README.Rmd

---
output: github_document
---

<p align="center">
  <a href="https://github.com/italo-granato/BGGE">
    <img src="Logo.png" alt="Bayesian Genomic Linear Models Applied to GE Genome Selection"/>
  </a>
  <h4 align="center">
  Bayesian Genomic Linear Models Applied to GE Genome Selection - Development version `r packageVersion('BGGE')`
  </h4>
  <h4 align="center">
    [Last README update: `r format(Sys.Date())`]
  </h4>
  <p align="center">
    <a href="https://www.tidyverse.org/lifecycle/#maturing">
    <img src="https://img.shields.io/badge/lifecycle-maturing-blue.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/#active">
    <img src="http://www.repostatus.org/badges/latest/active.svg" alt="Status of the Repo: Active">
    </a> <a href="">
    <img src="http://cranlogs.r-pkg.org/badges/BGGE" alt="Dowloads from the CRAN">
    </a> <a href="https://cran.r-project.org/package=BGGE">
    <img src="http://www.r-pkg.org/badges/version-ago/BGGE" alt="CRAN">
    </a>
  </p>
</p>

# Table of contents
  - [NEWS](#news)
  - [Instructions](#instructions)
    - [Installation](#install)
    - [Load the package](#package)
    - [Quick use](#example1)
    - [Other Params](#params)
  - [How to cite this package](#cite)
  - [Contributions](#contributions)
  - [Authors](#authors)

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

Changes:

* Added compatibility with the functions (print() and plot()).
* Include ORCID of the authors.
* Include url of the project.
* Now the `BGGE()` function exports the input parameters.

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

<h2 id="instructions">
  Instructions for proper implementation
</h2>

<h3 id="install">
  Installation
</h3>

To complete installation of dev version of BGGE from GitHub, you must have previously installed the devtools package.

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

If you want to use the stable version of BGGE package, install it from CRAN.
```{r CRAN, eval=FALSE}
install.packages('BGGE')
```

<h3 id="package">
  Load the package
</h3>

```{r}
library(BGGE)
```

<h3 id="example1">
  Example of simple usage of the package
</h3>

```{r BGGEUse}
library(BGGE)
library(BGLR)
data(wheat)

X <- scale(wheat.X, scale = TRUE, center = TRUE)
rownames(X) <- 1:599
pheno_geno <- data.frame(env = gl(n = 4, k = 599), 
                         GID = gl(n=599, k=1, length = 599*4),
                         value = as.vector(wheat.Y))

# Creating kernel for GE model

K <- getK(Y = pheno_geno, X = X, kernel = "GB", model = "MM")
y <- as.vector(wheat.Y)

fit <- BGGE(y = y, K = K, ne = rep(599, 4))
fit

plot(fit)
```


<h3 id="params">
  Others params
</h3>

| params |  Use    |
|--------|------|
| XF      | Design matrix for fixed effects. |
| ite     | Number of iterations. |
| ne      | Number of subjects by environment. |
| burn    | Number of iterations to be discarded as burn-in. |
|thin     | Thinin interval. |
| verbose | Should report be printed on screen? |
| tol      | tolerance for zero. Default is 1e-10 |
| R2      | the proportion of variance expected to be explained by the regression |


<h2 id="cite">
  Citation
</h2>

First option, by the paper.

```tex
@article {Granato2018,
	author = {Granato, Italo and Cuevas, Jaime and Luna-V{\'a}zquez, Francisco J. and Crossa, Jos{\'e} and Montesinos-L{\'o}pez, Osval A. and Burgue{\~n}o, Juan and Fritsche-Neto, Roberto},
	title = {BGGE: A New Package for Genomic-Enabled Prediction Incorporating Genotype {\texttimes} Environment Interaction Models},
	year = {2018},
	doi = {10.1534/g3.118.200435},
	publisher = {G3: Genes, Genomes, Genetics},
	URL = {http://www.g3journal.org/content/early/2018/07/25/g3.118.200435},
	eprint = {http://www.g3journal.org/content/early/2018/07/25/g3.118.200435.full.pdf},
	journal = {G3: Genes, Genomes, Genetics}
}
```


Second option, by the package
```{r}
citation('BGGE')
```

<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/italo/BGGE/issues/new), also if you want to request a feature/report a bug, or make a pull request if you can contribute.

<h2 id="contributions">
  Research and implementations
</h2>

* [BGGE: A New Package for Genomic-Enabled Prediction Incorporating Genotype × Environment Interaction Models](https://doi.org/10.1534/g3.118.200435)


<h2 id="authors">
  Authors
</h2> 
 - Italo Granato (Author, Maintainer)
 - Jaime D. Cuevas D. (Author)
 - Francisco J. Luna-Vázquez (Author, Maintainer)