README.Rmd

---
output: github_document
---
<p align="center">
  <a href="https://github.com/frahik/BMTME">
    <img src="Logo.png" alt="BMTME Logo"/>
  </a>
  <h3 align="center">
    Bayesian Multi-Trait Multi-Environment | Development version `r packageVersion('BMTME')` 
  </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">
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    <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.">
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    <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">
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      <img src='https://coveralls.io/repos/github/frahik/BMTME/badge.svg?branch=master' alt='Coverage Status'/>
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      <img src="http://www.r-pkg.org/badges/version-ago/BMTME" alt="CRAN">
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      <img src="https://cranchecks.info/badges/summary/BMTME" alt="CRAN">
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  </p>

  <h4 align="center">
    [Last README update: `r format(Sys.Date())`]
  </h4>
  
</p>


----------


# Table of contents
  - [NEWS](#news)
  - [Instructions](#instructions)
    - [Installation](#install)
    - [Dataset](#data)
  - [How to cite this package](#cite)
  - [Contributions](#contributions)
  - [Authors](#authors)

<h2 id="news">
  News of this version (`r packageVersion('BMTME')`)
</h2>

See the last updates on [NEWS](NEWS.md).

<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](https://cran.r-project.org/bin/windows/Rtools/) and a few packages first.

```{r installation, eval = FALSE}
install.packages('devtools')
devtools::install_github('frahik/BMTME')
```

<h3 id="data">
  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)`
<h2 id="cite">
  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

```{r}
citation('BMTME')
```

<h2 id="contributions">
  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](https://github.com/frahik/BMTME/issues/new), 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](https://www.g3journal.org/content/9/5/1355)
* [A Bayesian Multiple-Trait and Multiple-Environment Model Using the Matrix Normal Distribution](http://doi.org/10.5772/intechopen.71521)

<h2 id="authors">
  Authors
</h2>

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