rpcss

Constitution of Core Collections by Principal Component Scoring Strategy

https://github.com/aravind-j/rpcss

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 5 DOI reference(s) in README
✓
Academic publication links
Links to: zenodo.org
○
Academic email domains
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (12.4%) to scientific vocabulary

Keywords

core-collections genebank germplasm pgr plant-genetic-resources r

Last synced: 6 months ago · JSON representation ·

Repository

Constitution of Core Collections by Principal Component Scoring Strategy

Basic Info

Host: GitHub
Owner: aravind-j
Language: R
Default Branch: master
Homepage: https://aravind-j.github.io/rpcss/
Size: 39.3 MB

Statistics

Stars: 0
Watchers: 1
Forks: 0
Open Issues: 0
Releases: 1

Topics

core-collections genebank germplasm pgr plant-genetic-resources r

Created over 1 year ago · Last pushed 10 months ago

Metadata Files

Readme Changelog Citation Codemeta

README.Rmd

---
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.

***
[![minimal R version](https://img.shields.io/badge/R>%3D-3.5.0-6666ff.svg?logo=R)](https://cran.r-project.org/)
[![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
[![CRAN_Status_Badge](https://www.r-pkg.org/badges/version-last-release/rpcss)](https://cran.r-project.org/package=rpcss)
[![Dependencies](https://tinyverse.netlify.app/status/rpcss)](https://cran.r-project.org/package=rpcss)
[![rstudio mirror downloads](https://cranlogs.r-pkg.org/badges/grand-total/rpcss?color=green)](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 = ""))
```
[![Github Code Size](https://img.shields.io/github/languages/code-size/aravind-j/rpcss.svg)](https://github.com/aravind-j/rpcss)
[![R-CMD-check](https://github.com/aravind-j/rpcss/workflows/R-CMD-check/badge.svg)](https://github.com/aravind-j/rpcss/actions)
[![Project Status: WIP](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)
[![lifecycle](https://lifecycle.r-lib.org/articles/figures/lifecycle-maturing.svg)](https://lifecycle.r-lib.org/articles/stages.html#maturing)
[![Last-changedate](https://img.shields.io/badge/last%20change-`r gsub('-', '--', Sys.Date())`-yellowgreen.svg)](https://github.com/aravind-j/rpcss/)
[![Zenodo DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.zenodo.14889174.svg)](https://doi.org/10.5281/zenodo.14889174)
[![Website - pkgdown](https://img.shields.io/website-up-down-green-red/https/aravind-j.github.io/rpcss.svg)](https://aravind-j.github.io/rpcss/)
[![.](https://pro-pulsar-193905.appspot.com/G-B9EKQHWBD9/welcome-page)](https://github.com/aravind-j/google-analytics-beacon)
[![GoatCounter](https://rpcss-gh.goatcounter.com/count?p=/test)](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)



## 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
```

Owner

Name: J. Aravind
Login: aravind-j
Kind: user
Location: New Delhi, India

Website: https://aravind-j.github.io/R-packages-gallery/
Repositories: 11
Profile: https://github.com/aravind-j

Scientist, Division of Germplasm Conservation, ICAR-National Bureau of Plant Genetic Resources

Citation (CITATION.cff)

# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "rpcss" in publications use:'
type: software
license: GPL-2.0-or-later
title: 'rpcss: Constitution of Core Collections by Principal Component Scoring Strategy'
version: 0.1.0
identifiers:
- type: doi
  value: 10.32614/CRAN.package.rpcss
- type: url
  value: https://aravind-j.github.io/rpcss/
abstract: Generate a Core Collection with Principal Component Scoring Strategy (PCSS)
  using qualitative and/or quantitative trait data according to Hamon and Noirot (1990)
  <https://www.documentation.ird.fr/hor/fdi:36506>, Noirot et al. (1996) <https://doi.org/10.2307/2527837>
  and Noirot et al. (2003) <https://www.documentation.ird.fr/hor/fdi:010031886>.
authors:
- family-names: Aravind
  given-names: J.
  email: j.aravind@icar.gov.in
  orcid: https://orcid.org/0000-0002-4791-442X
preferred-citation:
  type: manual
  title: 'rpcss: Constitution of Core Collections by Principal Component Scoring Strategy'
  authors:
  - family-names: Aravind
    given-names: J.
    email: aravindj@nbpgr.ernet.in
    orcid: https://orcid.org/0000-0002-4791-442X
  notes: R package version 0.1.0 https://aravind-j.github.io/rpcss/ https://cran.r-project.org/package=rpcss
repository: https://CRAN.R-project.org/package=rpcss
repository-code: https://github.com/aravind-j/rpcss
url: https://cran.r-project.org/package=rpcss
contact:
- family-names: Aravind
  given-names: J.
  email: j.aravind@icar.gov.in
  orcid: https://orcid.org/0000-0002-4791-442X

CodeMeta (codemeta.json)

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  "description": "Generate a Core Collection with Principal Component Scoring Strategy (PCSS) (Noirot et al. 1996 <doi:10.2307/2527837> ; Noirot et al. 2003 <https://horizon.documentation.ird.fr/exl-doc/pleins_textes/divers21-03/010031886.pdf>) using qualitative and/or quantitative trait data.",
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GitHub Events

Total

Release event: 3
Delete event: 1
Push event: 47
Create event: 2

Last Year

Release event: 3
Delete event: 1
Push event: 47
Create event: 2

Issues and Pull Requests

Last synced: 11 months ago

All Time

Total issues: 0
Total pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Total issue authors: 0
Total pull request authors: 0
Average comments per issue: 0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 0
Pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 0
Pull request authors: 0
Average comments per issue: 0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

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Total packages: 1
Total downloads:
- cran 351 last-month

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 1
Total maintainers: 1

cran.r-project.org: rpcss

Constitution of Core Collections by Principal Component Scoring Strategy

Homepage: https://github.com/aravind-j/rpcss
Documentation: http://cran.r-project.org/web/packages/rpcss/rpcss.pdf
License: GPL-2 | GPL-3
Status: removed
Latest release: 0.1.0
published about 1 year ago

Versions: 1
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 351 Last month

Rankings

Dependent packages count: 27.2%

Dependent repos count: 33.5%

Average: 49.2%

Downloads: 87.0%

Maintainers (1)

j.aravind@icar.gov.in

Last synced: 10 months ago

Dependencies

DESCRIPTION cran

R >= 3.5.0 depends
FactoMineR * imports
Rdpack * imports
ggplot2 * imports
ggrepel * imports
gslnls * imports
knitr * suggests
pander * suggests
rmarkdown * suggests

.github/workflows/update-citation-cff.yaml actions

actions/checkout v3 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/pkgdown.yaml actions

actions/checkout v3 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2-branch composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/render-readme.yaml actions

actions/checkout v3 composite
peter-evans/repository-dispatch v2 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2-branch composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/R-CMD-check.yaml actions

actions/checkout v3 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite
r-lib/actions/setup-tinytex v2 composite

ecosyste.ms

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Experiments

Open Source Science

rpcss

Science Score: 67.0%

Keywords

Repository

Basic Info

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Topics

Metadata Files

README.Rmd

Owner

Citation (CITATION.cff)

CodeMeta (codemeta.json)

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Last Year

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cran.r-project.org: rpcss

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Dependencies