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README.Rmd
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---
output: rmarkdown::github_document
always_allow_html: true
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "",
fig.path = "inst/extdata/"
)
```
## `toolStability`: Tool for Stability Indices Calculation <img src="https://raw.githubusercontent.com/Illustratien/toolStability/master/inst/extdata/toolStability.png" align="right" alt="logo" width="200" height = "200" style = "padding: 10px; border: none; float: right;">
```{r,echo = FALSE, message = FALSE}
suppressWarnings(devtools::load_all("."))
wholetext <- packageDescription("toolStability", fields = "Description")
Section<- strsplit(wholetext,"This R")
text1 <- Section[[1]][1]
text2 <- unlist(strsplit(paste0("This R",Section[[1]][2]),"\n"))
```
###### License: [GPL-3](https://www.r-project.org/Licenses/)
<!-- Version : [`r getNamespaceVersion("toolStability")`](https://illustratien.github.io/toolStability/articles/toolStability.html#version-history); -->
##### *Wang, T-C. and Chen, T-W.*
<!-- badges: start -->
[](https://link.springer.com/article/10.1007/s00122-023-04264-7)
[](https://Illustratien.github.io/toolStability/)
[](https://zenodo.org/badge/latestdoi/203346020)
[](https://cran.r-project.org/)
<!-- [](https://www.gnu.org/licenses/gpl-3.0) -->
<!-- [](https://cran.r-project.org/package=toolStability) -->
<!-- # ```{r, results='asis', echo=FALSE} -->
<!-- # dver <- ifelse(test = gsub("(.\\.)(\\d+)(\\..)", "", getNamespaceVersion("toolStability")) != "", -->
<!-- # yes = getNamespaceVersion("toolStability"), -->
<!-- # no = gsub("Version:\\s*", "", readLines(paste0("https://raw.githubusercontent.com/", "Illustratien/toolStability", "/master/DESCRIPTION"))[grep("Version:", readLines(paste0("https://raw.githubusercontent.com/", "Illustratien/toolStability", "/master/DESCRIPTION")))])) -->
<!-- # -->
<!-- # # cat(paste("[![develVersion](https://img.shields.io/badge/devel%20version-", dver, "-orange.svg)](https://github.com/Illustratien/toolStability)", sep = "")) -->
<!-- # ``` -->
[](https://github.com/Illustratien/toolStability)
[](https://app.codecov.io/gh/Illustratien/toolStability?branch=master)
[](https://github.com/Illustratien/toolStability/actions)
<!-- [)`-yellowgreen.svg)](https://github.com/Illustratien/toolStability/commits/master) -->
<!-- [](https://github.com/Illustratien/google-analytics-beacon) -->
<!-- [](https://CRAN.R-project.org/package=toolStability) -->
<!-- badges: end -->
## Description
<!-- `r packageDescription("toolStability", fields = "Description")` -->
<!-- `r gsub("\\n", " ", packageDescription("toolStability", fields = "Description"))` -->
`r text1` `r "There are 11 stability indices in this package."`
`r text2[1]`
`r text2[2]`
`r text2[3]`
`r text2[4]`
`r text2[5]`
`r text2[6]`
<!-- `r text2[7]``r " (see tutorial for detailed information)"` -->
<!-- `r text2[8]` -->
<!-- `r text2[9]` -->
<!-- `r text2[10]` -->
<!-- `r text2[11]` -->
<!-- `r text2[12]` -->
<!-- `r text2[13]` -->
<!-- `r text2[14]` `r " https://www.jstor.org/stable/2531698"` -->
<!-- `r text2[15]` -->
<!-- `r text2[16]` `r " https://www.nature.com/articles/hdy197287"` -->
<!-- `r text2[17]` -->
<!-- `r text2[18]` -->
## Installation
The package can be installed from CRAN as follows:
```{r, eval=FALSE}
install.packages('toolStability', dependencies=TRUE)
```
The development version can be installed from github as follows:
```{r, eval=FALSE}
if (!require('devtools')) install.packages('devtools')
devtools::install_github("Illustratien/toolStability")
# or
if (!require('remotes')) install.packages('remotes')
remotes::install_github("Illustratien/toolStability")
```
## Tutorial
There are 11 stability indices in this package. A detailed tutorial with examples and references:
[click here](https://illustratien.github.io/toolStability/articles/toolStability.html).
## What's new
To know whats new in this version type:
```{r, eval=FALSE}
news(package='toolStability')
```
## Links
[Main publication](https://link.springer.com/article/10.1007/s00122-023-04264-7)
[Main publication analysis pipeline](https://github.com/Illustratien/Wang_2023_TAAG/tree/V1.0.0)
[Dataset documentation](https://doi.org/10.5281/zenodo.4729636)
[CRAN page](https://cran.r-project.org/package=toolStability)
[Package documentation](https://doi.org/10.5281/zenodo.5804212)
## Citing `toolStability`
To cite the methods in the package please use:
```{r, eval = FALSE}
Wang, TC., Casadebaig, P. & Chen, TW. More than 1000 genotypes are required to derive robust relationships between yield, yield stability and physiological parameters: a computational study on wheat crop. Theor Appl Genet 136, 34 (2023). https://doi.org/10.1007/s00122-023-04264-7
```
<!-- # ```{r, echo = FALSE} -->
<!-- # detach("package:toolStability", unload=TRUE) -->
<!-- # suppressPackageStartupMessages(library(toolStability)) -->
<!-- # cit <- citation("toolStability") -->
<!-- # yr <- format(Sys.Date(), "%Y") -->
<!-- # cit[1]$year <- yr -->
<!-- # oc <- class(cit) -->
<!-- # -->
<!-- # cit <- unclass(cit) -->
<!-- # attr(cit[[1]],"textVersion") <- gsub("\\(\\)", -->
<!-- # paste("\\(", yr, "\\)", sep = ""), -->
<!-- # attr(cit[[1]],"textVersion")) -->
<!-- # class(cit) <- oc -->
<!-- # cit -->
<!-- ``` -->