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EvaluateCore

Quality Evaluation of Core Collections

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

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
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.4%) to scientific vocabulary

Keywords

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

Keywords from Contributors

interpretability standardization hack
Last synced: 6 months ago · JSON representation ·

Repository

Quality Evaluation of Core Collections

Basic Info
Statistics
  • Stars: 1
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 3
Topics
core-collections core-evaluation genebank germplasm pgr plant-genetic-resources r
Created over 6 years 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 = "inst/extdata/"
)
```



## `EvaluateCore`: Quality Evaluation of Core Collections logo

```{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.

***
[![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/EvaluateCore)](https://cran.r-project.org/package=EvaluateCore)
[![Dependencies](https://tinyverse.netlify.app/status/EvaluateCore)](https://cran.r-project.org/package=EvaluateCore)
[![rstudio mirror downloads](https://cranlogs.r-pkg.org/badges/grand-total/EvaluateCore?color=green)](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 = ""))
```
[![Github Code Size](https://img.shields.io/github/languages/code-size/aravind-j/EvaluateCore.svg)](https://github.com/aravind-j/EvaluateCore)
[![R-CMD-check](https://github.com/aravind-j/EvaluateCore/workflows/R-CMD-check/badge.svg)](https://github.com/aravind-j/EvaluateCore/actions)
[![Project Status: WIP](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
[![lifecycle](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
[![Last-changedate](https://img.shields.io/badge/last%20change-`r gsub('-', '--', Sys.Date())`-yellowgreen.svg)](https://github.com/aravind-j/EvaluateCore/)
[![Zenodo DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3875930.svg)](https://doi.org/10.5281/zenodo.3875930)
[![Website - pkgdown](https://img.shields.io/website-up-down-green-red/https/aravind-j.github.io/EvaluateCore.svg)](https://aravind-j.github.io/EvaluateCore/)
[![.](https://pro-pulsar-193905.appspot.com/UA-148941781-1/welcome-page)](https://github.com/aravind-j/google-analytics-beacon)




***

## Description
`r gsub("()", "[doi:\\2](https://doi.org/\\2)", gsub("\\n", " ", packageDescription("EvaluateCore", fields = "Description")))`



## 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")
```



## 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",
    "[![Linux](https://img.shields.io/badge/Linux-FCC624?style=for-the-badge&logo=linux&logoColor=black)](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",
    "[![Windows](https://img.shields.io/badge/Windows-0078D6?style=for-the-badge&logo=windows&logoColor=white)](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",
    "[![MacOS](https://img.shields.io/badge/mac%20os-000000?style=for-the-badge&logo=apple&logoColor=white)](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("[![Linux](https://shields.io/badge/Linux--9cf?logo=Linux&style=social)]",
                           chklink, sep = ""),
                     # paste("[![Solaris](https://shields.io/badge/Solaris--9cf?logo=Oracle&style=social)]",
                     #       chklink, sep = ""),
                     paste("[![Windows](https://shields.io/badge/Windows--9cf?logo=Windows&style=social)]",
                           chklink, sep = ""),
                     paste("[![MacOS](https://shields.io/badge/MacOS--9cf?logo=Apple&style=social)]",
                           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
```

Owner

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

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

Citation (CITATION.cff) 

# -----------------------------------------------------------
# CITATION file created with {cffr} R package, v0.5.0
# See also: https://docs.ropensci.org/cffr/
# -----------------------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "EvaluateCore" in publications use:'
type: software
license:
- GPL-2.0-only
- GPL-3.0-only
title: 'EvaluateCore: Quality Evaluation of Core Collections'
version: 0.1.3.9000
abstract: Implements various quality evaluation statistics to assess the value of
  plant germplasm core collections using qualitative and quantitative phenotypic trait
  data according to Odong et al. (2015) <doi:10.1007/s00122-012-1971-y>.
authors:
- family-names: Aravind
  given-names: J.
  email: j.aravind@icar.gov.in
  orcid: https://orcid.org/0000-0002-4791-442X
- family-names: Kaur
  given-names: Vikender
  email: vikender.kaur@icar.gov.in
  orcid: https://orcid.org/0000-0001-9698-7329
- family-names: Wankhede
  given-names: Dhammaprakash Pandhari
  email: d.wankhede@icar.gov.in
  orcid: https://orcid.org/0000-0001-6384-8664
- family-names: Nanjundan
  given-names: Joghee
  email: j.nanjundan@icar.gov.in
  orcid: https://orcid.org/0000-0001-6254-7341
preferred-citation:
  type: manual
  title: 'EvaluateCore: Quality Evaluation of Core Collections'
  authors:
  - family-names: Aravind
    given-names: J.
    email: aravindj@nbpgr.ernet.in
    orcid: https://orcid.org/0000-0002-4791-442X
  - family-names: Kaur
    given-names: Vikender
    email: vikender.kaur@icar.gov.in
    orcid: https://orcid.org/0000-0001-9698-7329
  - family-names: Wankhede
    given-names: Dhammaprakash Pandhari
    email: d.wankhede@icar.gov.in
    orcid: https://orcid.org/0000-0001-6384-8664
  - family-names: Nanjundan
    given-names: J.
    email: j.nanjundan@icar.gov.in
  notes: R package version 0.1.3.9000 https://aravind-j.github.io/EvaluateCore/ https://CRAN.R-project.org/package=EvaluateCore
repository: https://CRAN.R-project.org/package=EvaluateCore
repository-code: https://github.com/aravind-j/EvaluateCore
url: https://CRAN.R-project.org/package=EvaluateCore
contact:
- family-names: Aravind
  given-names: J.
  email: j.aravind@icar.gov.in
  orcid: https://orcid.org/0000-0002-4791-442X
keywords:
- core-collections
- core-evaluation
- genebank
- germplasm
- pgr
- plant-genetic-resources
- r
identifiers:
- type: url
  value: https://aravind-j.github.io/EvaluateCore/
- type: url
  value: https://doi.org/10.5281/zenodo.3875930

CodeMeta (codemeta.json) 

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  "fileSize": "431.483KB",
  "citation": [
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      "author": [
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          "@type": "Person",
          "givenName": "J.",
          "familyName": "Aravind",
          "email": "aravindj@nbpgr.ernet.in",
          "@id": "https://orcid.org/0000-0002-4791-442X"
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          "email": "j.nanjundan@icar.gov.in"
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}

GitHub Events

Total
  • Push event: 17
Last Year
  • Push event: 17

Committers

Last synced: over 1 year ago

All Time
  • Total Commits: 178
  • Total Committers: 2
  • Avg Commits per committer: 89.0
  • Development Distribution Score (DDS): 0.006
Past Year
  • Commits: 13
  • Committers: 2
  • Avg Commits per committer: 6.5
  • Development Distribution Score (DDS): 0.077
Top Committers
Name Email Commits
J. Aravind a****i@g****m 177
github-actions[bot] 4****] 1

Issues and Pull Requests

Last synced: 12 months ago

All Time
  • Total issues: 1
  • Total pull requests: 0
  • Average time to close issues: 10 months
  • Average time to close pull requests: N/A
  • Total issue authors: 1
  • Total pull request authors: 0
  • Average comments per issue: 2.0
  • 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
View more stats
Top Authors
Issue Authors
  • sckott (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 704 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 3
  • Total maintainers: 1
cran.r-project.org: EvaluateCore

Quality Evaluation of Core Collections

  • Versions: 3
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 704 Last month
Rankings
Forks count: 28.8%
Dependent packages count: 29.8%
Downloads: 31.0%
Average: 32.0%
Stargazers count: 35.2%
Dependent repos count: 35.5%
Maintainers (1)
j.aravind@icar.gov.in
Last synced: 10 months ago

Dependencies

.github/workflows/R-CMD-check.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
  • r-lib/actions/setup-tinytex 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/update-citation-cff.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/setup-r v2-branch composite
  • r-lib/actions/setup-r-dependencies v2 composite
DESCRIPTION cran
  • R >= 3.5.0 depends
  • Rdpack * imports
  • agricolae * imports
  • boot * imports
  • car * imports
  • cluster * imports
  • dplyr * imports
  • entropy * imports
  • ggcorrplot * imports
  • ggplot2 * imports
  • ggtext * imports
  • grDevices * imports
  • gridExtra * imports
  • kSamples * imports
  • mathjaxr * imports
  • psych * imports
  • reshape2 * imports
  • stats * imports
  • tibble * imports
  • vegan * imports
  • RCurl * suggests
  • XML * suggests
  • corehunter * suggests
  • httr * suggests
  • pander * suggests
  • rJava >= 0.9 suggests