In frahik/BMTME: Bayesian Multi-Trait Multi-Environment for Genomic Selection Analysis

Bayesian Multi-Trait Multi-Environment | Development version `r packageVersion('BMTME')`

[Last README update: `r format(Sys.Date())`]

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Table of contents

• NEWS
• Instructions
  • Installation
  • Dataset
• How to cite this package
• Contributions
• Authors

News of this version (`r packageVersion('BMTME')`)

See the last updates on NEWS.

Instructions for proper implementation

Installation

To complete installation of dev version of BMTME from GitHub, you have to install Rtools Software and a few packages first.

install.packages('devtools')
devtools::install_github('frahik/BMTME')

Datasets

The package include 6 sample datasets

|Name |Lines|Environment|Traits|Total of observations| ME models | MTME models | |-------------|-----|-----------|------|---------------------|-----------|-------------| |MaizeToy | 30 | 3 | 3 | 270 | * | * | |WheatIranian | 30 | 2 | 2 | 120 | * | * | |WheatJapa30 | 30 | 1 | 6 | 180 | * | | |WheatJapa50 | 50 | 1 | 3 | 150 | * | | |WheatMadaToy | 50 | 1 | 6 | 300 | * | | |WheatToy | 30 | 3 | 2 | 180 | * | * |

To load one dataset, use the function data(datasetName)

How to cite this package

First option, by the article paper

@article {Montesinos-L{\'o}pez1355,
    author = {Montesinos-L{\'o}pez, Osval A. and Montesinos-L{\'o}pez, Abelardo and Luna-V{\'a}zquez, Francisco Javier and Toledo, Fernando H. and P{\'e}rez-Rodr{\'\i}guez, Paulino and Lillemo, Morten and Crossa, Jos{\'e}},
    title = {An R Package for Bayesian Analysis of Multi-environment and Multi-trait Multi-environment Data for Genome-Based Prediction},
    volume = {9},
    number = {5},
    pages = {1355--1369},
    year = {2019},
    doi = {10.1534/g3.119.400126},
    publisher = {G3: Genes, Genomes, Genetics},
    URL = {https://www.g3journal.org/content/9/5/1355},
    eprint = {https://www.g3journal.org/content/9/5/1355.full.pdf},
    journal = {G3: Genes, Genomes, Genetics}
}

Second option, by the manual package

citation('BMTME')

Contributions

If you have any suggestions or feedback, I would love to hear about it. Feel free to report new issues in this link, also if you want to request a feature/report a bug, or make a pull request if you can contribute.

Research and implementations

• An R Package for Bayesian Analysis of Multi-environment and Multi-trait Multi-environment Data for Genome-Gased Prediction
• A Bayesian Multiple-Trait and Multiple-Environment Model Using the Matrix Normal Distribution

Authors

• Francisco Javier Luna-Vázquez (Author, Maintainer)
• Osval Antonio Montesinos-López (Author)
• Abelardo Montesinos-López (Author)
• José Crossa (Author)
• Fernando Tolero (Author)

frahik/BMTME documentation built on Aug. 29, 2020, 10 p.m.