BMTME

Bayesian Multi-Trait Multi-Environment for genomic selection[R package] [Dev version]

https://github.com/frahik/bmtme

Science Score: 13.0%

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Found 3 DOI reference(s) in README
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Low similarity (16.4%) to scientific vocabulary

Keywords

cross-validation genomic-selection package parallel-processing r

Last synced: 6 months ago · JSON representation

Repository

Bayesian Multi-Trait Multi-Environment for genomic selection[R package] [Dev version]

Basic Info

Host: GitHub
Owner: frahik
License: lgpl-3.0
Language: R
Default Branch: master
Homepage:
Size: 1.07 MB

Statistics

Stars: 13
Watchers: 2
Forks: 10
Open Issues: 6
Releases: 17

Topics

cross-validation genomic-selection package parallel-processing r

Created over 7 years ago · Last pushed over 2 years ago

Metadata Files

Readme License

README.Rmd

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


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


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


  Instructions for proper implementation




  Installation


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')
```


  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

```{r}
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](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.


  Research and implementations


* [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)


  Authors


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