Author: Diego Hernangómez

# From R to CFF

### Crosswalk

#### Diego Hernangómez

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.

Back to summary.

### authors

This key is parsed from the “Authors” or “Authors@R” field of the DESCRIPTION file. Only persons with the role “aut” or “cre” are considered.

Example

    cff_obj <- cff_create("rmarkdown")
    pkg <- desc::desc(file.path(find.package("rmarkdown"), "DESCRIPTION"))

    cff_obj$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

    authors <- pkg$get_authors()

    authors[vapply(authors, function(x) {
      "aut" %in% x$role || "cre" %in% x$role
    }, logical(1))]
    #>  [1] "JJ Allaire <jj@rstudio.com> [aut]"
    #>  [2] "Yihui Xie <xie@yihui.name> [aut, cre] (<https://orcid.org/0000-0003-0645-5666>)"
    #>  [3] "Jonathan McPherson <jonathan@rstudio.com> [aut]"
    #>  [4] "Javier Luraschi <javier@rstudio.com> [aut]"
    #>  [5] "Kevin Ushey <kevin@rstudio.com> [aut]"
    #>  [6] "Aron Atkins <aron@rstudio.com> [aut]"
    #>  [7] "Hadley Wickham <hadley@rstudio.com> [aut]"
    #>  [8] "Joe Cheng <joe@rstudio.com> [aut]"
    #>  [9] "Winston Chang <winston@rstudio.com> [aut]"
    #> [10] "Richard Iannone <rich@rstudio.com> [aut] (<https://orcid.org/0000-0003-3925-190X>)"

Back to summary.

### cff-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`)
    #> v1.1.0

Back to summary.

### commit

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"

Back to summary.

### 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: xie@yihui.name
    #>   orcid: https://orcid.org/0000-0003-0645-5666

    pkg$get_author()
    #> [1] "Yihui Xie <xie@yihui.name> [aut, cre] (<https://orcid.org/0000-0003-0645-5666>)"

Back to summary.

### date-released

This key is parsed from the “Date” field or, if not present, from the “Date/Publication” field that is present on packages built on CRAN.

Example

    # From an installed package

    cff_obj <- cff_create("rmarkdown")
    pkg <- desc::desc(file.path(find.package("rmarkdown"), "DESCRIPTION"))

    cat(pkg$get("Date/Publication"))
    #> 2021-09-14 14:10:02 UTC

    cat(cff_obj$`date-released`)
    #> 2021-09-14

    # 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 <marcbasic@gmail.com> [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 <marcbasic@gmail.com> [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`)
    #> 1999-01-01

Back to summary.

### doi

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.03900

Back to summary.

### identifiers

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/behaviorchange

Back to summary.

### keywords

This key is extracted from the DESCRIPTION file. The keywords should appear in the DESCRIPTION as:

    ...
    X-schema.org-keywords: keyword1, keyword2, keyword3

Example

    # 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 <marcbasic@gmail.com> [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 <marcbasic@gmail.com> [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 keyword3

Additionally, 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: 1.3.2
    #> 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: rich.fitzjohn@gmail.com
    #> - family-names: Ashton
    #>   given-names: Rob
    #> - family-names: Buus
    #>   given-names: Mathias
    #> - family-names: Poberezkin
    #>   given-names: Evgeny
    #> preferred-citation:
    #>   type: manual
    #>   title: 'jsonvalidate: Validate ''JSON'' Schema'
    #>   authors:
    #>   - family-names: FitzJohn
    #>     given-names: Rich
    #>     email: rich.fitzjohn@gmail.com
    #>   - family-names: Ashton
    #>     given-names: Rob
    #>   - family-names: Buus
    #>     given-names: Mathias
    #>   - family-names: Poberezkin
    #>     given-names: Evgeny
    #>   year: '2021'
    #>   notes: R package version 1.3.2
    #>   url: https://CRAN.R-project.org/package=jsonvalidate
    #> repository: https://CRAN.R-project.org/package=jsonvalidate
    #> repository-code: https://github.com/ropensci/jsonvalidate
    #> url: https://docs.ropensci.org/jsonvalidate/
    #> date-released: '2021-11-03'
    #> contact:
    #> - family-names: FitzJohn
    #>   given-names: Rich
    #>   email: rich.fitzjohn@gmail.com
    #> keywords:
    #> - json
    #> - json-validation
    #> - jsonvalidate
    #> - r
    #> - r-package
    #> - rstats
    #> references:
    #> - type: software
    #>   title: 'V8: Embedded JavaScript and WebAssembly Engine for R'
    #>   authors:
    #>   - family-names: Ooms
    #>     given-names: Jeroen
    #>     email: jeroen@berkeley.edu
    #>     orcid: https://orcid.org/0000-0002-4035-0289
    #>   year: '2022'
    #>   notes: Imports
    #>   url: https://CRAN.R-project.org/package=V8
    #> - type: software
    #>   title: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
    #>   authors:
    #>   - family-names: Xie
    #>     given-names: Yihui
    #>     email: xie@yihui.name
    #>     orcid: https://orcid.org/0000-0003-0645-5666
    #>   year: '2022'
    #>   notes: Suggests
    #>   url: https://CRAN.R-project.org/package=knitr
    #> - type: software
    #>   title: 'jsonlite: A Simple and Robust JSON Parser and Generator for R'
    #>   authors:
    #>   - family-names: Ooms
    #>     given-names: Jeroen
    #>     email: jeroen@berkeley.edu
    #>     orcid: https://orcid.org/0000-0002-4035-0289
    #>   year: '2022'
    #>   notes: Suggests
    #>   url: https://CRAN.R-project.org/package=jsonlite
    #> - type: software
    #>   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: Suggests
    #>   url: https://CRAN.R-project.org/package=rmarkdown
    #> - type: software
    #>   title: 'testthat: Unit Testing for R'
    #>   authors:
    #>   - family-names: Wickham
    #>     given-names: Hadley
    #>     email: hadley@rstudio.com
    #>   year: '2022'
    #>   notes: Suggests
    #>   url: https://CRAN.R-project.org/package=testthat
    #> - type: software
    #>   title: 'withr: Run Code ''With'' Temporarily Modified Global State'
    #>   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'
    #>   notes: Suggests
    #>   url: https://CRAN.R-project.org/package=withr

    # Check keywords
    jsonval$keywords
    #> [1] "json"            "json-validation" "jsonvalidate"
    #> [4] "r"               "r-package"       "rstats"

    # The repo
    jsonval$`repository-code`
    #> [1] "https://github.com/ropensci/jsonvalidate"

Back to summary.

### 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 LICENSE

Back to summary.

### license-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"`

Back to summary.

### 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:

Back to summary.

### 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: 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: '2021'
    #> notes: R package version 2.11
    #> url: https://github.com/rstudio/rmarkdown

    citation("rmarkdown")[1]
    #>
    #>   JJ Allaire and Yihui Xie and Jonathan McPherson and
    #>   Javier Luraschi and Kevin Ushey and Aron Atkins and
    #>   Hadley Wickham and Joe Cheng and Winston Chang and
    #>   Richard Iannone (2021). rmarkdown: Dynamic
    #>   Documents for R. R package version 2.11. URL
    #>   https://rmarkdown.rstudio.com.
    #>
    #> A BibTeX entry for LaTeX users is
    #>
    #>   @Manual{,
    #>     title = {rmarkdown: Dynamic Documents for R},
    #>     author = {JJ Allaire and Yihui Xie 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 = {2021},
    #>     note = {R package version 2.11},
    #>     url = {https://github.com/rstudio/rmarkdown},
    #>   }

Back to summary.

### 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'
    #>   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'
    #>   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'
    #>   notes: Depends
    #> - type: software
    #>   title: 'R: A Language and Environment for Statistical Computing'
    #>   authors:
    #>   - name: R Core Team
    #>   location:
    #>     name: Vienna, Austria
    #>   year: '2022'
    #>   url: https://www.R-project.org/
    #>   institution:
    #>     name: R Foundation for Statistical Computing
    #>   notes: Imports
    #> - type: software
    #>   title: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
    #>   authors:
    #>   - family-names: Xie
    #>     given-names: Yihui
    #>     email: xie@yihui.name
    #>     orcid: https://orcid.org/0000-0003-0645-5666
    #>   year: '2022'
    #>   notes: Imports
    #>   url: https://CRAN.R-project.org/package=knitr
    #>   version: '>= 1.22'
    #> - type: software
    #>   title: 'yaml: Methods to Convert R Data to YAML and Back'
    #>   authors:
    #>   - 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.
    #>   year: '2022'
    #>   notes: Imports
    #>   url: https://CRAN.R-project.org/package=yaml
    #>   version: '>= 2.1.19'
    #> - type: software
    #>   title: 'htmltools: Tools for HTML'
    #>   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'
    #>   notes: Imports
    #>   url: https://CRAN.R-project.org/package=htmltools
    #>   version: '>= 0.3.5'
    #> - type: software
    #>   title: 'evaluate: Parsing and Evaluation Tools that Provide More Details than the
    #>     Default'
    #>   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'
    #>   notes: Imports
    #>   url: https://CRAN.R-project.org/package=evaluate
    #>   version: '>= 0.13'
    #> - type: software
    #>   title: 'jsonlite: A Simple and Robust JSON Parser and Generator for R'
    #>   authors:
    #>   - family-names: Ooms
    #>     given-names: Jeroen
    #>     email: jeroen@berkeley.edu
    #>     orcid: https://orcid.org/0000-0002-4035-0289
    #>   year: '2022'
    #>   notes: Imports
    #>   url: https://CRAN.R-project.org/package=jsonlite
    #> - type: software
    #>   title: 'tinytex: Helper Functions to Install and Maintain TeX Live, and Compile
    #>     LaTeX Documents'
    #>   authors:
    #>   - family-names: Xie
    #>     given-names: Yihui
    #>     email: xie@yihui.name
    #>     orcid: https://orcid.org/0000-0003-0645-5666
    #>   year: '2022'
    #>   notes: Imports
    #>   url: https://CRAN.R-project.org/package=tinytex
    #>   version: '>= 0.31'
    #> - type: software
    #>   title: 'xfun: Supporting Functions for Packages Maintained by ''Yihui Xie'''
    #>   authors:
    #>   - family-names: Xie
    #>     given-names: Yihui
    #>     email: xie@yihui.name
    #>     orcid: https://orcid.org/0000-0003-0645-5666
    #>   year: '2022'
    #>   notes: Imports
    #>   url: https://CRAN.R-project.org/package=xfun
    #>   version: '>= 0.21'
    #> - type: software
    #>   title: 'jquerylib: Obtain ''jQuery'' as an HTML Dependency Object'
    #>   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'
    #>   notes: Imports
    #>   url: https://CRAN.R-project.org/package=jquerylib
    #> - type: software
    #>   title: 'stringr: Simple, Consistent Wrappers for Common String Operations'
    #>   authors:
    #>   - family-names: Wickham
    #>     given-names: Hadley
    #>     email: hadley@rstudio.com
    #>   year: '2022'
    #>   notes: Imports
    #>   url: https://CRAN.R-project.org/package=stringr
    #>   version: '>= 1.2.0'
    #> - type: software
    #>   title: 'shiny: Web Application Framework for R'
    #>   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'
    #>   notes: Suggests
    #>   url: https://CRAN.R-project.org/package=shiny
    #>   version: '>= 1.6.0'
    #> - type: software
    #>   title: 'testthat: Unit Testing for R'
    #>   authors:
    #>   - family-names: Wickham
    #>     given-names: Hadley
    #>     email: hadley@rstudio.com
    #>   year: '2022'
    #>   notes: Suggests
    #>   url: https://CRAN.R-project.org/package=testthat
    #>   version: '>= 3.0.0'
    #> - type: software
    #>   title: 'digest: Create Compact Hash Digests of R Objects'
    #>   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'
    #>   notes: Suggests
    #>   url: https://CRAN.R-project.org/package=digest
    #> - type: software
    #>   title: 'vctrs: Vector Helpers'
    #>   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'
    #>   notes: Suggests
    #>   url: https://CRAN.R-project.org/package=vctrs
    #> - type: software
    #>   title: 'tibble: Simple Data Frames'
    #>   authors:
    #>   - family-names: Müller
    #>     given-names: Kirill
    #>     email: krlmlr+r@mailbox.org
    #>   - family-names: Wickham
    #>     given-names: Hadley
    #>     email: hadley@rstudio.com
    #>   year: '2022'
    #>   notes: Suggests
    #>   url: https://CRAN.R-project.org/package=tibble
    #> - type: software
    #>   title: 'fs: Cross-Platform File System Operations Based on ''libuv'''
    #>   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'
    #>   notes: Suggests
    #>   url: https://CRAN.R-project.org/package=fs
    #> - type: software
    #>   title: 'rsconnect: Deployment Interface for R Markdown Documents and Shiny Applications'
    #>   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'
    #>   notes: Suggests
    #>   url: https://CRAN.R-project.org/package=rsconnect
    #> - type: software
    #>   title: 'withr: Run Code ''With'' Temporarily Modified Global State'
    #>   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'
    #>   notes: Suggests
    #>   url: https://CRAN.R-project.org/package=withr
    #>   version: '>= 2.4.2'
    #> - type: software
    #>   title: 'bslib: Custom ''Bootstrap'' ''Sass'' Themes for ''shiny'' and ''rmarkdown'''
    #>   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'
    #>   notes: Suggests
    #>   url: https://CRAN.R-project.org/package=bslib
    #>   version: '>= 0.2.5.1'
    #> - type: software
    #>   title: 'sass: Syntactically Awesome Style Sheets (''Sass'')'
    #>   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'
    #>   notes: Suggests
    #>   url: https://CRAN.R-project.org/package=sass
    #>   version: '>= 0.4.0'

    citation("rmarkdown")[-1]
    #>
    #>   Yihui Xie and J.J. Allaire and Garrett Grolemund
    #>   (2018). R Markdown: The Definitive Guide. Chapman
    #>   and Hall/CRC. ISBN 9781138359338. URL
    #>   https://bookdown.org/yihui/rmarkdown.
    #>
    #>   Yihui Xie and Christophe Dervieux and Emily
    #>   Riederer (2020). R Markdown Cookbook. Chapman and
    #>   Hall/CRC. ISBN 9780367563837. URL
    #>   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)'.

Back to summary.

### 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 <marcbasic@gmail.com> [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")
    #>     CRAN
    #> "@CRAN@"

    # 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")
    #>     CRAN
    #> "@CRAN@"

Back to summary.

### 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"

Back to summary.

### 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:

- GitHub.
- GitLab.
- R-Forge.
- Bitbucket.

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 <cboettig@gmail.com> [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-data

Back to summary.

### title

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 R

Back to summary.

### type

Fixed value equal to “software.” The other possible value is “dataset.” See the description on the Guide to CFF schema v1.2.0.

Back to summary.

### 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 <marcbasic@gmail.com> [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-8

Back to summary.

### version

This key is extracted from the “Version” field on the DESCRIPTION file.

    # Should be (>= 3.0.0)
    cat(cff_create("testthat")$version)
    #> 3.1.1

Back to summary.

## References

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.