sommer: Solving Mixed Model Equations in R

Structural multivariate-univariate linear mixed model solver for estimation of multiple random effects with unknown variance-covariance structures (e.g., heterogeneous and unstructured) and known covariance among levels of random effects (e.g., pedigree and genomic relationship matrices) (Covarrubias-Pazaran, 2016 <doi:10.1371/journal.pone.0156744>; Maier et al., 2015 <doi:10.1016/j.ajhg.2014.12.006>). REML estimates can be obtained using the Direct-Inversion Newton-Raphson and Direct-Inversion Average Information algorithms for the problems r x r (r being the number of records) or using the mixed-model-equations-based average information algorithm for the problem c x c (c being the number of coefficients to estimate). Spatial models can also be fitted using the two-dimensional spline functionality available in sommer.

Version: 4.2.0
Depends: R (≥ 3.5.0), Matrix (≥ 1.1.1), methods, stats, MASS, lattice, crayon
Imports: Rcpp (≥ 0.12.19)
LinkingTo: Rcpp, RcppArmadillo, RcppProgress
Suggests: rmarkdown, knitr, plyr, parallel, orthopolynom, testthat (≥ 3.0.0)
Published: 2022-09-10
Author: Giovanny Covarrubias-Pazaran
Maintainer: Giovanny Covarrubias-Pazaran <cova_ruber at live.com.mx>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation: yes
Citation: sommer citation info
Materials: README ChangeLog
In views: Agriculture, MixedModels
CRAN checks: sommer results

Documentation:

Reference manual: sommer.pdf
Vignettes: Quick start for the sommer package
Moving to newer versions of sommer
Quantitative genetics using the sommer package
GxE models in sommer
translate lme4 to sommer
Spatial modeling using the sommer package

Downloads:

Package source: sommer_4.2.0.tar.gz
Windows binaries: r-devel: sommer_4.2.0.zip, r-release: sommer_4.2.0.zip, r-oldrel: sommer_4.2.0.zip
macOS binaries: r-release (arm64): sommer_4.2.0.tgz, r-oldrel (arm64): sommer_4.2.0.tgz, r-release (x86_64): sommer_4.2.0.tgz, r-oldrel (x86_64): sommer_4.2.0.tgz
Old sources: sommer archive

Reverse dependencies:

Reverse imports: IPLGP, lmDiallel, mlmm.gwas, pcgen, statgenGWAS
Reverse suggests: lucid, MoBPS
Reverse enhances: biometryassist, emmeans

Linking:

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