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README.Rmd
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---
output: rmarkdown::github_document
always_allow_html: true
---
```{r, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "",
fig.path = "inst/extdata/"
)
```
<!--
```{r, out.width = '20%', echo = FALSE, eval = TRUE}
knitr::include_graphics("https://raw.githubusercontent.com/aravind-j/EvaluateCore/master/inst/extdata/EvaluateCore.png")
```
-->
## `EvaluateCore`: Quality Evaluation of Core Collections <img src="https://raw.githubusercontent.com/aravind-j/EvaluateCore/master/inst/extdata/EvaluateCore.png" align="right" alt="logo" width="173" height = "200" style = "border: none; float: right;">
```{r,echo = FALSE, message = FALSE}
devtools::load_all(".")
```
###### Version : [`r getNamespaceVersion("EvaluateCore")`](https://aravind-j.github.io/EvaluateCore/); Copyright (C) 2018-`r format(Sys.Date(), "%Y")`: [ICAR-NBPGR](http://www.nbpgr.ernet.in/); License: [GPL-2|GPL-3](https://www.r-project.org/Licenses/)
##### *Aravind, J.^1^, Kaur, V.^2^, Wankhede, D. P.^3^ and Nanjundan, J.^4^*
1. Division of Germplasm Conservation, ICAR-National Bureau of Plant Genetic Resources, New Delhi.
2. Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, New Delhi.
3. Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi.
4. ICAR-Indian Agricultural Research Institute, Regional Station, Wellington, Tamil Nadu.
***
[](https://cran.r-project.org/)
[](https://www.gnu.org/licenses/gpl-3.0)
[](https://cran.r-project.org/package=EvaluateCore)
[](https://cran.r-project.org/package=EvaluateCore)
[](https://CRAN.R-project.org/package=EvaluateCore)
```{r, results='asis', echo=FALSE}
dver <- ifelse(test = gsub("(.\\.)(\\d+)(\\..)", "", getNamespaceVersion("EvaluateCore")) != "",
yes = getNamespaceVersion("EvaluateCore"),
no = gsub("Version:\\s*", "", readLines(paste0("https://raw.githubusercontent.com/", "aravind-j/EvaluateCore", "/master/DESCRIPTION"))[grep("Version:", readLines(paste0("https://raw.githubusercontent.com/", "aravind-j/EvaluateCore", "/master/DESCRIPTION")))]))
cat(paste("[![develVersion](https://img.shields.io/badge/devel%20version-", dver, "-orange.svg)](https://github.com/aravind-j/EvaluateCore)", sep = ""))
```
[](https://github.com/aravind-j/EvaluateCore)
[](https://github.com/aravind-j/EvaluateCore/actions)
[](https://www.repostatus.org/#active)
[](https://lifecycle.r-lib.org/articles/stages.html#stable)
[)`-yellowgreen.svg)](https://github.com/aravind-j/EvaluateCore/)
[](https://doi.org/10.5281/zenodo.3875930)
[](https://aravind-j.github.io/EvaluateCore/)
[](https://github.com/aravind-j/google-analytics-beacon)
<!-- [](https://github.com/aravind-j/EvaluateCore) -->
<!-- [] -->
<!-- [](http://www.rdocumentation.org/packages/EvaluateCore) -->
***
## Description
`r gsub("(<doi:)(.+)(>)", "[doi:\\2](https://doi.org/\\2)", gsub("\\n", " ", packageDescription("EvaluateCore", fields = "Description")))`
<!-- ## System Requirements
The function `dist.evaluate.core` is a wrapper around the `evaluateCore` function of the `corehunter` package which implemented in Java 8. Hence you need to have [Java Runtime Environment](http://www.oracle.com/technetwork/java/javase/downloads/jre8-downloads-2133155.html) (JRE) version 8 or higher for the package to work.-->
## Installation
The package can be installed from CRAN as follows:
```{r, eval=FALSE}
# Install from CRAN
install.packages('EvaluateCore', dependencies=TRUE)
```
The development version can be installed from github as follows:
```{r, eval=FALSE}
# Install development version from Github
devtools::install_github("aravind-j/EvaluateCore")
```
<!-- ## Detailed tutorial
For a detailed tutorial (vignette) on how to used this package type:
```{r, eval=FALSE}
browseVignettes(package = 'EvaluateCore')
```
The vignette for the latest version is also available [online](https://aravind-j.github.io/EvaluateCore/articles.html).-->
## What's new
To know whats new in this version type:
```{r, eval=FALSE}
news(package='EvaluateCore')
```
## Links
[CRAN page](https://cran.r-project.org/package=EvaluateCore)
[Github page](https://github.com/aravind-j/EvaluateCore)
[Documentation website](https://aravind-j.github.io/EvaluateCore/)
[Zenodo DOI](https://doi.org/10.5281/zenodo.3875930)
## CRAN checks
```{r, echo = FALSE}
pkgname <- "EvaluateCore"
osdf <-
rbind(data.frame(OS = "Linux",
Flavour = c("r-devel-linux-x86_64-debian-clang",
"r-devel-linux-x86_64-debian-gcc",
"r-devel-linux-x86_64-fedora-clang",
"r-devel-linux-x86_64-fedora-gcc",
"r-patched-linux-x86_64",
"r-release-linux-x86_64")),
# data.frame(OS = "Solaris",
# Flavour = c("r-patched-solaris-x86")),
data.frame(OS = "Windows",
Flavour = c("r-devel-windows-x86_64",
"r-release-windows-x86_64",
"r-oldrel-windows-x86_64")),
data.frame(OS = "macOS",
Flavour = c("r-release-macos-x86_64",
# "r-release-macos-arm64",
# "r-oldrel-macos-arm64",
"r-oldrel-macos-x86_64")))
chkurl <- paste("https://cran.r-project.org/web/checks/check_results_",
pkgname, ".html", sep = "")
library(RCurl)
if (url.exists(chkurl)) {
chklink <- paste("(", chkurl, ")", sep = "")
} else {
chklink <- "(https://cran.r-project.org/web/checks/check_results_j.aravind_at_icar.gov.in.html)"
}
osdf$`CRAN check` <- paste("[![CRAN check - ", osdf$Flavour, "]",
"(https://badges.cranchecks.info/flavor/",
osdf$Flavour, "/", pkgname, ".svg)]",
chklink,
sep = "")
```
```{r, echo = FALSE, results='asis'}
cat("\n",
"[](https://cran.r-project.org/web/checks/check_results_EvaluateCore.html)", "\n")
# knitr::kable(osdf[osdf$OS == "Linux", c(2, 3)], format = "simple",
# col.names = c("", ""),
# row.names = FALSE)
pander::pandoc.table(osdf[osdf$OS == "Linux", c(2, 3)], split.tables = Inf,
row.names = FALSE, justify = "ll", style = "grid")
cat("\n",
"[](https://cran.r-project.org/web/checks/check_results_EvaluateCore.html)", "\n")
# knitr::kable(osdf[osdf$OS == "Windows", c(2, 3)], format = "simple",
# col.names = c("", ""),
# row.names = FALSE)
pander::pandoc.table(osdf[osdf$OS == "Windows", c(2, 3)], split.tables = Inf,
row.names = FALSE, justify = "ll", style = "grid")
cat("\n",
"[](https://cran.r-project.org/web/checks/check_results_EvaluateCore.html)", "\n")
# knitr::kable(osdf[osdf$OS == "macOS", c(2, 3)], format = "simple",
# col.names = c("", ""),
# row.names = FALSE)
pander::pandoc.table(osdf[osdf$OS == "macOS", c(2, 3)], split.tables = Inf,
row.names = FALSE, justify = "ll", style = "grid")
cat("\n")
```
```{r, echo = FALSE, results='asis', eval = FALSE}
library(kableExtra, warn.conflicts = FALSE)
kosdf <- kbl(osdf[, c("Flavour", "CRAN check")], row.names = FALSE,
format = "simple")
kosdf2 <- kable_styling(kosdf, bootstrap_options = c("striped", "hover"),
full_width = F, position = "left")
# os_index <- c(6, 1, 3, 2)
os_index <- c(6, 3, 2)
names(os_index) <- c(paste("[]",
chklink, sep = ""),
# paste("[]",
# chklink, sep = ""),
paste("[]",
chklink, sep = ""),
paste("[]",
chklink, sep = ""))
pack_rows(kosdf2, index = os_index)
```
## Citing `EvaluateCore`
To cite the methods in the package use:
```{r, eval = FALSE}
citation("EvaluateCore")
```
```{r, echo = FALSE}
detach("package:EvaluateCore", unload = TRUE)
suppressPackageStartupMessages(library(EvaluateCore))
cit <- citation("EvaluateCore")
# 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
```