https://github.com/aravind-j/rpcss
Constitution of Core Collections by Principal Component Scoring Strategy
https://github.com/aravind-j/rpcss
Last synced: about 1 month ago
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Constitution of Core Collections by Principal Component Scoring Strategy
- Host: GitHub
- URL: https://github.com/aravind-j/rpcss
- Owner: aravind-j
- Created: 2024-08-04T05:02:34.000Z (10 months ago)
- Default Branch: master
- Last Pushed: 2025-03-10T12:56:10.000Z (2 months ago)
- Last Synced: 2025-03-10T13:24:36.942Z (2 months ago)
- Language: R
- Homepage: https://aravind-j.github.io/rpcss/
- Size: 39.5 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.Rmd
- Changelog: NEWS.md
- Citation: CITATION.cff
- Codemeta: codemeta.json
Awesome Lists containing this project
README
---
output: rmarkdown::github_document
always_allow_html: true
---
```{r, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "",
fig.path = "man/figures/README-"
)
```
## `rpcss`: Constitution of Core Collections by Principal Component Scoring Strategy 
```{r,echo = FALSE, message = FALSE}
devtools::load_all(".", quiet = TRUE) # quiet = T for hiding macOS compiler warnings
```
###### Version : [`r getNamespaceVersion("rpcss")`](https://aravind-j.github.io/rpcss/); License: [GPL-2|GPL-3](https://www.r-project.org/Licenses/)
##### Aravind, J.
Division of Germplasm Conservation, ICAR-National Bureau of Plant Genetic Resources, New Delhi.
***
[](https://cran.r-project.org/)
[](https://www.gnu.org/licenses/gpl-3.0)
[](https://cran.r-project.org/package=rpcss)
[](https://cran.r-project.org/package=rpcss)
[](https://CRAN.R-project.org/package=rpcss)
```{r, results='asis', echo=FALSE}
dver <- ifelse(test = gsub("(.\\.)(\\d+)(\\..)", "", getNamespaceVersion("rpcss")) != "",
yes = getNamespaceVersion("rpcss"),
no = gsub("Version:\\s*", "", readLines(paste0("https://raw.githubusercontent.com/", "aravind-j/rpcss", "/master/DESCRIPTION"))[grep("Version:", readLines(paste0("https://raw.githubusercontent.com/", "aravind-j/rpcss", "/master/DESCRIPTION")))]))
cat(paste("[![develVersion](https://img.shields.io/badge/devel%20version-", dver, "-orange.svg)](https://github.com/aravind-j/rpcss)", sep = ""))
```
[](https://github.com/aravind-j/rpcss)
[](https://github.com/aravind-j/rpcss/actions)
[](https://www.repostatus.org/#wip)
[](https://lifecycle.r-lib.org/articles/stages.html#maturing)
[)`-yellowgreen.svg)](https://github.com/aravind-j/rpcss/)
[](https://doi.org/10.5281/zenodo.14889174)
[](https://aravind-j.github.io/rpcss/)
[](https://github.com/aravind-j/google-analytics-beacon)
[](https://rpcss.goatcounter.com/)
***
## Description
`r gsub("\\n", "", pkgdown:::linkify(packageDescription("rpcss", fields = "Description")))`
```{r readme-plot, echo=FALSE, out.width='100%', fig.height=8, fig.width=12, out.width='100%', dpi = 250}
suppressPackageStartupMessages(library(EvaluateCore))
# Get data from EvaluateCore
data("cassava_EC", package = "EvaluateCore")
data = cbind(Genotypes = rownames(cassava_EC), cassava_EC)
quant <- c("NMSR", "TTRN", "TFWSR", "TTRW", "TFWSS", "TTSW", "TTPW", "AVPW",
"ARSR", "SRDM")
qual <- c("CUAL", "LNGS", "PTLC", "DSTA", "LFRT", "LBTEF", "CBTR", "NMLB",
"ANGB", "CUAL9M", "LVC9M", "TNPR9M", "PL9M", "STRP", "STRC",
"PSTR")
rownames(data) <- NULL
# Convert qualitative data columns to factor
data[, qual] <- lapply(data[, qual], as.factor)
out1 <- pcss.core(data = data, names = "Genotypes",
quantitative = quant,
qualitative = NULL, eigen.threshold = NULL, size = 0.2,
var.threshold = 0.75)
g1 <- coreplot(x = out1, criterion = "variance")
g2 <- coreplot(x = out1, criterion = "logistic")[[2]]
g3 <- screeplot(x = out1)
g4 <- biplot(out1, ndim = 3, highlight.core = "size", quant.scale = 5,
point.alpha = 0.5)[[1]]
library(patchwork)
(g1 + g2)/
(g3 + g4)
```
## Installation
The package can be installed from CRAN as follows:
```{r, eval=FALSE, echo=FALSE}
# Install from CRAN
install.packages('rpcss', 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/rpcss")
```
## What's new
To know whats new in this version type:
```{r, eval=FALSE}
news(package='rpcss')
```
## Links
[CRAN page](https://cran.r-project.org/package=rpcss)
[Github page](https://github.com/aravind-j/rpcss)
[Documentation website](https://aravind-j.github.io/rpcss/)
[Zenodo DOI](https://doi.org/10.5281/zenodo.14889174)
## CRAN checks
```{r, echo = FALSE}
pkgname <- "rpcss"
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_rpcss.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_rpcss.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_rpcss.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")
```
## Citing `rpcss`
To cite the methods in the package use:
```{r, eval = FALSE}
citation("rpcss")
```
```{r, echo = FALSE}
detach("package:rpcss", unload = TRUE)
suppressPackageStartupMessages(library(rpcss))
cit <- citation("rpcss")
# 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
```