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ammistability

Additive Main Effects and Multiplicative Interaction Model Stability Parameters

https://github.com/ajaygpb/ammistability

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 (12.9%) to scientific vocabulary

Keywords from Contributors

curve-fitting germination germination-indices seed seed-germination-curve seed-germination-indices augmented-block augmented-design augmented-rcbd
Last synced: 6 months ago · JSON representation ·

Repository

Additive Main Effects and Multiplicative Interaction Model Stability Parameters

Basic Info
Statistics
  • Stars: 3
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 5
Created almost 8 years ago · Last pushed over 2 years ago
Metadata Files
Readme Changelog Citation Codemeta

README.Rmd 

---
output: rmarkdown::github_document
always_allow_html: true
---

```{r, results='asis', echo=FALSE}
glue::glue('')
```

```{r, echo = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "",
  fig.path = "inst/extdata/"
)
```

## `ammistability`: Additive Main Effects and Multiplicative Interaction Model Stability Parameters logo

```{r,echo = FALSE, message = FALSE, eval = FALSE}
devtools::load_all(".")

```

###### Version : [`r getNamespaceVersion("ammistability")`](https://ajaygpb.github.io/ammistability/); Copyright (C) 2017-`r  format(Sys.Date(), "%Y")`: [ICAR-DGR](https://en.wikipedia.org/wiki/Directorate_of_Groundnut_Research); License: [GPL-2|GPL-3](https://www.r-project.org/Licenses/)

##### *Ajay, B. C.^1^, Aravind, J.^2^ and Abdul Fiyaz, R^3^*

1. RRS, ICAR-Directorate of Groundnut Research, Anantapur.
2. ICAR-National Bureau of Plant Genetic Resources, New Delhi.
3. ICAR-Indian Institute of Rice Research, Hyderabad.

***


[![minimal R version](https://img.shields.io/badge/R>%3D-3.0.2-6666ff.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/ammistability)](https://cran.r-project.org/package=ammistability)
[![Dependencies](https://tinyverse.netlify.com/badge/ammistability)](https://cran.r-project.org/package=ammistability)
[![rstudio mirror downloads](https://cranlogs.r-pkg.org/badges/grand-total/ammistability?color=green)](https://CRAN.R-project.org/package=ammistability)
```{r, results='asis', echo=FALSE}
dver <- ifelse(test = gsub("(.\\.)(\\d+)(\\..)", "", getNamespaceVersion("ammistability")) != "",
               yes = getNamespaceVersion("ammistability"),
               no = gsub("Version:\\s*", "", readLines(paste0("https://raw.githubusercontent.com/", "ajaygpb/ammistability", "/master/DESCRIPTION"))[grep("Version:", readLines(paste0("https://raw.githubusercontent.com/", "ajaygpb/ammistability", "/master/DESCRIPTION")))]))

cat(paste("[![develVersion](https://img.shields.io/badge/devel%20version-", dver, "-orange.svg)](https://github.com/ajaygpb/ammistability)", sep = ""))
```
[![Github Code Size](https://img.shields.io/github/languages/code-size/ajaygpb/ammistability.svg)](https://github.com/ajaygpb/ammistability)
[![R-CMD-check](https://github.com/ajaygpb/ammistability/workflows/R-CMD-check/badge.svg)](https://github.com/ajaygpb/ammistability/actions)
[![Project Status: Inactive](http://www.repostatus.org/badges/latest/inactive.svg)](https://www.repostatus.org/#inactive)
[![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/ajaygpb/ammistability/commits/master)
[![Zenodo DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1344756.svg)](https://doi.org/10.5281/zenodo.1344756)
[![Pub DOI](https://img.shields.io/badge/article-10.31742%2FIJGPB.79.2.10-blue.svg)](https://www.isgpb.org/journal/index.php/IJGPB/article/view/2848)
[![Website - pkgdown](https://img.shields.io/website-up-down-green-red/https/ajaygpb.github.io/ammistability.svg)](https://ajaygpb.github.io/ammistability/)
[![.](https://pro-pulsar-193905.appspot.com/UA-123032895-2/welcome-page)](https://github.com/aravind-j/google-analytics-beacon)





***

## Description
`r gsub("\\n", " ", packageDescription("ammistability", fields = "Description"))`

## Installation
The package can be installed from CRAN as follows:

```{r, eval=FALSE}
# Install from CRAN
install.packages('ammistability', dependencies=TRUE)
```

The development version can be installed from github as follows:

```{r, eval=FALSE}
# Install development version from Github
devtools::install_github("ajaygpb/ammistability")
```

## Detailed tutorial
For a detailed tutorial (vignette) on how to used this package type:

```{r, eval=FALSE}
browseVignettes(package = 'ammistability')
```
The vignette for the latest version is also available [online](https://ajaygpb.github.io/ammistability/articles/Introduction.html).

## What's new
To know whats new in this version type:

```{r, eval=FALSE}
news(package='ammistability')
```

## Links

[CRAN page](https://cran.r-project.org/package=ammistability)

[Github page](https://github.com/ajaygpb/ammistability)

[Documentation website](https://ajaygpb.github.io/ammistability/)

[Zenodo DOI](https://doi.org/10.5281/zenodo.1344756)

## CRAN checks

```{r, echo = FALSE}
pkgname <- "ammistability"

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("[![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_ammistability.html)", "\n")

knitr::kable(osdf[osdf$OS == "Linux", c(2, 3)], format = "simple", 
             col.names = c("", ""), 
             row.names = FALSE)

cat("[![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_ammistability.html)", "\n")

knitr::kable(osdf[osdf$OS == "Windows", c(2, 3)], format = "simple", 
             col.names = c("", ""),
             row.names = FALSE)

cat("[![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_ammistability.html)", "\n")

knitr::kable(osdf[osdf$OS == "macOS", c(2, 3)], format = "simple", 
             col.names = c("", ""),
             row.names = FALSE)

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 `ammistability`
To cite the methods in the package use:

```{r, eval = FALSE}
citation("ammistability")
```

```{r, echo = FALSE}
# detach("package:ammistability", unload=TRUE)
suppressPackageStartupMessages(library(ammistability))
cit <- citation("ammistability")
# 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: Ajay BC
  • Login: ajaygpb
  • Kind: user
  • Location: Anantapur
  • Company: ICAR-Directorate of Groundnut Research

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 "ammistability" in publications use:'
type: software
license:
- GPL-2.0-only
- GPL-3.0-only
title: 'ammistability: Additive Main Effects and Multiplicative Interaction Model
  Stability Parameters'
version: 0.1.4.9000
abstract: Computes various stability parameters from Additive Main Effects and Multiplicative
  Interaction (AMMI) analysis results such as Modified AMMI Stability Value (MASV),
  Sums of the Absolute Value of the Interaction Principal Component Scores (SIPC),
  Sum Across Environments of Genotype-Environment Interaction Modelled by AMMI (AMGE),
  Sum Across Environments of Absolute Value of Genotype-Environment Interaction Modelled
  by AMMI (AV_(AMGE)), AMMI Stability Index (ASI), Modified ASI (MASI), AMMI Based
  Stability Parameter (ASTAB), Annicchiarico's D Parameter (DA), Zhang's D Parameter
  (DZ), Averages of the Squared Eigenvector Values (EV), Stability Measure Based on
  Fitted AMMI Model (FA), Absolute Value of the Relative Contribution of IPCs to the
  Interaction (Za). Further calculates the Simultaneous Selection Index for Yield
  and Stability from the computed stability parameters. See the vignette for complete
  list of citations for the methods implemented.
authors:
- family-names: Ajay
  given-names: B. C.
  email: ajaygpb@yahoo.co.in
  orcid: https://orcid.org/0000-0001-7222-8483
- family-names: Aravind
  given-names: J.
  email: j.aravind@icar.gov.in
  orcid: https://orcid.org/0000-0002-4791-442X
- family-names: Abdul Fiyaz
  given-names: R.
  email: fiyaz.ra@icar.gov.in
  orcid: https://orcid.org/0000-0001-6261-7071
preferred-citation:
  type: article
  title: 'ammistability: R package for ranking genotypes based on stability parameters
    derived from AMMI model'
  authors:
  - family-names: Ajay
    given-names: B. C.
    email: ajaygpb@yahoo.co.in
    orcid: https://orcid.org/0000-0001-7222-8483
  - family-names: Aravind
    given-names: J.
    email: j.aravind@icar.gov.in
    orcid: https://orcid.org/0000-0002-4791-442X
  - family-names: Abdul Fiyaz
    given-names: R.
    email: fiyaz.ra@icar.gov.in
    orcid: https://orcid.org/0000-0001-6261-7071
  journal: Indian Journal of Genetics and Plant Breeding (The)
  year: '2019'
  volume: '79'
  issue: '2'
  url: https://www.isgpb.org/article/ammistability-r-package-for-ranking-genotypes-based-on-stability-parameters-derived-from-ammi-model
  start: '460'
  end: '466'
repository: https://CRAN.R-project.org/package=ammistability
repository-code: https://github.com/ajaygpb/ammistability
url: https://github.com/ajaygpb/ammistability/
contact:
- family-names: Ajay
  given-names: B. C.
  email: ajaygpb@yahoo.co.in
  orcid: https://orcid.org/0000-0001-7222-8483
references:
- type: manual
  title: 'ammistability: Additive Main Effects and Multiplicative Interaction Model
    Stability Parameters'
  authors:
  - family-names: Ajay
    given-names: B. C.
    email: ajaygpb@yahoo.co.in
    orcid: https://orcid.org/0000-0001-7222-8483
  - family-names: Aravind
    given-names: J.
    email: j.aravind@icar.gov.in
    orcid: https://orcid.org/0000-0002-4791-442X
  - family-names: Abdul Fiyaz
    given-names: R.
    email: fiyaz.ra@icar.gov.in
  notes:
  - R package version 0.1.4.9000
  - https://ajaygpb.github.io/ammistability/
  - https://CRAN.R-project.org/package=ammistability
identifiers:
- type: url
  value: https://CRAN.R-project.org/package=ammistability
- type: url
  value: https://ajaygpb.github.io/ammistability/
- type: url
  value: https://doi.org/10.5281/zenodo.1344756

CodeMeta (codemeta.json) 

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          "familyName": "Aravind",
          "email": "j.aravind@icar.gov.in",
          "@id": "https://orcid.org/0000-0002-4791-442X"
        },
        {
          "@type": "Person",
          "givenName": "R.",
          "familyName": "Abdul Fiyaz",
          "email": "fiyaz.ra@icar.gov.in"
        }
      ],
      "name": "ammistability: {R} package for ranking genotypes based on stability parameters derived from {AMMI} model",
      "url": "https://www.isgpb.org/article/ammistability-r-package-for-ranking-genotypes-based-on-stability-parameters-derived-from-ammi-model",
      "pagination": "460--466",
      "isPartOf": {
        "@type": "PublicationIssue",
        "issueNumber": "2",
        "datePublished": "2019",
        "isPartOf": {
          "@type": [
            "PublicationVolume",
            "Periodical"
          ],
          "volumeNumber": "79",
          "name": "Indian Journal of Genetics and Plant Breeding (The)"
        }
      }
    },
    {
      "@type": "SoftwareSourceCode",
      "author": [
        {
          "@type": "Person",
          "givenName": [
            "B.",
            "C."
          ],
          "familyName": "Ajay",
          "email": "ajaygpb@yahoo.co.in",
          "@id": "https://orcid.org/0000-0001-7222-8483"
        },
        {
          "@type": "Person",
          "givenName": "J.",
          "familyName": "Aravind",
          "email": "j.aravind@icar.gov.in",
          "@id": "https://orcid.org/0000-0002-4791-442X"
        },
        {
          "@type": "Person",
          "givenName": "R.",
          "familyName": "Abdul Fiyaz",
          "email": "fiyaz.ra@icar.gov.in"
        }
      ],
      "name": "ammistability: Additive Main Effects and Multiplicative Interaction Model Stability Parameters",
      "description": [
        "R package version 0.1.4.9000",
        "https://ajaygpb.github.io/ammistability/",
        "https://CRAN.R-project.org/package=ammistability"
      ]
    }
  ],
  "releaseNotes": "https://github.com/ajaygpb/ammistability/blob/master/NEWS.md",
  "readme": "https://github.com/ajaygpb/ammistability/blob/master/README.md",
  "contIntegration": "https://github.com/ajaygpb/ammistability/actions",
  "developmentStatus": [
    "https://www.repostatus.org/#inactive",
    "https://lifecycle.r-lib.org/articles/stages.html#stable"
  ]
}

GitHub Events

Total
Last Year

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 209
  • Total Committers: 4
  • Avg Commits per committer: 52.25
  • Development Distribution Score (DDS): 0.024
Past Year
  • Commits: 20
  • Committers: 2
  • Avg Commits per committer: 10.0
  • Development Distribution Score (DDS): 0.05
Top Committers
Name Email Commits
J. Aravind a****i@g****m 204
J. Aravind a****6@y****m 2
ajay a****b@y****n 2
GitHub Actions a****s@g****m 1
Committer Domains (Top 20 + Academic)
github.com: 1 yahoo.co.in: 1

Issues and Pull Requests

Last synced: 7 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 706 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
cran.r-project.org: ammistability

Additive Main Effects and Multiplicative Interaction Model Stability Parameters

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 706 Last month
Rankings
Stargazers count: 26.2%
Forks count: 28.8%
Dependent packages count: 29.8%
Dependent repos count: 35.5%
Average: 42.0%
Downloads: 89.7%
Maintainers (1)
ajaygpb@yahoo.co.in
Last synced: 7 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.5.0 depends
  • Rdpack * imports
  • agricolae * imports
  • ggcorrplot * imports
  • ggplot2 * imports
  • mathjaxr * imports
  • methods * imports
  • reshape2 * imports
  • stats * imports
  • RCurl * suggests
  • XML * suggests
  • httr * suggests
  • knitr * suggests
  • pander * suggests
  • rmarkdown * suggests
.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/render-readme-pkgdown.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
.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