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R-package-pointers.md

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R Packages for Mixed(-Effects) Models

The absolute core:

nlme

lme4

Other Packages with Mixed Effect Models as main purpose (and recommendable)

CRAN Task Views

There is none, with this topic Is there no good one ?

  • nlme is in ChemPhys, Econometrics, Environmetrics, Finance, OfficialStatistics, Psychometrics, SocialSciences, Spatial, SpatioTemporal,

    whereas

  • lme4 is in Bayesian, Econometrics, Environmetrics, OfficialStatistics, Psychometrics, SocialSciences, SpatioTemporal,

  • with the intersection

Task View URL CRAN packages comments
Econometrics https://CRAN.R-project.org/view=Econometrics nlme, lme4
Environmetrics https://CRAN.R-project.org/view=Environmetrics nlme, lme4 Modelling species responses and other data
OfficialStatistics https://CRAN.R-project.org/view=OfficialStatistics nlme, lme4, rsae (robust) Small Area Estimation
Psychometrics https://CRAN.R-project.org/view=Psychometrics nlme, lme4, ordinal, MCMCglmm, irtrees Item Response Theory (ITR), Rasch Mod.
SocialSciences https://CRAN.R-project.org/view=SocialSciences nlme, lme4, lmeSplines, lmm, MCMCglmm Other Regression Methods
SpatioTemporal https://CRAN.R-project.org/view=SpatioTemporal nlme, lme4 (spatio-temporal data)

R (CRAN) packages with LMM in their names:

ip <- installed.packages() # ~ 13'000 for Martin Maechler
str(ip)
##  chr [1:13265, 1:16] "BiocInstaller" "pkgA" "copula_" "copulaData" ...
##  - attr(*, "dimnames")=List of 2
##   ..$ : chr [1:13265] "BiocInstaller" "pkgA" "copula_" "copulaData" ...
##   ..$ : chr [1:16] "Package" "LibPath" "Version" "Priority" ...

pkgs <- rownames(ip)
str(LMMs <- grep("lmm", pkgs, ignore.case=TRUE, value=TRUE))
##  chr [1:36] "denseFLMM" "designGLMM" "glmm" "glmmADMB" "glmmAK" ...

pdLMM <- lapply(LMMs, packageDescription)
titLMM <-
    ttLMM <- gsub("\n", " ",
                  sapply(setNames(,LMMs), packageDescription, fields = "Title"))
longT <- nchar(ttLMM) > 80
ttLMM[longT] <- paste(substr(ttLMM[longT], 1, 77), "...")
cbind(ttLMM) # 80% are GLMM  amazing
##                ttLMM                                                                              
## denseFLMM      "Functional Linear Mixed Models for Densely Sampled Data"                          
## designGLMM     "Finding Optimal Block Designs for a Generalised Linear Mixed Model"               
## glmm           "Generalized Linear Mixed Models via Monte Carlo Likelihood Approximation"         
## glmmADMB       "Generalized Linear Mixed Models using AD Model Builder"                           
## glmmAK         "Generalized Linear Mixed Models"                                                  
## glmmBUGS       "Generalised Linear Mixed Models with BUGS and JAGS"                               
## glmmGS         "Gauss-Seidel Generalized Linear Mixed Model solver"                               
## glmmLasso      "Variable Selection for Generalized Linear Mixed Models by L1-Penalized Estima ..."
## glmmML         "Generalized Linear Models with Clustering"                                        
## GLMMRR         "Generalized Linear Mixed Model (GLMM) for Binary Randomized Response Data"        
## glmmsr         "Fit a Generalized Linear Mixed Model"                                             
## glmmTMB        "Generalized Linear Mixed Models using Template Model Builder"                     
## HGLMMM         "Hierarchical Generalized Linear Models"                                           
## HiLMM          "Estimation of Heritability in Linear Mixed Models"                                
## lmm            "Linear Mixed Models"                                                              
## lmmen          "Linear Mixed Model Elastic Net"                                                   
## lmmfit         "Goodness-of-fit-measures for linear mixed models with one-level-grouping"         
## lmmlasso       "Linear mixed-effects models with Lasso"                                           
## lmmot          "Multiple Ordinal Tobit (MOT) Model"                                               
## lmmpar         "Parallel Linear Mixed Model"                                                      
## lmms           "Linear Mixed Effect Model Splines for Modelling and Analysis of Time Course Data" 
## MCMCglmm       "MCMC Generalised Linear Mixed Models"                                             
## mlmm           "Multilevel Model for Multivariate Responses with Missing Values"                  
## mlmmm          "ML estimation under multivariate linear mixed models with missing values"         
## mvglmmRank     "Multivariate Generalized Linear Mixed Models for Ranking Sports Teams"            
## plmm           "Partially Linear Mixed Effects Model"                                             
## powerlmm       "Power Calculations for Longitudinal Multilevel Models"                            
## QGglmm         "Estimate Quantitative Genetics Parameters from Generalised Linear Mixed Models"   
## qrLMM          "Quantile Regression for Linear Mixed-Effects Models"                              
## qrNLMM         "Quantile Regression for Nonlinear Mixed-Effects Models"                           
## r2glmm         "Computes R Squared for Mixed (Multilevel) Models"                                 
## RLMM           "A Genotype Calling Algorithm for Affymetrix SNP Arrays"                           
## robustlmm      "Robust Linear Mixed Effects Models"                                               
## sparseFLMM     "Functional Linear Mixed Models for Irregularly or Sparsely Sampled Data"          
## StroupGLMM     "R Codes and Datasets for Generalized Linear Mixed Models: Modern Concepts, Me ..."
## VetResearchLMM "Linear Mixed Models - An Introduction with Applications in Veterinary Research"

Closely related packages

  • ordinal, fn clmm() for cumulative LMMs.

  • lmeSplines, based on pkg nlme, allows splines for linear and non-linear MM.

  • mgcv, Recommended pkg, has gamm(), based on pkg nlme. Alternatively, (and not possible inside rec. package mgcv):

  • gamm4, based on pkg lme4, has fn. gamm4() based on lmer() etc.

NB. "knit me" to markdown --> *.md simply by

knitr::knit("~/R/D/GH/MEMo/R-package-pointers.Rmd")