Package: plantmix 1.0.2

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.

Authors:Timothee Flutre [aut, ctb, cre], INRAE [cph, fnd], Jerome Enjalbert [ctb], Emma Forst [ctb], Maxence Remerand [ctb], Jemay Salomon [ctb]

plantmix_1.0.2.tar.gz
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plantmix_1.0.2.tgz(r-4.6-x86_64)plantmix_1.0.2.tgz(r-4.6-arm64)plantmix_1.0.2.tgz(r-4.5-x86_64)plantmix_1.0.2.tgz(r-4.5-arm64)
plantmix_1.0.2.tar.gz(r-4.7-arm64)plantmix_1.0.2.tar.gz(r-4.7-x86_64)plantmix_1.0.2.tar.gz(r-4.6-arm64)plantmix_1.0.2.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
card.svg |card.png
plantmix/json (API)
NEWS

# Install 'plantmix' in R:
install.packages('plantmix', repos = c('https://timflutre.r-universe.dev', 'https://cloud.r-project.org'))

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

3.18 score 39 exports 34 dependencies

Last updated from:24a33b86e4. Checks:12 OK, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK254
linux-devel-x86_64OK269
source / vignettesOK413
linux-release-arm64OK267
linux-release-x86_64OK244
macos-release-arm64OK273
macos-release-x86_64OK640
macos-oldrel-arm64OK405
macos-oldrel-x86_64OK467
windows-develOK1038
windows-releaseOK1096
windows-oldrelOK309
wasm-releaseFAIL161

Exports:CCestimGRMestimRYMRepestimRYRepfitDBVSBVinterfitGMASMAgetDesignBinaryCropMixgetDesignBinaryVarMixgetMixtureListgetMixturesPerGenoimageMatinfoCriterioninvvecinvvecMixesLERmixSowingWeightmkAllZSMAmkZGMAmkZinterspemkZSMAnbSeedsToSownInPurenormBiasErrorparamBoot4TMBpivotMixData2LongpivotMixData2WideplotDesignCropMixplotDesignVarMixplotDiallelRIIRIInetrmatnormRYRYMRYPRYTsimulDBVSBVintersimulGenosDoseStructsummarizeGMASMAsvec

Dependencies:bootclicpp11farverggplot2gluegtableigraphisobandlabelinglatticelifecyclelme4magrittrMASSMatrixminqanlmenloptrpkgconfigR6rbibutilsRColorBrewerRcppRcppEigenRdpackreformulasrlangS7scalesTMBvctrsviridisLitewithr

Introduction to GMA-SMA models

T. Flutre, J. Enjalbert

Rendered fromvig1_intro-GMA-SMA.Rmdusingknitr::rmarkdownon Jun 10 2026.

Last update: 2026-06-09
Started: 2026-06-09

Example of GMA-SMA models for varietal mixtures in microplots

T. Flutre

Rendered fromvig2_GMA-SMA_simul-infer.Rmdusingknitr::rmarkdownon Jun 10 2026.

Last update: 2026-06-09
Started: 2026-06-09

Example of DBV-SBV models for species mixtures in a tester-based design

J. Salomon, J. Enjalbert, T. Flutre

Rendered fromvig3_DBV-SBV_crop-mix_testers.Rmdusingknitr::rmarkdownon Jun 10 2026.

Last update: 2026-06-09
Started: 2026-06-09

Readme and manuals

Help Manual

Help pageTopics
Change in contributionCC
Estimate a GRMestimGRM
RYM with "rep" effectestimRYMRep
RY with "rep" effectestimRYRep
Fit DBV-SBV models for interspecific mixturesfitDBVSBVinter
Fit GMA-SMA modelsfitGMASMA
Optimize design for binary crop mixturesgetDesignBinaryCropMix
Optimize design for binary varietal mixturesgetDesignBinaryVarMix
Reformat composition of mixtures into a listgetMixtureList
Get mixture(s) per genotypegetMixturesPerGeno
Image of a matriximageMat
Information criterioninfoCriterion
Inverse vec operatorinvvec
Inverse vec for mixturesinvvecMixes
Land equivalent ratio (LER)LER
SowingmixSowingWeight
Design matrices of SMAs for GMA-SMA modelsmkAllZSMA
Design matrix of GMAs for GMA-SMA modelsmkZGMA
Design matrices for DBV-SBV models in an inter-specific trialmkZinterspe
Design matrix of SMAs for GMA-SMA modelsmkZSMA
SowingnbSeedsToSownInPure
Normalized bias errornormBiasError
Parametric bootstrap with TMBparamBoot4TMB
Pivot mixture data into the long formatpivotMixData2Long
Pivot mixture data into the wide formatpivotMixData2Wide
Plot design for crop mixturesplotDesignCropMix
Plot design for varietal mixturesplotDesignVarMix
Plot diallelplotDiallel
Relative interaction index (RII)RII
Net Relative interaction index (RIInet)RIInet
Matrix-variate Normal distributionrmatnorm
Relative yield (RY)RY
Relative yield of mixture (RYM)RYM
Relative yield per plant (RYP)RYP
Relative yield total (RYT)RYT
Simulate w.r.t. a DBV-SBV model for interspecific mixturessimulDBVSBVinter
Simulate SNP genotypessimulGenosDoseStruct
Model summarysummarizeGMASMAs
Vec operatorvec