cffr

CRAN-status CRAN-results Downloads R-CMD-check codecov r-universe CITATION-cff DOI Project Status: Active - The project has reached a stable, usable state and is being actively developed. GitHub code size in bytes peer-review pkgcheck

cffr provides utilities to generate, parse, modify and validate CITATION.cff files automatically for R packages, as well as tools and examples for working with .cff more generally.

What is a CITATION.cff file?

Citation File Format (CFF) (Druskat et al. 2021) (v1.2.0) are plain text files with human- and machine-readable citation information for software (and datasets). Code developers can include them in their repositories to let others know how to correctly cite their software.

This format is becoming popular within the software citation ecosystem. Recently GitHub, Zenodo and Zotero have included full support of this citation format (Druskat 2021). GitHub support is of special interest:

GitHub-link

— Nat Friedman (@natfriedman) July 27, 2021

See Enhanced support for citations on GitHub (Smith 2021) for more info.

The CodeMeta Project (Jones et al. 2017) creates a concept vocabulary that can be used to standardize the exchange of software metadata across repositories and organizations. One of the many uses of a codemeta.json file (created following the standards defined on The CodeMeta Project) is to provide citation metadata such as title, authors, publication year, and venue (Fenner 2021). The packages codemeta/ codemetar allows to generate codemeta.json files from R packages metadata.

The cffr package

cffr maximizes the data extraction by using both the DESCRIPTION file and the CITATION file (if present) of your package. Note that cffr works best if your package pass R CMD check/devtools::check().

As per 2022-04-08 there are at least 115 repos on GitHub using cffr. Check them out here.

Installation

Install cffr from CRAN:

install.packages("cffr")

You can install the developing version of cffr with:

devtools::install_github("ropensci/cffr")

Alternatively, you can install cffr using the r-universe:

# Enable this universe
options(repos = c(
  ropensci = "https://ropensci.r-universe.dev",
  CRAN = "https://cloud.r-project.org"
))

# Install some packages
install.packages("cffr")

Example

By default most often from within your package folder you’ll simply run cff_write(), that creates a cff object, write it on a CITATION.cff file and validates it on a single command:

library(cffr)

# For in-development packages
cff_write()
#>
#> CITATION.cff generated
#>
#> cff_validate results-----
#> Congratulations! This .cff file is valid

However, cffr provides also custom print methods and mechanisms that allows you to customize the CITATION.cff and integrate them in your workflows.

This is a basic example which shows you how to create a cff object (see ?cff for more info). In this case, we are creating a cff object from the metadata of the rmarkdown package:

library(cffr)

# Example with an installed package
test <- cff_create("rmarkdown")
#> Warning in citation(n$package, auto = TRUE): no date field in DESCRIPTION file
#> of package 'testthat'

CITATION.cff for rmarkdown 

cff-version: 1.2.0
message: 'To cite package "rmarkdown" in publications use:'
type: software
license: GPL-3.0-only
title: 'rmarkdown: Dynamic Documents for R'
version: '2.13'
abstract: Convert R Markdown documents into a variety of formats.
authors:
- family-names: Allaire
  given-names: JJ
  email: jj@rstudio.com
- family-names: Xie
  given-names: Yihui
  email: xie@yihui.name
  orcid: https://orcid.org/0000-0003-0645-5666
- family-names: McPherson
  given-names: Jonathan
  email: jonathan@rstudio.com
- family-names: Luraschi
  given-names: Javier
  email: javier@rstudio.com
- family-names: Ushey
  given-names: Kevin
  email: kevin@rstudio.com
- family-names: Atkins
  given-names: Aron
  email: aron@rstudio.com
- family-names: Wickham
  given-names: Hadley
  email: hadley@rstudio.com
- family-names: Cheng
  given-names: Joe
  email: joe@rstudio.com
- family-names: Chang
  given-names: Winston
  email: winston@rstudio.com
- family-names: Iannone
  given-names: Richard
  email: rich@rstudio.com
  orcid: https://orcid.org/0000-0003-3925-190X
preferred-citation:
  type: manual
  title: 'rmarkdown: Dynamic Documents for R'
  authors:
  - family-names: Allaire
    given-names: JJ
    email: jj@rstudio.com
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  - family-names: McPherson
    given-names: Jonathan
    email: jonathan@rstudio.com
  - family-names: Luraschi
    given-names: Javier
    email: javier@rstudio.com
  - family-names: Ushey
    given-names: Kevin
    email: kevin@rstudio.com
  - family-names: Atkins
    given-names: Aron
    email: aron@rstudio.com
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
  - family-names: Cheng
    given-names: Joe
    email: joe@rstudio.com
  - family-names: Chang
    given-names: Winston
    email: winston@rstudio.com
  - family-names: Iannone
    given-names: Richard
    email: rich@rstudio.com
    orcid: https://orcid.org/0000-0003-3925-190X
  year: '2022'
  notes: R package version 2.13
  url: https://github.com/rstudio/rmarkdown
repository: https://CRAN.R-project.org/package=rmarkdown
repository-code: https://github.com/rstudio/rmarkdown
url: https://pkgs.rstudio.com/rmarkdown/
date-released: '2022-03-10'
contact:
- family-names: Xie
  given-names: Yihui
  email: xie@yihui.name
  orcid: https://orcid.org/0000-0003-0645-5666
keywords:
- literate-programming
- markdown
- pandoc
- r
- r-package
- rmarkdown
references:
- type: book
  title: 'R Markdown: The Definitive Guide'
  authors:
  - family-names: Xie
    given-names: Yihui
  - family-names: Allaire
    given-names: J.J.
  - family-names: Grolemund
    given-names: Garrett
  publisher:
    name: Chapman and Hall/CRC
    address: Boca Raton, Florida
  year: '2018'
  notes: ISBN 9781138359338
  url: https://bookdown.org/yihui/rmarkdown
- type: book
  title: R Markdown Cookbook
  authors:
  - family-names: Xie
    given-names: Yihui
  - family-names: Dervieux
    given-names: Christophe
  - family-names: Riederer
    given-names: Emily
  publisher:
    name: Chapman and Hall/CRC
    address: Boca Raton, Florida
  year: '2020'
  notes: ISBN 9780367563837
  url: https://bookdown.org/yihui/rmarkdown-cookbook
- type: software
  title: 'R: A Language and Environment for Statistical Computing'
  notes: Depends
  authors:
  - name: R Core Team
  location:
    name: Vienna, Austria
  year: '2022'
  url: https://www.R-project.org/
  institution:
    name: R Foundation for Statistical Computing
  version: '>= 3.0'
- type: software
  title: bslib
  abstract: 'bslib: Custom ''Bootstrap'' ''Sass'' Themes for ''shiny'' and ''rmarkdown'''
  notes: Imports
  authors:
  - family-names: Sievert
    given-names: Carson
    email: carson@rstudio.com
    orcid: https://orcid.org/0000-0002-4958-2844
  - family-names: Cheng
    given-names: Joe
    email: joe@rstudio.com
  year: '2022'
  url: https://CRAN.R-project.org/package=bslib
  version: '>= 0.2.5.1'
- type: software
  title: evaluate
  abstract: 'evaluate: Parsing and Evaluation Tools that Provide More Details than
    the Default'
  notes: Imports
  authors:
  - family-names: Wickham
    given-names: Hadley
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  year: '2022'
  url: https://CRAN.R-project.org/package=evaluate
  version: '>= 0.13'
- type: software
  title: htmltools
  abstract: 'htmltools: Tools for HTML'
  notes: Imports
  authors:
  - family-names: Cheng
    given-names: Joe
    email: joe@rstudio.com
  - family-names: Sievert
    given-names: Carson
    email: carson@rstudio.com
    orcid: https://orcid.org/0000-0002-4958-2844
  - family-names: Schloerke
    given-names: Barret
    email: barret@rstudio.com
    orcid: https://orcid.org/0000-0001-9986-114X
  - family-names: Chang
    given-names: Winston
    email: winston@rstudio.com
    orcid: https://orcid.org/0000-0002-1576-2126
  - family-names: Xie
    given-names: Yihui
    email: yihui@rstudio.com
  - family-names: Allen
    given-names: Jeff
    email: jeff@rstudio.com
  year: '2022'
  url: https://CRAN.R-project.org/package=htmltools
  version: '>= 0.3.5'
- type: software
  title: jquerylib
  abstract: 'jquerylib: Obtain ''jQuery'' as an HTML Dependency Object'
  notes: Imports
  authors:
  - family-names: Sievert
    given-names: Carson
    email: carson@rstudio.com
    orcid: https://orcid.org/0000-0002-4958-2844
  - family-names: Cheng
    given-names: Joe
    email: joe@rstudio.com
  year: '2022'
  url: https://CRAN.R-project.org/package=jquerylib
- type: software
  title: jsonlite
  abstract: 'jsonlite: A Simple and Robust JSON Parser and Generator for R'
  notes: Imports
  authors:
  - family-names: Ooms
    given-names: Jeroen
    email: jeroen@berkeley.edu
    orcid: https://orcid.org/0000-0002-4035-0289
  year: '2022'
  url: https://CRAN.R-project.org/package=jsonlite
- type: software
  title: knitr
  abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
  notes: Imports
  authors:
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  year: '2022'
  url: https://CRAN.R-project.org/package=knitr
  version: '>= 1.22'
- type: software
  title: methods
  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Imports
  authors:
  - name: R Core Team
  location:
    name: Vienna, Austria
  year: '2022'
  url: https://www.R-project.org/
  institution:
    name: R Foundation for Statistical Computing
- type: software
  title: stringr
  abstract: 'stringr: Simple, Consistent Wrappers for Common String Operations'
  notes: Imports
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
  year: '2022'
  url: https://CRAN.R-project.org/package=stringr
  version: '>= 1.2.0'
- type: software
  title: tinytex
  abstract: 'tinytex: Helper Functions to Install and Maintain TeX Live, and Compile
    LaTeX Documents'
  notes: Imports
  authors:
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  year: '2022'
  url: https://CRAN.R-project.org/package=tinytex
  version: '>= 0.31'
- type: software
  title: tools
  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Imports
  authors:
  - name: R Core Team
  location:
    name: Vienna, Austria
  year: '2022'
  url: https://www.R-project.org/
  institution:
    name: R Foundation for Statistical Computing
- type: software
  title: utils
  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Imports
  authors:
  - name: R Core Team
  location:
    name: Vienna, Austria
  year: '2022'
  url: https://www.R-project.org/
  institution:
    name: R Foundation for Statistical Computing
- type: software
  title: xfun
  abstract: 'xfun: Supporting Functions for Packages Maintained by ''Yihui Xie'''
  notes: Imports
  authors:
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  year: '2022'
  url: https://CRAN.R-project.org/package=xfun
  version: '>= 0.30'
- type: software
  title: yaml
  abstract: 'yaml: Methods to Convert R Data to YAML and Back'
  notes: Imports
  authors:
  - family-names: Garbett
    given-names: Shawn P
  - family-names: Stephens
    given-names: Jeremy
  - family-names: Simonov
    given-names: Kirill
  - family-names: Xie
    given-names: Yihui
  - family-names: Dong
    given-names: Zhuoer
  - family-names: Wickham
    given-names: Hadley
  - family-names: Horner
    given-names: Jeffrey
  - name: reikoch
  - family-names: Beasley
    given-names: Will
  - family-names: O'Connor
    given-names: Brendan
  - family-names: Warnes
    given-names: Gregory R.
  - family-names: Quinn
    given-names: Michael
  - family-names: Kamvar
    given-names: Zhian N.
  year: '2022'
  url: https://CRAN.R-project.org/package=yaml
  version: '>= 2.1.19'
- type: software
  title: digest
  abstract: 'digest: Create Compact Hash Digests of R Objects'
  notes: Suggests
  authors:
  - family-names: Lucas
    given-names: Dirk Eddelbuettel with contributions by Antoine
    email: edd@debian.org
  - family-names: Tuszynski
    given-names: Jarek
  - family-names: Bengtsson
    given-names: Henrik
  - family-names: Urbanek
    given-names: Simon
  - family-names: Frasca
    given-names: Mario
  - family-names: Lewis
    given-names: Bryan
  - family-names: Stokely
    given-names: Murray
  - family-names: Muehleisen
    given-names: Hannes
  - family-names: Murdoch
    given-names: Duncan
  - family-names: Hester
    given-names: Jim
  - family-names: Wu
    given-names: Wush
  - family-names: Kou
    given-names: Qiang
  - family-names: Onkelinx
    given-names: Thierry
  - family-names: Lang
    given-names: Michel
  - family-names: Simko
    given-names: Viliam
  - family-names: Hornik
    given-names: Kurt
  - family-names: Neal
    given-names: Radford
  - family-names: Bell
    given-names: Kendon
  - family-names: de Queljoe
    given-names: Matthew
  - family-names: Suruceanu
    given-names: Ion
  - family-names: Denney
    given-names: Bill
  - family-names: Schumacher
    given-names: Dirk
  - family-names: Chang.
    given-names: and Winston
  year: '2022'
  url: https://CRAN.R-project.org/package=digest
- type: software
  title: fs
  abstract: 'fs: Cross-Platform File System Operations Based on ''libuv'''
  notes: Suggests
  authors:
  - family-names: Hester
    given-names: Jim
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
  - family-names: Csárdi
    given-names: Gábor
    email: csardi.gabor@gmail.com
  year: '2022'
  url: https://CRAN.R-project.org/package=fs
- type: software
  title: rsconnect
  abstract: 'rsconnect: Deployment Interface for R Markdown Documents and Shiny Applications'
  notes: Suggests
  authors:
  - family-names: Atkins
    given-names: Aron
    email: aron@rstudio.com
  - family-names: McPherson
    given-names: Jonathan
    email: jonathan@rstudio.com
  - family-names: Allaire
    given-names: JJ
  year: '2022'
  url: https://CRAN.R-project.org/package=rsconnect
- type: software
  title: downlit
  abstract: 'downlit: Syntax Highlighting and Automatic Linking'
  notes: Suggests
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
  year: '2022'
  url: https://CRAN.R-project.org/package=downlit
  version: '>= 0.4.0'
- type: software
  title: sass
  abstract: 'sass: Syntactically Awesome Style Sheets (''Sass'')'
  notes: Suggests
  authors:
  - family-names: Cheng
    given-names: Joe
    email: joe@rstudio.com
  - family-names: Mastny
    given-names: Timothy
    email: tim.mastny@gmail.com
  - family-names: Iannone
    given-names: Richard
    email: rich@rstudio.com
    orcid: https://orcid.org/0000-0003-3925-190X
  - family-names: Schloerke
    given-names: Barret
    email: barret@rstudio.com
    orcid: https://orcid.org/0000-0001-9986-114X
  - family-names: Sievert
    given-names: Carson
    email: carson@rstudio.com
    orcid: https://orcid.org/0000-0002-4958-2844
  year: '2022'
  url: https://CRAN.R-project.org/package=sass
  version: '>= 0.4.0'
- type: software
  title: shiny
  abstract: 'shiny: Web Application Framework for R'
  notes: Suggests
  authors:
  - family-names: Chang
    given-names: Winston
    email: winston@rstudio.com
    orcid: https://orcid.org/0000-0002-1576-2126
  - family-names: Cheng
    given-names: Joe
    email: joe@rstudio.com
  - family-names: Allaire
    given-names: JJ
    email: jj@rstudio.com
  - family-names: Sievert
    given-names: Carson
    email: carson@rstudio.com
    orcid: https://orcid.org/0000-0002-4958-2844
  - family-names: Schloerke
    given-names: Barret
    email: barret@rstudio.com
    orcid: https://orcid.org/0000-0001-9986-114X
  - family-names: Xie
    given-names: Yihui
    email: yihui@rstudio.com
  - family-names: Allen
    given-names: Jeff
    email: jeff@rstudio.com
  - family-names: McPherson
    given-names: Jonathan
    email: jonathan@rstudio.com
  - family-names: Dipert
    given-names: Alan
  - family-names: Borges
    given-names: Barbara
  year: '2022'
  url: https://CRAN.R-project.org/package=shiny
  version: '>= 1.6.0'
- type: software
  title: testthat
  abstract: 'testthat: Unit Testing for R'
  notes: Suggests
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
  year: '2022'
  version: '>= 3.0.3'
- type: software
  title: tibble
  abstract: 'tibble: Simple Data Frames'
  notes: Suggests
  authors:
  - family-names: Müller
    given-names: Kirill
    email: krlmlr+r@mailbox.org
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
  year: '2022'
  url: https://CRAN.R-project.org/package=tibble
- type: software
  title: vctrs
  abstract: 'vctrs: Vector Helpers'
  notes: Suggests
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
  - family-names: Henry
    given-names: Lionel
    email: lionel@rstudio.com
  - family-names: Vaughan
    given-names: Davis
    email: davis@rstudio.com
  year: '2022'
  url: https://CRAN.R-project.org/package=vctrs
- type: software
  title: withr
  abstract: 'withr: Run Code ''With'' Temporarily Modified Global State'
  notes: Suggests
  authors:
  - family-names: Hester
    given-names: Jim
  - family-names: Henry
    given-names: Lionel
    email: lionel@rstudio.com
  - family-names: Müller
    given-names: Kirill
    email: krlmlr+r@mailbox.org
  - family-names: Ushey
    given-names: Kevin
    email: kevinushey@gmail.com
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
  - family-names: Chang
    given-names: Winston
  year: '2022'
  url: https://CRAN.R-project.org/package=withr
  version: '>= 2.4.2'

We can validate the result using cff_validate():

cff_validate(test)
#> 
#> cff_validate results-----
#> Congratulations! This cff object is valid

Check the docs and vignette("cffr", package = "cffr") to learn how to work with cff objects.

Keep your CITATION.cff file up-to-date

GitHub Actions

The easiest way for keeping you CITATION.cff file up-to-date is using GitHub Actions. Use cff_gha_update()function to install a GitHub Action that would update your CITATION.cff file on the following events:

cff_gha_update()

#> Installing update-citation-cff.yaml on './.github/workflows'
#> Adding .github to .Rbuildignore

See the example workflow file here.

Git pre-commit hook Experimental

You can also use a git pre-commit hook:

The pre-commit hook is run first, before you even type in a commit message. It’s used to inspect the snapshot that’s about to be committed, to see if you’ve forgotten something, to make sure tests run, or to examine whatever you need to inspect in the code. Exiting non-zero from this hook aborts the commit, although you can bypass it with git commit --no-verify.

A specific pre-commit hook can be installed with cff_git_hook_install(). If you want to use a pre-commit hook, please make sure you have the testthat package installed.

Learn more

Check the following articles to learn more about cffr:

Citation

Hernangómez D (2021). “cffr: Generate Citation File Format Metadata for R Packages.” Journal of Open Source Software, 6(67), 3900. doi: 10.21105/joss.03900 (URL: https://doi.org/10.21105/joss.03900), <URL: https://doi.org/10.21105/joss.03900>.

A BibTeX entry for LaTeX users is

@Article{hernangomez2021,
  doi = {10.21105/joss.03900},
  url = {https://doi.org/10.21105/joss.03900},
  year = {2021},
  publisher = {The Open Journal},
  volume = {6},
  number = {67},
  pages = {3900},
  author = {Diego Hernangómez},
  title = {cffr: Generate Citation File Format Metadata for R Packages},
  journal = {Journal of Open Source Software},
}

You can also use the citation provided by GitHub, that is generated from the information of a CITATION.cff created with cffr. See About CITATION files for more info.

References

Druskat, Stephan. 2021. “Making Software Citation Easi(er) - The Citation File Format and Its Integrations.” https://doi.org/10.5281/zenodo.5529914.

Druskat, Stephan, Jurriaan H. Spaaks, Neil Chue Hong, Robert Haines, James Baker, Spencer Bliven, Egon Willighagen, David Pérez-Suárez, and Alexander Konovalov. 2021. “Citation File Format.” https://doi.org/10.5281/zenodo.5171937.

Fenner, Martin. 2021. “We Need Your Feedback: Aligning the CodeMeta Vocabulary for Scientific Software with Schema.org.” https://doi.org/10.5438/a49j-x692.

Jones, Matthew B, Carl Boettiger, Abby Cabunoc Mayes, Arfon Smith, Peter Slaughter, Kyle Niemeyer, Yolanda Gil, et al. 2017. CodeMeta: An Exchange Schema for Software Metadata. KNB Data Repository. https://doi.org/10.5063/SCHEMA/CODEMETA-2.0.

Smith, Arfon. 2021. “Enhanced Support for Citations on GitHub.” https://github.blog/2021-08-19-enhanced-support-citations-github/.

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