= 2013.8.6) , PKPDmodels , plyr , Rcpp (>= 0.10.1) , RcppEigen (>= 0.3.1.2) , reshape , testthat |
| imports | graphics , grid , MASS , minqa (>= 1.1.15) , nlme , splines |
| Contributors | Steven Walker, Ben Bolker, Douglas Bates, Martin Maechler |
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