BMTME
Bayesian Multi-Trait Multi-Environment for genomic selection[R package] [Dev version]
Install / Use
/learn @frahik/BMTMEREADME
Bayesian Multi-Trait Multi-Environment | Development version 1.0.19
</h4> <p align="center"> <a href="https://www.tidyverse.org/lifecycle/#stable"> <img src="https://img.shields.io/badge/lifecycle-stable-green.svg" alt="Maturing"> </a> <a href="https://www.gnu.org/licenses/lgpl-3.0"> <img src="https://img.shields.io/badge/License-LGPL%20v3-blue.svg" alt="LGPL, Version 3.0"> </a> <a href="http://www.repostatus.org/#inactive"> <img src="https://www.repostatus.org/badges/latest/inactive.svg" alt="The project has reached a stable, usable state and is being actively developed."> </a> <a href="https://cran.r-project.org/package=BMTME"> <img src="http://cranlogs.r-pkg.org/badges/BMTME" alt="Dowloads from the CRAN"> </a> </p> <p align="center"> <a href="https://travis-ci.org/frahik/BMTME"> <img src="https://travis-ci.org/frahik/BMTME.svg?branch=master" alt="Travis build status"> </a> <a href="https://ci.appveyor.com/project/frahik/bmtme"> <img src="https://ci.appveyor.com/api/projects/status/r2vog9sa30yutl5n?svg=true" alt="Appveyor build status"> </a> <a href="https://github.com/frahik/BMTME/actions?query=workflow%3AR-CMD-check"> <img src="https://github.com/frahik/BMTME/workflows/R-CMD-check/badge.svg?branch=master" alt="Github Actions"> </a> <a href='https://coveralls.io/github/frahik/BMTME'> <img src='https://coveralls.io/repos/github/frahik/BMTME/badge.svg?branch=master' alt='Coverage Status'/> </a> <a href="https://cran.r-project.org/package=BMTME"> <img src="http://www.r-pkg.org/badges/version-ago/BMTME" alt="CRAN"> </a> <a href="https://cran.r-project.org/package=BMTME"> <img src="https://cranchecks.info/badges/summary/BMTME" alt="CRAN"> </a> </p> <h4 align="center">[Last README update: 2020-08-26]
</h4> </p>Table of contents
<h2 id="news">News of this version (1.0.19)
</h2>See the last updates on NEWS.
<h2 id="instructions">Instructions for proper implementation
</h2> <h3 id="install">Installation
</h3>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
</h3>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
</h2>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
</h2>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.
<h2 id="research">Research and implementations
</h2>- 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
</h2>- Francisco Javier Luna-Vázquez (Author, Maintainer)
- Osval Antonio Montesinos-López (Author)
- Abelardo Montesinos-López (Author)
- José Crossa (Author)
- Fernando Tolero (Author)
