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plantmix: Genetic Study of Plant Mixtures

Fit linear mixed models dedicated to the genetic study of plant mixtures, such as those based on general and specific mixing abilities (GMA-SMA) as well as direct and social breeding values (DBV-SBV), also known as direct and indirect genetic effects (DGE-IGE). More details in Forst et al (2019, <doi:10.1016/j.fcr.2019.107571>) for GMA-SMA models, and Salomon et al (2026, <doi:10.64898/2026.03.27.714849>) for DBV-SBV models. The package also provides functions to optimize experimental designs, simulate data sets and compute interaction indices.

Version: 1.0.2
Depends: R (≥ 4.0.0), ggplot2, lme4
Imports: graphics, igraph, MASS, Matrix, methods, Rcpp (≥ 1.0.13), stats, TMB (≥ 1.9.17), utils
LinkingTo: TMB, Rcpp, RcppEigen
Suggests: breedR, INLA, emmeans, knitr, MM4LMM, rmarkdown, testthat
Published: 2026-06-09
DOI: 10.32614/CRAN.package.plantmix
Author: Timothee Flutre ORCID iD [aut, ctb, cre], INRAE [cph, fnd], Jerome Enjalbert ORCID iD [ctb], Emma Forst ORCID iD [ctb], Maxence Remerand ORCID iD [ctb], Jemay Salomon ORCID iD [ctb]
Maintainer: Timothee Flutre <timothee.flutre at inrae.fr>
License: AGPL-3
Copyright: INRAE
NeedsCompilation: yes
Additional_repositories: https://famuvie.github.io/breedR, https://inla.r-inla-download.org/R/stable
Citation: plantmix citation info
Materials: README, NEWS
CRAN checks: plantmix results

Documentation:

Reference manual: plantmix.html , plantmix.pdf
Vignettes: 1) Introduction to GMA-SMA models (source, R code)
2) Example of GMA-SMA models for varietal mixtures in microplots (source, R code)
3) Example of DBV-SBV models for species mixtures in a tester-based design (source, R code)

Downloads:

Package source: plantmix_1.0.2.tar.gz
Windows binaries: r-devel: plantmix_1.0.2.zip, r-release: not available, r-oldrel: plantmix_1.0.2.zip
macOS binaries: r-release (arm64): plantmix_1.0.2.tgz, r-oldrel (arm64): plantmix_1.0.2.tgz, r-release (x86_64): plantmix_1.0.2.tgz, r-oldrel (x86_64): plantmix_1.0.2.tgz

Linking:

Please use the canonical form https://CRAN.R-project.org/package=plantmix to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.