The goal of this vignette is to provide an explicit map between the metadata fields used by cffr and each one of the valid keys of the Citation File Format schema version 1.2.0.
Summary
We summarize here the fields that cffr can parse and the original source of information for each one of them. The details on each key are presented on the next section of the document. The assessment of fields are based on the Guide to Citation File Format schema version 1.2.0 (Druskat et al. 2021).
| key | source |
|---|---|
| abstract | DESCRIPTION file |
| authors | DESCRIPTION file |
| cff-version | parameter on function |
| commit | Not parsed by cffr |
| contact | DESCRIPTION file |
| date-released | DESCRIPTION file |
| doi | CITATION file |
| identifiers | DESCRIPTION/CITATION files |
| keywords | DESCRIPTION file |
| license | DESCRIPTION file |
| license-url | Not parsed by cffr |
| message | DESCRIPTION file |
| preferred-citation | CITATION file |
| references | DESCRIPTION/CITATION files |
| repository | DESCRIPTION file |
| repository-artifact | Not parsed by cffr |
| repository-code | DESCRIPTION file |
| title | DESCRIPTION file |
| type | Fixed value: ‘software’ |
| url | DESCRIPTION file |
| version | DESCRIPTION file |
Details
abstract
This key is extracted from the “Description” field of the DESCRIPTION file.
Example
library(cffr)
# Create cffr for yaml
cff_obj <- cff_create("rmarkdown")
# Get DESCRIPTION of rmarkdown to check
pkg <- desc::desc(file.path(find.package("rmarkdown"), "DESCRIPTION"))
cat(cff_obj$abstract)
#> Convert R Markdown documents into a variety of formats.
cat(pkg$get("Description"))
#> Convert R Markdown documents into a variety of formats.authors
This key is parsed from the “Authors” or “Authors@R” field of the DESCRIPTION file. By default persons with the role “aut” or “cre” are considered, however this can be modified via the authors_roles parameter.
Example
# An example DESCRIPTION
path <- system.file("examples/DESCRIPTION_many_persons", package = "cffr")
pkg <- desc::desc(path)
# See persons listed
pkg$get_authors()
#> [1] "Diego Hernangómez <[email protected]> [aut, cre] (<https://orcid.org/0000-0001-8457-4658>, error, error)"
#> [2] "Joe Doe <I am a wrong email> [aut] (This One, ES, error)"
#> [3] "Pepe Doe <[email protected]> [aut] (error)"
#> [4] "I am an entity [cre] (2020-01-01, error)"
#> [5] "ERROR entity [cph] (for the administrative boundaries.)"
#> [6] "ERROR person [cph] (<https://orcid.org/0000-0003-2042-7063>, for the gisco_countrycode dataset.)"
# Default behaviour, use authors and creators (maintainers)
cff_obj <- cff_create(path)
cff_obj$authors
#> - family-names: Hernangómez
#> given-names: Diego
#> email: [email protected]
#> orcid: https://orcid.org/0000-0001-8457-4658
#> - family-names: Doe
#> given-names: Joe
#> affiliation: This One
#> country: ES
#> - family-names: Doe
#> given-names: Pepe
#> email: [email protected]
#> - name: I am an entity
#> date-end: '2020-01-01'
# Use now Copyright holders and maintainers
cff_obj_alt <- cff_create(path, authors_roles = c("cre", "cph"))
cff_obj_alt$authors
#> - family-names: Hernangómez
#> given-names: Diego
#> email: [email protected]
#> orcid: https://orcid.org/0000-0001-8457-4658
#> - name: I am an entity
#> date-end: '2020-01-01'
#> - name: ERROR entity
#> - family-names: person
#> given-names: ERROR
#> orcid: https://orcid.org/0000-0003-2042-7063cff-version
This key can be set via the parameters of the cff_create()/cff_write() functions:
Example
cff_objv110 <- cff_create("jsonlite", cff_version = "v1.1.0")
cat(cff_objv110$`cff-version`)
#> v1.1.0commit
This key is not extracted from the metadata of the package. See the description on the Guide to CFF schema v1.2.0.
description: The commit hash or revision number of the software version.
usage:
commit: 1ff847d81f29c45a3a1a5ce73d38e45c2f319bba commit: "Revision: 8612"
contact
This key is parsed from the “Authors” or “Authors@R” field of the DESCRIPTION file. Only persons with the role “cre” (i.e, the maintainer(s)) are considered.
Example
cff_obj <- cff_create("rmarkdown")
pkg <- desc::desc(file.path(find.package("rmarkdown"), "DESCRIPTION"))
cff_obj$contact
#> - family-names: Xie
#> given-names: Yihui
#> email: [email protected]
#> orcid: https://orcid.org/0000-0003-0645-5666
pkg$get_author()
#> [1] "Yihui Xie <[email protected]> [aut, cre] (<https://orcid.org/0000-0003-0645-5666>)"date-released
This key is extracted following this logic:
“Date” field or,
If not present, from “Date/Publication”. This is present on packages built on CRAN and Bioconductor. Or,
If not present, from “Packaged”, that is present on packages built by the r-universe.
Example
# From an installed package
cff_obj <- cff_create("rmarkdown")
pkg <- desc::desc(file.path(find.package("rmarkdown"), "DESCRIPTION"))
cat(pkg$get("Date/Publication"))
#> 2023-09-18 09:30:02 UTC
cat(cff_obj$`date-released`)
#> 2023-09-18
# A DESCRIPTION file without a Date
nodate <- system.file("examples/DESCRIPTION_basic", package = "cffr")
tmp <- tempfile("DESCRIPTION")
# Create a temporary file
file.copy(nodate, tmp)
#> [1] TRUE
pkgnodate <- desc::desc(tmp)
cffnodate <- cff_create(tmp)
# Won't appear
cat(cffnodate$`date-released`)
pkgnodate
#> Type: Package
#> Package: basicdesc
#> Title: A Basic Description
#> Version: 0.1.6
#> Authors@R (parsed):
#> * Marc Basic <[email protected]> [aut, cre, cph]
#> Description: A very basic description. Should parse without
#> problems.
#> License: GPL-3
#> URL: https://github.com/basic/package,
#> https://basic.github.io/package
#> BugReports: https://github.com/basic/package/issues
#> Encoding: UTF-8
#> LazyData: true
#> RoxygenNote: 6.0.1.9000
# Adding a Date
desc::desc_set("Date", "1999-01-01", file = tmp)
#> Type: Package
#> Package: basicdesc
#> Title: A Basic Description
#> Version: 0.1.6
#> Date: 1999-01-01
#> Authors@R (parsed):
#> * Marc Basic <[email protected]> [aut, cre, cph]
#> Description: A very basic description. Should parse without
#> problems.
#> License: GPL-3
#> URL: https://github.com/basic/package,
#> https://basic.github.io/package
#> BugReports: https://github.com/basic/package/issues
#> Encoding: UTF-8
#> LazyData: true
#> RoxygenNote: 6.0.1.9000
cat(cff_create(tmp)$`date-released`)
#> 1999-01-01doi
This key is parsed from the “doi” field of the preferred-citation object.
Example
cff_doi <- cff_create("cffr")
cat(cff_doi$doi)
#> 10.21105/joss.03900
cat(cff_doi$`preferred-citation`$doi)
#> 10.21105/joss.03900identifiers
This key includes all the possible identifiers of the package:
From the DESCRIPTION field, it includes all the urls not included in url or repository-code.
From the CITATION file, it includes all the dois not included in doi and the identifiers (if any) not included in the “identifiers” key of preferred-citation.
Example
file <- system.file("examples/DESCRIPTION_many_urls", package = "cffr")
pkg <- desc::desc(file)
cat(pkg$get_urls())
#> https://github.com/test/package https://test.github.io/package/ https://r-forge.r-project.org/projects/test/ http://google.ru https://gitlab.com/r-packages/behaviorchange
cat(cff_create(file)$url)
#> https://test.github.io/package/
cat(cff_create(file)$`repository-code`)
#> https://github.com/test/package
cff_create(file)$identifiers
#> - type: url
#> value: https://r-forge.r-project.org/projects/test/
#> - type: url
#> value: http://google.ru
#> - type: url
#> value: https://gitlab.com/r-packages/behaviorchangekeywords
This key is extracted from the DESCRIPTION file. The keywords should appear in the DESCRIPTION as:
...
X-schema.org-keywords: keyword1, keyword2, keyword3Example
# A DESCRIPTION file without keywords
nokeywords <- system.file("examples/DESCRIPTION_basic", package = "cffr")
tmp2 <- tempfile("DESCRIPTION")
# Create a temporary file
file.copy(nokeywords, tmp2)
#> [1] TRUE
pkgnokeywords <- desc::desc(tmp2)
cffnokeywords <- cff_create(tmp2)
# Won't appear
cat(cffnokeywords$keywords)
pkgnokeywords
#> Type: Package
#> Package: basicdesc
#> Title: A Basic Description
#> Version: 0.1.6
#> Authors@R (parsed):
#> * Marc Basic <[email protected]> [aut, cre, cph]
#> Description: A very basic description. Should parse without
#> problems.
#> License: GPL-3
#> URL: https://github.com/basic/package,
#> https://basic.github.io/package
#> BugReports: https://github.com/basic/package/issues
#> Encoding: UTF-8
#> LazyData: true
#> RoxygenNote: 6.0.1.9000
# Adding Keywords
desc::desc_set("X-schema.org-keywords", "keyword1, keyword2, keyword3",
file = tmp2
)
#> Type: Package
#> Package: basicdesc
#> Title: A Basic Description
#> Version: 0.1.6
#> Authors@R (parsed):
#> * Marc Basic <[email protected]> [aut, cre, cph]
#> Description: A very basic description. Should parse without
#> problems.
#> License: GPL-3
#> URL: https://github.com/basic/package,
#> https://basic.github.io/package
#> BugReports: https://github.com/basic/package/issues
#> Encoding: UTF-8
#> LazyData: true
#> RoxygenNote: 6.0.1.9000
#> X-schema.org-keywords: keyword1, keyword2, keyword3
cat(cff_create(tmp2)$keywords)
#> keyword1 keyword2 keyword3Additionally, if the source code of the package is hosted on GitHub, cffr can retrieve the topics of your repo via the GitHub API and include those topics as keywords. This option is controlled via the gh_keywords parameter:
Example
# Get cff object from jsonvalidate
jsonval <- cff_create("jsonvalidate")
# Keywords are retrieved from the GitHub repo
jsonval
#> cff-version: 1.2.0
#> message: 'To cite package "jsonvalidate" in publications use:'
#> type: software
#> license: MIT
#> title: 'jsonvalidate: Validate ''JSON'' Schema'
#> version: 1.4.2
#> abstract: Uses the node library 'is-my-json-valid' or 'ajv' to validate 'JSON' against
#> a 'JSON' schema. Drafts 04, 06 and 07 of 'JSON' schema are supported.
#> authors:
#> - family-names: FitzJohn
#> given-names: Rich
#> email: [email protected]
#> - family-names: Ashton
#> given-names: Rob
#> - family-names: Buus
#> given-names: Mathias
#> - family-names: Poberezkin
#> given-names: Evgeny
#> repository: https://ropensci.r-universe.dev
#> repository-code: https://github.com/ropensci/jsonvalidate
#> url: https://docs.ropensci.org/jsonvalidate/
#> date-released: '2023-08-27'
#> contact:
#> - family-names: FitzJohn
#> given-names: Rich
#> email: [email protected]
#> keywords:
#> - json
#> - json-validation
#> - jsonvalidate
#> - r
#> - r-package
#> - rstats
#> references:
#> - type: software
#> title: R6
#> abstract: 'R6: Encapsulated Classes with Reference Semantics'
#> notes: Imports
#> url: https://r6.r-lib.org
#> repository: https://CRAN.R-project.org/package=R6
#> authors:
#> - family-names: Chang
#> given-names: Winston
#> email: [email protected]
#> year: '2023'
#> - type: software
#> title: V8
#> abstract: 'V8: Embedded JavaScript and WebAssembly Engine for R'
#> notes: Imports
#> url: https://jeroen.r-universe.dev/V8
#> repository: https://CRAN.R-project.org/package=V8
#> authors:
#> - family-names: Ooms
#> given-names: Jeroen
#> email: [email protected]
#> orcid: https://orcid.org/0000-0002-4035-0289
#> year: '2023'
#> - 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: [email protected]
#> orcid: https://orcid.org/0000-0003-0645-5666
#> year: '2023'
#> - type: software
#> title: jsonlite
#> abstract: 'jsonlite: A Simple and Robust JSON Parser and Generator for R'
#> notes: Suggests
#> url: https://jeroen.r-universe.dev/jsonlite
#> repository: https://CRAN.R-project.org/package=jsonlite
#> authors:
#> - family-names: Ooms
#> given-names: Jeroen
#> email: [email protected]
#> orcid: https://orcid.org/0000-0002-4035-0289
#> year: '2023'
#> identifiers:
#> - type: url
#> value: https://arxiv.org/abs/1403.2805
#> - 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: [email protected]
#> - family-names: Xie
#> given-names: Yihui
#> email: [email protected]
#> orcid: https://orcid.org/0000-0003-0645-5666
#> - family-names: Dervieux
#> given-names: Christophe
#> email: [email protected]
#> orcid: https://orcid.org/0000-0003-4474-2498
#> - family-names: McPherson
#> given-names: Jonathan
#> email: [email protected]
#> - family-names: Luraschi
#> given-names: Javier
#> - family-names: Ushey
#> given-names: Kevin
#> email: [email protected]
#> - family-names: Atkins
#> given-names: Aron
#> email: [email protected]
#> - family-names: Wickham
#> given-names: Hadley
#> email: [email protected]
#> - family-names: Cheng
#> given-names: Joe
#> email: [email protected]
#> - family-names: Chang
#> given-names: Winston
#> email: [email protected]
#> - family-names: Iannone
#> given-names: Richard
#> email: [email protected]
#> orcid: https://orcid.org/0000-0003-3925-190X
#> year: '2023'
#> - type: software
#> title: testthat
#> 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: [email protected]
#> year: '2023'
#> - 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
#> email: [email protected]
#> - family-names: Müller
#> given-names: Kirill
#> email: [email protected]
#> - family-names: Ushey
#> given-names: Kevin
#> email: [email protected]
#> - family-names: Wickham
#> given-names: Hadley
#> email: [email protected]
#> - family-names: Chang
#> given-names: Winston
#> year: '2023'
# Check keywords
jsonval$keywords
#> [1] "json" "json-validation" "jsonvalidate" "r"
#> [5] "r-package" "rstats"
# The repo
jsonval$`repository-code`
#> [1] "https://github.com/ropensci/jsonvalidate"license
This key is extracted from the “License” field of the DESCRIPTION file.
Example
cff_obj <- cff_create("yaml")
cat(cff_obj$license)
#> BSD-3-Clause
pkg <- desc::desc(file.path(find.package("yaml"), "DESCRIPTION"))
cat(pkg$get("License"))
#> BSD_3_clause + file LICENSElicense-url
This key is not extracted from the metadata of the package. See the description on the Guide to CFF schema v1.2.0.
- description: The URL of the license text under which the software or dataset is licensed (only for non-standard licenses not included in the SPDX License List).
- usage:
yaml license-url: "https://obscure-licenses.com?id=1234"
message
This key is extracted from the DESCRIPTION field, specifically as:
msg <- paste0(
'To cite package "',
"NAME_OF_THE_PACKAGE",
'" in publications use:'
)Example
cat(cff_create("jsonlite")$message)
#> To cite package "jsonlite" in publications use:preferred-citation
This key is extracted from the CITATION file. If several references are provided, it would select the first citation as the “preferred-citation” and the rest of them as references.
Example
cffobj <- cff_create("rmarkdown")
cffobj$`preferred-citation`
#> type: manual
#> title: 'rmarkdown: Dynamic Documents for R'
#> authors:
#> - family-names: Allaire
#> given-names: JJ
#> email: [email protected]
#> - family-names: Xie
#> given-names: Yihui
#> email: [email protected]
#> orcid: https://orcid.org/0000-0003-0645-5666
#> - family-names: Dervieux
#> given-names: Christophe
#> email: [email protected]
#> orcid: https://orcid.org/0000-0003-4474-2498
#> - family-names: McPherson
#> given-names: Jonathan
#> email: [email protected]
#> - family-names: Luraschi
#> given-names: Javier
#> - family-names: Ushey
#> given-names: Kevin
#> email: [email protected]
#> - family-names: Atkins
#> given-names: Aron
#> email: [email protected]
#> - family-names: Wickham
#> given-names: Hadley
#> email: [email protected]
#> - family-names: Cheng
#> given-names: Joe
#> email: [email protected]
#> - family-names: Chang
#> given-names: Winston
#> email: [email protected]
#> - family-names: Iannone
#> given-names: Richard
#> email: [email protected]
#> orcid: https://orcid.org/0000-0003-3925-190X
#> year: '2023'
#> notes: R package version 2.25
#> url: https://github.com/rstudio/rmarkdown
citation("rmarkdown")[1]
#> Allaire J, Xie Y, Dervieux C, McPherson J, Luraschi J, Ushey K, Atkins
#> A, Wickham H, Cheng J, Chang W, Iannone R (2023). _rmarkdown: Dynamic
#> Documents for R_. R package version 2.25,
#> <https://github.com/rstudio/rmarkdown>.
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Manual{,
#> title = {rmarkdown: Dynamic Documents for R},
#> author = {JJ Allaire and Yihui Xie and Christophe Dervieux and Jonathan McPherson and Javier Luraschi and Kevin Ushey and Aron Atkins and Hadley Wickham and Joe Cheng and Winston Chang and Richard Iannone},
#> year = {2023},
#> note = {R package version 2.25},
#> url = {https://github.com/rstudio/rmarkdown},
#> }references
This key is extracted from the CITATION file if several references are provided. The first citation is considered as the preferred-citation and the rest of them as “references”. It also extracts the package dependencies and adds those to this fields using citation(auto = TRUE) on each dependency.
Example
cffobj <- cff_create("rmarkdown")
cffobj$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'
#> 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'
#> isbn: '9780367563837'
#> url: https://bookdown.org/yihui/rmarkdown-cookbook
#> - type: software
#> title: 'R: A Language and Environment for Statistical Computing'
#> notes: Depends
#> url: https://www.R-project.org/
#> authors:
#> - name: R Core Team
#> location:
#> name: Vienna, Austria
#> year: '2023'
#> 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
#> url: https://rstudio.github.io/bslib/
#> repository: https://CRAN.R-project.org/package=bslib
#> authors:
#> - family-names: Sievert
#> given-names: Carson
#> email: [email protected]
#> orcid: https://orcid.org/0000-0002-4958-2844
#> - family-names: Cheng
#> given-names: Joe
#> email: [email protected]
#> - family-names: Aden-Buie
#> given-names: Garrick
#> email: [email protected]
#> orcid: https://orcid.org/0000-0002-7111-0077
#> year: '2023'
#> version: '>= 0.2.5.1'
#> - type: software
#> title: evaluate
#> abstract: 'evaluate: Parsing and Evaluation Tools that Provide More Details than
#> the Default'
#> notes: Imports
#> url: https://github.com/r-lib/evaluate
#> repository: https://CRAN.R-project.org/package=evaluate
#> authors:
#> - family-names: Wickham
#> given-names: Hadley
#> - family-names: Xie
#> given-names: Yihui
#> email: [email protected]
#> orcid: https://orcid.org/0000-0003-0645-5666
#> year: '2023'
#> version: '>= 0.13'
#> - type: software
#> title: fontawesome
#> abstract: 'fontawesome: Easily Work with ''Font Awesome'' Icons'
#> notes: Imports
#> url: https://rstudio.github.io/fontawesome/
#> repository: https://CRAN.R-project.org/package=fontawesome
#> authors:
#> - family-names: Iannone
#> given-names: Richard
#> email: [email protected]
#> orcid: https://orcid.org/0000-0003-3925-190X
#> year: '2023'
#> version: '>= 0.5.0'
#> - type: software
#> title: htmltools
#> abstract: 'htmltools: Tools for HTML'
#> notes: Imports
#> url: https://rstudio.github.io/htmltools/
#> repository: https://CRAN.R-project.org/package=htmltools
#> authors:
#> - family-names: Cheng
#> given-names: Joe
#> email: [email protected]
#> - family-names: Sievert
#> given-names: Carson
#> email: [email protected]
#> orcid: https://orcid.org/0000-0002-4958-2844
#> - family-names: Schloerke
#> given-names: Barret
#> email: [email protected]
#> orcid: https://orcid.org/0000-0001-9986-114X
#> - family-names: Chang
#> given-names: Winston
#> email: [email protected]
#> orcid: https://orcid.org/0000-0002-1576-2126
#> - family-names: Xie
#> given-names: Yihui
#> email: [email protected]
#> - family-names: Allen
#> given-names: Jeff
#> year: '2023'
#> version: '>= 0.5.1'
#> - type: software
#> title: jquerylib
#> abstract: 'jquerylib: Obtain ''jQuery'' as an HTML Dependency Object'
#> notes: Imports
#> repository: https://CRAN.R-project.org/package=jquerylib
#> authors:
#> - family-names: Sievert
#> given-names: Carson
#> email: [email protected]
#> orcid: https://orcid.org/0000-0002-4958-2844
#> - family-names: Cheng
#> given-names: Joe
#> email: [email protected]
#> year: '2023'
#> - type: software
#> title: jsonlite
#> abstract: 'jsonlite: A Simple and Robust JSON Parser and Generator for R'
#> notes: Imports
#> url: https://jeroen.r-universe.dev/jsonlite
#> repository: https://CRAN.R-project.org/package=jsonlite
#> authors:
#> - family-names: Ooms
#> given-names: Jeroen
#> email: [email protected]
#> orcid: https://orcid.org/0000-0002-4035-0289
#> year: '2023'
#> identifiers:
#> - type: url
#> value: https://arxiv.org/abs/1403.2805
#> - type: software
#> title: knitr
#> abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
#> notes: Imports
#> url: https://yihui.org/knitr/
#> repository: https://CRAN.R-project.org/package=knitr
#> authors:
#> - family-names: Xie
#> given-names: Yihui
#> email: [email protected]
#> orcid: https://orcid.org/0000-0003-0645-5666
#> year: '2023'
#> 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: '2023'
#> institution:
#> name: R Foundation for Statistical Computing
#> - type: software
#> title: stringr
#> abstract: 'stringr: Simple, Consistent Wrappers for Common String Operations'
#> notes: Imports
#> url: https://stringr.tidyverse.org
#> repository: https://CRAN.R-project.org/package=stringr
#> authors:
#> - family-names: Wickham
#> given-names: Hadley
#> email: [email protected]
#> year: '2023'
#> version: '>= 1.2.0'
#> - type: software
#> title: tinytex
#> abstract: 'tinytex: Helper Functions to Install and Maintain TeX Live, and Compile
#> LaTeX Documents'
#> notes: Imports
#> url: https://github.com/rstudio/tinytex
#> repository: https://CRAN.R-project.org/package=tinytex
#> authors:
#> - family-names: Xie
#> given-names: Yihui
#> email: [email protected]
#> orcid: https://orcid.org/0000-0003-0645-5666
#> year: '2023'
#> 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: '2023'
#> 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: '2023'
#> institution:
#> name: R Foundation for Statistical Computing
#> - type: software
#> title: xfun
#> abstract: 'xfun: Supporting Functions for Packages Maintained by ''Yihui Xie'''
#> notes: Imports
#> url: https://github.com/yihui/xfun
#> repository: https://CRAN.R-project.org/package=xfun
#> authors:
#> - family-names: Xie
#> given-names: Yihui
#> email: [email protected]
#> orcid: https://orcid.org/0000-0003-0645-5666
#> year: '2023'
#> version: '>= 0.36'
#> - type: software
#> title: yaml
#> abstract: 'yaml: Methods to Convert R Data to YAML and Back'
#> notes: Imports
#> url: https://github.com/vubiostat/r-yaml/
#> repository: https://CRAN.R-project.org/package=yaml
#> 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: '2023'
#> version: '>= 2.1.19'
#> - type: software
#> title: digest
#> abstract: 'digest: Create Compact Hash Digests of R Objects'
#> notes: Suggests
#> url: https://dirk.eddelbuettel.com/code/digest.html
#> repository: https://CRAN.R-project.org/package=digest
#> authors:
#> - family-names: Lucas
#> given-names: Dirk Eddelbuettel with contributions by Antoine
#> email: [email protected]
#> - 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: Winston
#> - family-names: Attali.
#> given-names: Dean
#> year: '2023'
#> - type: software
#> title: fs
#> abstract: 'fs: Cross-Platform File System Operations Based on ''libuv'''
#> notes: Suggests
#> url: https://fs.r-lib.org
#> repository: https://CRAN.R-project.org/package=fs
#> authors:
#> - family-names: Hester
#> given-names: Jim
#> - family-names: Wickham
#> given-names: Hadley
#> email: [email protected]
#> - family-names: Csárdi
#> given-names: Gábor
#> email: [email protected]
#> year: '2023'
#> - type: software
#> title: downlit
#> abstract: 'downlit: Syntax Highlighting and Automatic Linking'
#> notes: Suggests
#> url: https://downlit.r-lib.org/
#> repository: https://CRAN.R-project.org/package=downlit
#> authors:
#> - family-names: Wickham
#> given-names: Hadley
#> email: [email protected]
#> year: '2023'
#> version: '>= 0.4.0'
#> - type: software
#> title: sass
#> abstract: 'sass: Syntactically Awesome Style Sheets (''Sass'')'
#> notes: Suggests
#> url: https://rstudio.github.io/sass/
#> repository: https://CRAN.R-project.org/package=sass
#> authors:
#> - family-names: Cheng
#> given-names: Joe
#> email: [email protected]
#> - family-names: Mastny
#> given-names: Timothy
#> email: [email protected]
#> - family-names: Iannone
#> given-names: Richard
#> email: [email protected]
#> orcid: https://orcid.org/0000-0003-3925-190X
#> - family-names: Schloerke
#> given-names: Barret
#> email: [email protected]
#> orcid: https://orcid.org/0000-0001-9986-114X
#> - family-names: Sievert
#> given-names: Carson
#> email: [email protected]
#> orcid: https://orcid.org/0000-0002-4958-2844
#> year: '2023'
#> version: '>= 0.4.0'
#> - type: software
#> title: testthat
#> 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: [email protected]
#> year: '2023'
#> version: '>= 3.0.3'
#> - type: software
#> title: tibble
#> abstract: 'tibble: Simple Data Frames'
#> notes: Suggests
#> url: https://tibble.tidyverse.org/
#> repository: https://CRAN.R-project.org/package=tibble
#> authors:
#> - family-names: Müller
#> given-names: Kirill
#> email: [email protected]
#> orcid: https://orcid.org/0000-0002-1416-3412
#> - family-names: Wickham
#> given-names: Hadley
#> email: [email protected]
#> year: '2023'
#> - type: software
#> title: vctrs
#> abstract: 'vctrs: Vector Helpers'
#> notes: Suggests
#> url: https://vctrs.r-lib.org/
#> repository: https://CRAN.R-project.org/package=vctrs
#> authors:
#> - family-names: Wickham
#> given-names: Hadley
#> email: [email protected]
#> - family-names: Henry
#> given-names: Lionel
#> email: [email protected]
#> - family-names: Vaughan
#> given-names: Davis
#> email: [email protected]
#> year: '2023'
#> - 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
#> email: [email protected]
#> - family-names: Müller
#> given-names: Kirill
#> email: [email protected]
#> - family-names: Ushey
#> given-names: Kevin
#> email: [email protected]
#> - family-names: Wickham
#> given-names: Hadley
#> email: [email protected]
#> - family-names: Chang
#> given-names: Winston
#> year: '2023'
#> version: '>= 2.4.2'
citation("rmarkdown")[-1]
#> Xie Y, Allaire J, Grolemund G (2018). _R Markdown: The Definitive
#> Guide_. Chapman and Hall/CRC, Boca Raton, Florida. ISBN 9781138359338,
#> <https://bookdown.org/yihui/rmarkdown>.
#>
#> Xie Y, Dervieux C, Riederer E (2020). _R Markdown Cookbook_. Chapman
#> and Hall/CRC, Boca Raton, Florida. ISBN 9780367563837,
#> <https://bookdown.org/yihui/rmarkdown-cookbook>.
#>
#> To see these entries in BibTeX format, use 'print(<citation>,
#> bibtex=TRUE)', 'toBibtex(.)', or set
#> 'options(citation.bibtex.max=999)'.repository
This key is extracted from the “Repository” field of the DESCRIPTION file. Usually, this field is auto-populated when a package is hosted on a repo (like CRAN or the r-universe). For packages without this field on the DESCRIPTION (that is the typical case for an in-development package), cffr would try to search the package on any of the default repositories specified on options("repos").
In the case of Bioconductor packages, those are identified if a “biocViews” is present on the DESCRIPTION file.
If cffr detects that the package is available on CRAN, it would return the canonical url form of the package (i.e. https://CRAN.R-project.org/package=jsonlite).
Example
# Installed package
inst <- cff_create("jsonlite")
cat(inst$repository)
#> https://CRAN.R-project.org/package=jsonlite
# Demo file downloaded from the r-universe
runiv <- system.file("examples/DESCRIPTION_r_universe", package = "cffr")
runiv_cff <- cff_create(runiv)
cat(runiv_cff$repository)
#> https://ropensci.r-universe.dev
desc::desc(runiv)$get("Repository")
#> Repository
#> "https://ropensci.r-universe.dev"
# For in development package
norepo <- system.file("examples/DESCRIPTION_basic", package = "cffr")
# No repo
norepo_cff <- cff_create(norepo)
cat(norepo_cff[["repository"]])
# Change the name to a known package on CRAN: ggplot2
tmp <- tempfile("DESCRIPTION")
file.copy(norepo, tmp)
#> [1] TRUE
# Change name
desc::desc_set("Package", "ggplot2", file = tmp)
#> Type: Package
#> Package: ggplot2
#> Title: A Basic Description
#> Version: 0.1.6
#> Authors@R (parsed):
#> * Marc Basic <[email protected]> [aut, cre, cph]
#> Description: A very basic description. Should parse without
#> problems.
#> License: GPL-3
#> URL: https://github.com/basic/package,
#> https://basic.github.io/package
#> BugReports: https://github.com/basic/package/issues
#> Encoding: UTF-8
#> LazyData: true
#> RoxygenNote: 6.0.1.9000
cat(cff_create(tmp)[["repository"]])
#> https://CRAN.R-project.org/package=ggplot2
# Show what happens if another repo is set
# Save original config
orig_options <- options()
getOption("repos")
#> binaries
#> "https://ropensci.r-universe.dev/bin/linux/jammy/4.3"
#> universe
#> "https://ropensci.r-universe.dev"
#> CRAN
#> "https://packagemanager.posit.co/all/__linux__/jammy/latest"
#> BioCsoft
#> "https://bioconductor.org/packages/3.17/bioc"
#> BioCann
#> "https://bioconductor.org/packages/3.17/data/annotation"
#> BioCexp
#> "https://bioconductor.org/packages/3.17/data/experiment"
#> fallback
#> "https://cloud.r-project.org"
# Set new repos
options(repos = c(
tidyverse = "https://tidyverse.r-universe.dev",
CRAN = "https://cloud.r-project.org"
))
# Load again the library
# Repos are evaluated on load
unloadNamespace("cffr")
library(cffr)
cat(cff_create(tmp)[["repository"]])
#> https://tidyverse.r-universe.dev/
# Now it is the tidyverse repo, due to our new config!
# Reset original config
options(orig_options)
getOption("repos")
#> binaries
#> "https://ropensci.r-universe.dev/bin/linux/jammy/4.3"
#> universe
#> "https://ropensci.r-universe.dev"
#> CRAN
#> "https://packagemanager.posit.co/all/__linux__/jammy/latest"
#> BioCsoft
#> "https://bioconductor.org/packages/3.17/bioc"
#> BioCann
#> "https://bioconductor.org/packages/3.17/data/annotation"
#> BioCexp
#> "https://bioconductor.org/packages/3.17/data/experiment"
#> fallback
#> "https://cloud.r-project.org"repository-artifact
This key is not extracted from the metadata of the package. See the description on the Guide to CFF schema v1.2.0.
description: The URL of the work in a build artifact/binary repository (when the work is software).
usage:
repository-artifact: "https://search.maven.org/artifact/org.corpus-tools/cff-maven-plugin/0.4.0/maven-plugin"
repository-code
This key is extracted from the “BugReports” or “URL” fields on the DESCRIPTION file. cffr tries to identify the url of the source on the following repositories:
Example
# Installed package on GitHub
cff_create("jsonlite")$`repository-code`
#> [1] "https://github.com/jeroen/jsonlite"
# GitLab
gitlab <- system.file("examples/DESCRIPTION_gitlab", package = "cffr")
cat(cff_create(gitlab)$`repository-code`)
#> https://gitlab.com/ninijay/methoden
# Check
desc::desc(gitlab)
#> Type: Package
#> Package: codemetar
#> Title: Generate 'CodeMeta' Metadata for R Packages
#> Version: 0.1.6
#> Authors@R (parsed):
#> * Carl Boettiger <[email protected]> [aut, cre, cph] (<https://orcid.org/0000-0002-1642-628X>)
#> * Anna Krystalli [rev, ctb] (<https://orcid.org/0000-0002-2378-4915>)
#> * Toph Allen [rev] (<https://orcid.org/0000-0003-4580-091X>)
#> * Maëlle Salmon [ctb, aut] (<https://orcid.org/0000-0002-2815-0399>)
#> * rOpenSci [fnd] (https://ropensci.org/)
#> * Katrin Leinweber [ctb]
#> * Noam Ross [ctb]
#> * Arfon Smith [ctb]
#> Description: The 'Codemeta' Project defines a 'JSON-LD' format for
#> describing software metadata, as detailed at
#> <https://codemeta.github.io>. This package provides utilities to
#> generate, parse, and modify 'codemeta.json' files automatically for R
#> packages, as well as tools and examples for working with
#> 'codemeta.json' 'JSON-LD' more generally.
#> License: GPL-3
#> URL: https://gitlab.com/ninijay/methoden,
#> https://ropensci.github.io/codemetar
#> BugReports: https://gitlab.com/ninijay/methoden/-/issues
#> Depends:
#> R (>= 3.0.0)
#> Imports:
#> crul,
#> desc,
#> devtools,
#> gh,
#> git2r,
#> jsonld,
#> jsonlite (>= 1.3),
#> memoise,
#> methods,
#> purrr,
#> readr,
#> sessioninfo,
#> stats,
#> stringi,
#> stringr,
#> tibble,
#> usethis,
#> whisker
#> Suggests:
#> covr,
#> dplyr (>= 0.7.0),
#> jsonvalidate,
#> knitr,
#> magrittr,
#> printr,
#> rmarkdown,
#> testthat,
#> xml2
#> VignetteBuilder:
#> knitr
#> Encoding: UTF-8
#> LazyData: true
#> RoxygenNote: 6.0.1.9000
#> X-schema.org-isPartOf: https://ropensci.org
#> X-schema.org-keywords: metadata, codemeta, ropensci, citation,
#> credit, linked-datatitle
This key is extracted from the “Description” field of the DESCRIPTION file.
title <- paste0(
"NAME_OF_THE_PACKAGE",
": ",
"TITLE_OF_THE_PACKAGE"
)Example
# Installed package
cat(cff_create("testthat")$title)
#> testthat: Unit Testing for Rtype
Fixed value equal to “software”. The other possible value is “dataset”. See the description on the Guide to CFF schema v1.2.0.
url
This key is extracted from the “BugReports” or “URL” fields on the DESCRIPTION file. It corresponds to the first url that is different to repository-code.
Example
# Many urls
manyurls <- system.file("examples/DESCRIPTION_many_urls", package = "cffr")
cat(cff_create(manyurls)$url)
#> https://test.github.io/package/
# Check
desc::desc(manyurls)
#> Type: Package
#> Package: manyurls
#> Title: A lot of urls
#> Version: 0.1.6
#> Authors@R (parsed):
#> * Marc Basic <[email protected]> [aut, cre, cph]
#> Description: This package has many urls. Specifically, 1 Bug
#> Reports and 6 URLs. Expected is to have 1 repository-code, 1 url and 3
#> URLs, since there is 1 duplicate and 1 invalid url.
#> License: GPL-3
#> URL: https://github.com/test/package,
#> https://test.github.io/package/,
#> https://r-forge.r-project.org/projects/test/, http://google.ru,
#> https://gitlab.com/r-packages/behaviorchange, this.is.not.an.url
#> BugReports: https://github.com/test/package/issues
#> Encoding: UTF-8version
This key is extracted from the “Version” field on the DESCRIPTION file.
# Should be (>= 3.0.0)
cat(cff_create("testthat")$version)
#> 3.1.10References
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.