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Open Source Science

fairpub

:package: Fair publications

https://github.com/frbcesab/fairpub

Science Score: 44.0%

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
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.7%) to scientific vocabulary

Keywords from Contributors

interactive mesh interpretability profiles sequences generic projection standardization optim embedded
Last synced: 9 months ago · JSON representation ·

Repository

:package: Fair publications

Basic Info
Statistics
  • Stars: 1
  • Watchers: 0
  • Forks: 0
  • Open Issues: 3
  • Releases: 2
Created 11 months ago · Last pushed 10 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation Codemeta

README.Rmd 

---
output: github_document
---




```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/",
  out.width = "100%"
)
```



fairpub: How fair are you when you publish/cite scientific works? 
=========================================================


![Package](https://img.shields.io/static/v1?message=Package&logo=r&labelColor=5c5c5c&color=yellowgreen&logoColor=white&label=%20)
![Lifecycle Maturing](https://img.shields.io/badge/Lifecycle-Maturing-007EC6)
[![CRAN status](https://www.r-pkg.org/badges/version/fairpub)](https://CRAN.R-project.org/package=fairpub)
[![R CMD Check](https://github.com/frbcesab/fairpub/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/frbcesab/fairpub/actions/workflows/R-CMD-check.yaml)
[![Website](https://github.com/frbcesab/fairpub/actions/workflows/pkgdown.yaml/badge.svg)](https://github.com/frbcesab/fairpub/actions/workflows/pkgdown.yaml)
[![codecov](https://codecov.io/gh/frbcesab/fairpub/graph/badge.svg?token=pTqQ0978iE)](https://codecov.io/gh/frbcesab/fairpub)
[![License: GPL (>= 2)](https://img.shields.io/badge/License-GPL%20%28%3E%3D%202%29-blue.svg)](https://choosealicense.com/licenses/gpl-2.0/)






  • Overview

  • Features

  • Limitation

  • Installation

  • Get started

  • Citation

  • Contributing

  • Acknowledgments

  • References





## Overview


Scientific journals operate over a broad spectrum of publishing strategies, 
from strictly for-profit, to non-profit, and in-between business models 
(e.g. for-profit but academic friendly journals). Scientific publishing is 
increasingly dominated by for-profit journals, many of which attract prestige 
and submissions through high impact factors. In contrast, non-profit journals 
– those that reinvest revenue into the academic community – struggle to maintain
visibility despite offering more equitable publishing models.

The R package `fairpub` aims to provide a user-friendly toolbox to investigate 
the fairness of a research (article, bibliographic list, citation list, 
etc.). The fairness is measured according to two dimensions: 

- the **business model** of the journal: for-profit vs. non-profit
- the **academic friendly** status of the journal: yes or no

A journal with a non-profit business model is fairer than an academic friendly 
journal with a for-profit business model. But the later is still fairer than a
non-academic friendly journal with a for-profit business model.

This information comes from the 
[DAFNEE initiative](https://dafnee.isem-evolution.fr/), a Database of Academia 
Friendly jourNals in Ecology and Evolution.

The package `fairpub` also implements the method proposed by Beck _et al._ 
(in revision): the strategic citation. By deliberately choosing to cite relevant
articles from non-profit journals when multiple references would be equally 
valid, researchers can contribute to increasing their visibility and future 
impact factor. This method is implemented in the `fp_compute_ratio()` function 
and can answer the question **How fair am I when I cite previous works?** by 
computing the fairness ratio on the references cited in a manuscript.

The package can also answer the question **How fair is my publication list?**.
See the [Get started](https://frbcesab.github.io/fairpub/articles/fairpub.html) 
vignette for more information.


## Features

The `fairpub` package can:

- retrieve the fairness status of a journal with the [`fp_journal_fairness()`](https://frbcesab.github.io/fairpub/reference/fp_journal_fairness.html) function
- retrieve the fairness status of an article with the [`fp_article_fairness()`](https://frbcesab.github.io/fairpub/reference/fp_article_fairness.html) function and by querying the [OpenAlex](https://openalex.org) bibliographic database
- compute the fairness ratio of a list references cited in a manuscript with the [`fp_compute_ratio()`](https://frbcesab.github.io/fairpub/reference/fp_compute_ratio.html) function
- compute the fairness ratio of all publications of an author (or a team) with the [`fp_compute_ratio()`](https://frbcesab.github.io/fairpub/reference/fp_compute_ratio.html) function

In addition, the [`fp_doi_from_bibtex()`](https://frbcesab.github.io/fairpub/reference/fp_doi_from_bibtex.html) function helps user to easily extract DOI from a BibTeX file. The list of DOI can then be pass to the [`fp_compute_ratio()`](https://frbcesab.github.io/fairpub/reference/fp_compute_ratio.html) function. 


## Limitation

The package `fairpub` provides a small subset of the journals indexed in the DAFNEE database.
We are currently working to increase this list of journals.


## Installation

You can install the development version from [GitHub](https://github.com/) with:

```{r eval=FALSE}
# Install < remotes > package (if not already installed) ----
if (!requireNamespace("remotes", quietly = TRUE)) {
  install.packages("remotes")
}

# Install < fairpub > from GitHub ----
remotes::install_github("frbcesab/fairpub")
```

Then you can attach the package `fairpub`:

```{r eval=FALSE}
library("fairpub")
```



## Get started

The main function of `fairpub` is [`fp_compute_ratio()`](https://frbcesab.github.io/fairpub/reference/fp_compute_ratio.html). From a vector of article DOI, this function will report the following metrics:

```{r eval=FALSE}
fp_compute_ratio(doi = list_of_doi)
```

```
## $summary
##                                     metric value
##                           Total references    33
##                        References with DOI    33
##                    Deduplicated references    33
##               References found in OpenAlex    30
##                 References found in DAFNEE    10
##     Non-profit & acad. friendly references     9
##     For-profit & acad. friendly references     1
## For-profit & non-acad. friendly references     0
## 
## $ratios
## Non-profit & acad. friendly  For-profit & acad. friendly  For-profit & non-acad. friendly 
##                         0.9                          0.1                              0.0 
```

In this example, this list of references has a fairness ratio 
(`Non-profit and academic friendly`) of 90%. But this value must be interpreted 
with caution. Indeed this ratio has been computed on 26% (10 over 38) of the 
references, because the journal of 20 articles is not indexed in the DAFNEE 
database.


Visit the [**Get started**](https://frbcesab.github.io/fairpub/articles/fairpub.html) vignette for a complete usage of the `fairpub` package.



## Citation

Please cite `fairpub` as: 

> Casajus Nicolas (`r format(Sys.Date(), "%Y")`) fairpub: How fair are you
when you publish/cite scientific works? R package version 1.0.0. 




## Contributing

All types of contributions are encouraged and valued. For more information, 
check out our [Contributor Guidelines](https://github.com/frbcesab/fairpub/blob/main/CONTRIBUTING.md).

Please note that the `fairpub` project is released with a 
[Contributor Code of Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html). 
By contributing to this project, you agree to abide by its terms.



## Acknowledgments

This project is a collaborative work among 
[FRB-CESAB](https://www.fondationbiodiversite.fr/en/about-the-foundation/le-cesab/) 
scientific team.

We want to thanks the [DAFNEE team](https://dafnee.isem-evolution.fr/) for his 
incredible work in gathering information about scientific journals.



## References

Beck M _et al._ (in revision) Strategic citations for a fairer academic landscape. 
Submitted to Proc B - Biological Science Practices.

Owner

  • Name: FRB CESAB
  • Login: FRBCesab
  • Kind: organization
  • Location: Montpellier, FRANCE

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 "fairpub" in publications use:'
type: software
license: GPL-2.0-or-later
title: 'fairpub: How Fair Are You When You Publish/Cite Scientific Works?'
version: 1.0.0
abstract: Provides a user-friendly way to compute the non-profit and academic friendly
  ratio of the bibliographic reference list before submitting a manuscript for peer
  review.
authors:
- family-names: Casajus
  given-names: Nicolas
  email: rdev.nc@gmail.com
  orcid: https://orcid.org/0000-0002-5537-5294
preferred-citation:
  type: manual
  title: 'fairpub: How fair are you when you publish/cite scientific works?'
  authors:
  - name: Casajus Nicolas
  year: '2025'
  notes: R package version 1.0.0
  url: https://github.com/frbcesab/fairpub
repository-code: https://github.com/frbcesab/fairpub
url: https://github.com/frbcesab/fairpub
contact:
- family-names: Casajus
  given-names: Nicolas
  email: rdev.nc@gmail.com
  orcid: https://orcid.org/0000-0002-5537-5294
references:
- type: software
  title: 'R: A Language and Environment for Statistical Computing'
  notes: Depends
  url: https://www.R-project.org/
  authors:
  - name: R Core Team
  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2025'
  version: '>= 3.5'
- type: software
  title: openalexR
  abstract: 'openalexR: Getting Bibliographic Records from ''OpenAlex'' Database Using
    ''DSL'' API'
  notes: Imports
  url: https://docs.ropensci.org/openalexR/
  repository: https://CRAN.R-project.org/package=openalexR
  authors:
  - family-names: Aria
    given-names: Massimo
    email: aria@unina.it
    orcid: https://orcid.org/0000-0002-8517-9411
  - family-names: Le
    given-names: Trang
    email: grixor@gmail.com
    orcid: https://orcid.org/0000-0003-3737-6565
  - family-names: Choe
    given-names: June
    email: jchoe001@gmail.com
    orcid: https://orcid.org/0000-0002-0701-921X
  year: '2025'
  doi: 10.32614/CRAN.package.openalexR
- type: software
  title: RefManageR
  abstract: 'RefManageR: Straightforward ''BibTeX'' and ''BibLaTeX'' Bibliography
    Management'
  notes: Imports
  url: https://github.com/ropensci/RefManageR/
  repository: https://CRAN.R-project.org/package=RefManageR
  authors:
  - family-names: McLean
    given-names: Mathew W.
    email: mathew.w.mclean@gmail.com
    orcid: https://orcid.org/0000-0002-7891-9645
  year: '2025'
  doi: 10.32614/CRAN.package.RefManageR
- type: software
  title: stringdist
  abstract: 'stringdist: Approximate String Matching, Fuzzy Text Search, and String
    Distance Functions'
  notes: Imports
  url: https://github.com/markvanderloo/stringdist
  repository: https://CRAN.R-project.org/package=stringdist
  authors:
  - family-names: Loo
    given-names: Mark
    name-particle: van der
    email: mark.vanderloo@gmail.com
    orcid: https://orcid.org/0000-0002-9807-4686
  year: '2025'
  doi: 10.32614/CRAN.package.stringdist
- type: software
  title: knitr
  abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
  notes: Suggests
  url: https://yihui.org/knitr/
  repository: https://CRAN.R-project.org/package=knitr
  authors:
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  year: '2025'
  doi: 10.32614/CRAN.package.knitr
- type: software
  title: rmarkdown
  abstract: 'rmarkdown: Dynamic Documents for R'
  notes: Suggests
  url: https://pkgs.rstudio.com/rmarkdown/
  repository: https://CRAN.R-project.org/package=rmarkdown
  authors:
  - family-names: Allaire
    given-names: JJ
    email: jj@posit.co
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  - family-names: Dervieux
    given-names: Christophe
    email: cderv@posit.co
    orcid: https://orcid.org/0000-0003-4474-2498
  - family-names: McPherson
    given-names: Jonathan
    email: jonathan@posit.co
  - family-names: Luraschi
    given-names: Javier
  - family-names: Ushey
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  - family-names: Atkins
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  - family-names: Wickham
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    email: hadley@posit.co
  - family-names: Cheng
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    email: joe@posit.co
  - family-names: Chang
    given-names: Winston
    email: winston@posit.co
  - family-names: Iannone
    given-names: Richard
    email: rich@posit.co
    orcid: https://orcid.org/0000-0003-3925-190X
  year: '2025'
  doi: 10.32614/CRAN.package.rmarkdown
- type: software
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  abstract: 'testthat: Unit Testing for R'
  notes: Suggests
  url: https://testthat.r-lib.org
  repository: https://CRAN.R-project.org/package=testthat
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  year: '2025'
  doi: 10.32614/CRAN.package.testthat
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- type: software
  title: withr
  abstract: 'withr: Run Code ''With'' Temporarily Modified Global State'
  notes: Suggests
  url: https://withr.r-lib.org
  repository: https://CRAN.R-project.org/package=withr
  authors:
  - family-names: Hester
    given-names: Jim
  - family-names: Henry
    given-names: Lionel
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  - family-names: Müller
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  - family-names: Ushey
    given-names: Kevin
    email: kevinushey@gmail.com
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  - family-names: Chang
    given-names: Winston
  year: '2025'
  doi: 10.32614/CRAN.package.withr

CodeMeta (codemeta.json) 

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GitHub Events

Total
  • Create event: 1
  • Release event: 1
  • Issues event: 6
  • Watch event: 1
  • Push event: 18
  • Pull request event: 1
Last Year
  • Create event: 1
  • Release event: 1
  • Issues event: 6
  • Watch event: 1
  • Push event: 18
  • Pull request event: 1

Committers

Last synced: 10 months ago

All Time
  • Total Commits: 68
  • Total Committers: 2
  • Avg Commits per committer: 34.0
  • Development Distribution Score (DDS): 0.029
Past Year
  • Commits: 68
  • Committers: 2
  • Avg Commits per committer: 34.0
  • Development Distribution Score (DDS): 0.029
Top Committers
Name Email Commits
Nicolas Casajus r****c@g****m 66
dependabot[bot] 4****] 2

Issues and Pull Requests

Last synced: 9 months ago

Dependencies

.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/check-r-package v2 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/pkgdown.yaml actions
  • JamesIves/github-pages-deploy-action v4.4.1 composite
  • 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
DESCRIPTION cran
  • R >= 3.5 depends
  • openalexR * imports
  • RefManageR * suggests
  • knitr * suggests
  • rmarkdown * suggests
.github/workflows/test-coverage.yaml actions
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  • actions/upload-artifact v4 composite
  • codecov/codecov-action v5 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite