search

frahik / BMTME

Bayesian Multi-Trait Multi-Environment for genomic selection[R package] [Dev version]
GNU Lesser General Public License v3.0
17 stars 9 forks source link
cross-validation genomic-selection package parallel-processing r

readme

BMTME Logo

Bayesian Multi-Trait Multi-Environment | Development version 1.0.19

Maturing LGPL, Version 3.0 The project has reached a stable, usable state and is being actively developed. Dowloads from the CRAN

Travis build status Appveyor build status Github Actions Coverage Status CRAN CRAN

\[Last README update: 2020-08-26\]

Table of contents

News of this version (1.0.19)

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')
## 
## To cite package 'BMTME' in publications use:
## 
##   Francisco Javier Luna-Vazquez, Fernando H. Toledo, Osval Antonio
##   Montesinos-Lopez, Abelardo Montesinos-Lopez and Jose Crossa (2020).
##   BMTME: Bayesian Multi-Trait Multi-Environment for Genomic Selection
##   Analysis. R package version 1.0.19. https://github.com/frahik/BMTME
## 
## A BibTeX entry for LaTeX users is
## 
##   @Manual{,
##     title = {BMTME: Bayesian Multi-Trait Multi-Environment for Genomic Selection Analysis},
##     author = {Francisco Javier Luna-Vazquez and Fernando H. Toledo and Osval Antonio Montesinos-Lopez and Abelardo Montesinos-Lopez and Jose Crossa},
##     year = {2020},
##     note = {R package version 1.0.19},
##     url = {https://github.com/frahik/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

Authors