lme4 v1.1-8
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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 | |
| GQdk | Sparse Gaussian / Gauss-Hermite Quadrature grid | |
| hatvalues.merMod | Diagonal elements of the hat matrix | |
| lme4-package | Linear, generalized linear, and nonlinear mixed models | |
| confint.merMod | Compute Confidence Intervals for Parameters of a [ng]lmer Fit | |
| ranef | Extract the modes of the random effects | |
| VerbAgg | Verbal Aggression item responses | |
| GHrule | Univariate Gauss-Hermite quadrature rule | |
| devcomp | Extract the deviance component list | |
| VarCorr | Extract Variance and Correlation Components | |
| Pastes | Paste strength by batch and cask | |
| lmList4-class | Class "lmList4" of 'lm' Objects on Common Model | |
| subbars | "Sub[stitute] Bars" | |
| Penicillin | Variation in penicillin testing | |
| mkReTrms | Make Random Effect Terms: Create Z, Lambda, Lind, etc. | |
| lmerControl | Control of Mixed Model Fitting | |
| sigma | Extract Residual Standard Deviation 'Sigma' | |
| dummy | Dummy variables (experimental) | |
| golden | Generator object for the golden search optimizer class. | |
| merPredD-class | Class "merPredD" - a Dense Predictor Reference Class | |
| glmer.nb | glmer() for Negative Binomial | |
| predict.merMod | Predictions from a model at new data values | |
| lmList | Fit List of lm Objects with a Common Model | |
| mkdevfun | Create Deviance Evaluation Function from Predictor and Response Module | |
| plots.thpr | Mixed-Effects Profile Plots (Regular / Density / Pairs) | |
| nobars | Omit terms separated by vertical bars in a formula | |
| simulate.merMod | Simulate Responses From merMod Object | |
| glmer | Fitting Generalized Linear Mixed-Effects Models | |
| NelderMead | Nelder-Mead Optimization of Parameters, Possibly (Box) Constrained | |
| findbars | Determine random-effects expressions from a formula | |
| cbpp | Contagious bovine pleuropneumonia | |
| pvalues | Getting p-values for fitted models | |
| cake | Breakage Angle of Chocolate Cakes | |
| NelderMead-class | Class "NelderMead" of Nelder-Mead optimizers and its Generator | |
| refitML | Refit a Model by Maximum Likelihood Criterion | |
| golden-class | Class "golden" | |
| Dyestuff | Yield of dyestuff by batch | |
| glmFamily | Generator object for the glmFamily class | |
| isNested | Is f1 nested within f2? | |
| plot.merMod | diagnostic plots for merMod fits | |
| troubleshooting | Troubleshooting | |
| mkMerMod | Create a merMod object | |
| lmResp | Generator objects for the response classes | |
| mkRespMod | Create an lmerResp, glmResp or nlsResp instance | |
| nlmer | Fitting Nonlinear Mixed-Effects Models | |
| residuals.merMod | residuals of merMod objects | |
| rePos-class | Class "rePos" | |
| Arabidopsis | Arabidopsis clipping/fertilization data | |
| fortify | add information to data based on a fitted model | |
| merMod-class | Class "merMod" of Fitted Mixed-Effect Models | |
| expandDoubleVerts | Expand terms with '||' notation into separate '|' terms | |
| lmer | Fit Linear Mixed-Effects Models | |
| ngrps | Number of Levels of a Factor or a "merMod" Model | |
| drop1.merMod | Drop all possible single fixed-effect terms from a mixed effect model | |
| isREML | Check characteristics of models | |
| vcconv | Convert between representations of (co-)variance structures | |
| refit | Refit a (merMod) Model with a Different Response | |
| convergence | Assessing Convergence for Fitted Models | |
| mkSimulateTemplate | Make templates suitable for guiding mixed model simulations | |
| bootMer | Model-based (Semi-)Parametric Bootstrap for Mixed Models | |
| mkVarCorr | Make Variance and Correlation Matrices from theta | |
| sleepstudy | Reaction times in a sleep deprivation study | |
| nloptwrap | Wrappers for additional optimizers | |
| glmerLaplaceHandle | Handle for glmerLaplace | |
| glmFamily-class | Class "glmFamily" - a reference class for family | |
| grouseticks | Data on red grouse ticks from Elston et al. 2001 | |
| rePos | Generator object for the rePos (random-effects positions) class | |
| getME | Extract or Get Generalized Components from a Fitted Mixed Effects Model | |
| modular | Modular Functions for Mixed Model Fits | |
| varianceProf | Transform Profile to the variance scale | |
| factorize | Attempt to convert grouping variables to factors | |
| fixef | Extract fixed-effects estimates | |
| plot.lmList4 | plots for lmList4 objects | |
| profile-methods | Profile method for merMod objects | |
| lmResp-class | Classes "lmResp", "glmResp", "nlsResp" and "lmerResp" | |
| InstEval | University Lecture/Instructor Evaluations by Students at ETH | |
| merPredD | Generator object for the merPredD class | |
| nlformula | Manipulate a Nonlinear Model Formula | |
| No Results! | ||
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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 | 2015-06-20 21:23:09 UTC; bolker |
| Repository | CRAN |
| Date/Publication | 2015-06-22 09:09:58 |
| 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 , 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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