Fits generalized linear and non linear mixed models with flexible covariance structures for multiple random effects. Supports structured random-effect and Gaussian residual covariances, including unstructured, autoregressive, spatial, factor-analytic and reduced-rank models. These structures can be combined using Kronecker products and user-defined covariance functions. Known relationships among random-effect levels, including pedigree and genomic relationship matrices, can be incorporated. Gaussian models are fitted by maximum likelihood or restricted maximum likelihood using complementary coefficient-space Henderson and observation-space direct-inversion engines, with average-information optimization and expectation-maximization recovery. Numerical methods include sparse matrix factorization, preconditioned iterative solvers and stochastic trace and log-determinant approximations for eligible large-scale problems. Generalized models are fitted by penalized quasi-likelihood or native Laplace-approximated maximum likelihood, including joint models of responses from different families linked through shared random effects. Provides prediction, uncertainty quantification and inference tools for applications including quantitative genetics, genomic prediction, multi-environment trials and spatial analysis (Covarrubias-Pazaran, 2016 <doi:10.1371/journal.pone.0156744>; Maier et al., 2015 <doi:10.1016/j.ajhg.2014.12.006>; Jensen et al., 1997).
| Version: |
4.5.27 |
| Depends: |
R (≥ 3.5.0), Matrix (≥ 1.6-2), methods, stats, enhancer |
| Imports: |
Rcpp (≥ 0.12.19), MASS, crayon |
| LinkingTo: |
Rcpp, RcppArmadillo, RcppProgress, RcppEigen, Matrix |
| Suggests: |
RcppArmadillo, flexiblas, RhpcBLASctl, parallelly, rmarkdown, knitr, plyr, parallel, orthopolynom, RSpectra, lattice, emmeans (≥ 1.4), estimability, testthat (≥ 3.0.0), rrBLUP, litedown |
| Published: |
2026-11-14 |
| DOI: |
10.32614/CRAN.package.sommer |
| Author: |
Giovanny Covarrubias-Pazaran
 [aut, cre] |
| Maintainer: |
Giovanny Covarrubias-Pazaran <cova_ruber at live.com.mx> |
| BugReports: |
https://github.com/covaruber/sommer/issues |
| License: |
GPL-3 |
| URL: |
https://github.com/covaruber/sommer |
| NeedsCompilation: |
yes |
| SystemRequirements: |
METIS graph partitioning library (optional; enables
nested-dissection sparse ordering for large relationship
matrices, auto-detected at configure time, falls back to AMD
ordering when absent), NVIDIA GPU toolkit with cuBLAS and
cuSOLVER (optional; enables GPU kernels on Linux through
SOMMER_CUDA_HOME; the GPU libraries are loaded dynamically at
run time and are not needed to build the package) |
| Citation: |
sommer citation info |
| Materials: |
README, ChangeLog |
| In views: |
Agriculture, MixedModels |
| CRAN checks: |
sommer results |