cffr is a tool whose target audience are
R package developers. The main goal of
cffr is to create a CITATION.cff file
using the metadata information of the following files:
DESCRIPTION file.inst/CITATION.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 data sets). 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:
— Nat Friedman (@natfriedman) July 27, 2021
See Customize your repository/About CITATION files for more info.
CITATION.cff file for my R packageWith cffr creating a CITATION.cff file
is quite straightforward. You just need to run
cff_write():
Under the hood, cff_write() performs the following
tasks:
cff_create().cff_modify().CITATION.cff file.cff_validate().Congratulations! Now you have a full CITATION.cff file
for your R package.
CITATION.cff fileYou can easily customize the cff object (a custom class
of cffr) using the coercion system provided in the
package, as well as making use of the keys parameter.
We would create a cff object using cff()
(for example purposes only) and we would add or modify contents of
it.
newobject <- cff()
newobject
#> cff-version: 1.2.0
#> message: If you use this software, please cite it using these metadata.
#> title: My Research Software
#> authors:
#> - family-names: Doe
#> given-names: JohnThe valid keys of the Citation
File Format schema version 1.2.0 can be displayed with
cff_schema_keys():
cff_schema_keys()
#> [1] "cff-version" "message" "type"
#> [4] "license" "title" "version"
#> [7] "doi" "identifiers" "abstract"
#> [10] "authors" "preferred-citation" "repository"
#> [13] "repository-artifact" "repository-code" "commit"
#> [16] "url" "date-released" "contact"
#> [19] "keywords" "references" "license-url"In this case, we are going to add url,
version and repository. We would also
overwrite the title key. We just need to add those
parameters to cff_modify():
modobject <- cff_modify(newobject,
url = "https://ropensci.org/",
version = "0.0.1",
repository = "https://github.com/ropensci/cffr",
# If the field is already present, it would be overridden
title = "Modifying a 'cff' object"
)
modobject
#> cff-version: 1.2.0
#> message: If you use this software, please cite it using these metadata.
#> title: Modifying a 'cff' object
#> authors:
#> - family-names: Doe
#> given-names: John
#> url: https://ropensci.org/
#> version: 0.0.1
#> repository: https://github.com/ropensci/cffr
# Validate against the schema
cff_validate(modobject)
#> ══ Validating cff ══════════════════════════════════════════════════════════════
#> ✔ Congratulations! This <cff> is validcffr provides two functions that convert
person and bibentry objects (see
?person and ?bibentry) according to the Citation
File Format schema.
Following the previous example, we are going to add a new author first. For doing that, we need first to extract the current author of the package and append the coerced person:
# Valid person keys
cff_schema_definitions_person()
#> [1] "address" "affiliation" "alias" "city"
#> [5] "country" "email" "family-names" "fax"
#> [9] "given-names" "name-particle" "name-suffix" "orcid"
#> [13] "post-code" "region" "tel" "website"
# Create the person
chiquito <- person("Gregorio",
"Sánchez Fernández",
email = "fake@email2.com",
comment = c(
alias = "Chiquito de la Calzada",
city = "Malaga",
country = "ES",
ORCID = "0000-0000-0000-0001"
)
)
chiquito
#> [1] "Gregorio Sánchez Fernández <fake@email2.com> (Chiquito de la Calzada, Malaga, ES, <https://orcid.org/0000-0000-0000-0001>)"
# To cff
chiquito_cff <- as_cff_person(chiquito)
chiquito_cff
#> - family-names: Sánchez Fernández
#> given-names: Gregorio
#> email: fake@email2.com
#> alias: Chiquito de la Calzada
#> city: Malaga
#> country: ES
#> orcid: https://orcid.org/0000-0000-0000-0001
# Append to previous authors
newauthors <- c(modobject$authors, chiquito_cff)
newauthors
#> - family-names: Doe
#> given-names: John
#> - family-names: Sánchez Fernández
#> given-names: Gregorio
#> email: fake@email2.com
#> alias: Chiquito de la Calzada
#> city: Malaga
#> country: ES
#> orcid: https://orcid.org/0000-0000-0000-0001
newauthorobject <- cff_modify(modobject, authors = newauthors)
newauthorobject
#> cff-version: 1.2.0
#> message: If you use this software, please cite it using these metadata.
#> title: Modifying a 'cff' object
#> authors:
#> - family-names: Doe
#> given-names: John
#> - family-names: Sánchez Fernández
#> given-names: Gregorio
#> email: fake@email2.com
#> alias: Chiquito de la Calzada
#> city: Malaga
#> country: ES
#> orcid: https://orcid.org/0000-0000-0000-0001
#> url: https://ropensci.org/
#> version: 0.0.1
#> repository: https://github.com/ropensci/cffr
cff_validate(newauthorobject)
#> ══ Validating cff ══════════════════════════════════════════════════════════════
#> ✔ Congratulations! This <cff> is validNow, we may want to add references to our data. On the
following example, we would add two references, one created with
bibentry() and another with citation():
# Valid reference keys
cff_schema_definitions_refs()
#> [1] "abbreviation" "abstract" "authors"
#> [4] "collection-doi" "collection-title" "collection-type"
#> [7] "commit" "conference" "contact"
#> [10] "copyright" "data-type" "database-provider"
#> [13] "database" "date-accessed" "date-downloaded"
#> [16] "date-published" "date-released" "department"
#> [19] "doi" "edition" "editors"
#> [22] "editors-series" "end" "entry"
#> [25] "filename" "format" "identifiers"
#> [28] "institution" "isbn" "issn"
#> [31] "issue" "issue-date" "issue-title"
#> [34] "journal" "keywords" "languages"
#> [37] "license" "license-url" "loc-end"
#> [40] "loc-start" "location" "medium"
#> [43] "month" "nihmsid" "notes"
#> [46] "number" "number-volumes" "pages"
#> [49] "patent-states" "pmcid" "publisher"
#> [52] "recipients" "repository" "repository-artifact"
#> [55] "repository-code" "scope" "section"
#> [58] "senders" "start" "status"
#> [61] "term" "thesis-type" "title"
#> [64] "translators" "type" "url"
#> [67] "version" "volume" "volume-title"
#> [70] "year" "year-original"
# Auto coercion from another R package
base_r <- citation("base")
bib <- bibentry("Book",
title = "This is a book",
author = "Lisa Lee",
year = 1980,
publisher = "McGraw Hill",
volume = 2
)
refs <- c(base_r, bib)
refs
#> R Core Team (2024). _R: A Language and Environment for Statistical
#> Computing_. R Foundation for Statistical Computing, Vienna, Austria.
#> <https://www.R-project.org/>.
#>
#> Lee L (1980). _This is a book_, volume 2. McGraw Hill.
# Now to cff
refs_cff <- as_cff(refs)
refs_cff
#> - type: manual
#> title: 'R: A Language and Environment for Statistical Computing'
#> authors:
#> - name: R Core Team
#> institution:
#> name: R Foundation for Statistical Computing
#> address: Vienna, Austria
#> year: '2024'
#> url: https://www.R-project.org/
#> - type: book
#> title: This is a book
#> authors:
#> - family-names: Lee
#> given-names: Lisa
#> year: '1980'
#> publisher:
#> name: McGraw Hill
#> volume: '2'Now the process is similar to the example with person:
we just modify our cff object:
finalobject <- cff_modify(newauthorobject, references = refs_cff)
finalobject
#> cff-version: 1.2.0
#> message: If you use this software, please cite it using these metadata.
#> title: Modifying a 'cff' object
#> authors:
#> - family-names: Doe
#> given-names: John
#> - family-names: Sánchez Fernández
#> given-names: Gregorio
#> email: fake@email2.com
#> alias: Chiquito de la Calzada
#> city: Malaga
#> country: ES
#> orcid: https://orcid.org/0000-0000-0000-0001
#> url: https://ropensci.org/
#> version: 0.0.1
#> repository: https://github.com/ropensci/cffr
#> references:
#> - type: manual
#> title: 'R: A Language and Environment for Statistical Computing'
#> authors:
#> - name: R Core Team
#> institution:
#> name: R Foundation for Statistical Computing
#> address: Vienna, Austria
#> year: '2024'
#> url: https://www.R-project.org/
#> - type: book
#> title: This is a book
#> authors:
#> - family-names: Lee
#> given-names: Lisa
#> year: '1980'
#> publisher:
#> name: McGraw Hill
#> volume: '2'
cff_validate(finalobject)
#> ══ Validating cff ══════════════════════════════════════════════════════════════
#> ✔ Congratulations! This <cff> is validCITATION.cff fileThe results can be written with cff_write():
# For example
tmp <- tempfile(fileext = ".cff")
see_res <- cff_write(finalobject, outfile = tmp)
#> ✔ 'C:\Users\diego\AppData\Local\Temp\RtmpygP3mt\file1ed84bba7528.cff' generated
#> ══ Validating cff ══════════════════════════════════════════════════════════════
#> ✔ Congratulations! 'C:\Users\diego\AppData\Local\Temp\RtmpygP3mt\file1ed84bba7528.cff' is valid
cat(readLines(tmp), sep = "\n")
#> # --------------------------------------------
#> # CITATION file created with {cffr} R package
#> # See also: https://docs.ropensci.org/cffr/
#> # --------------------------------------------
#>
#> cff-version: 1.2.0
#> message: If you use this software, please cite it using these metadata.
#> title: Modifying a 'cff' object
#> version: 0.0.1
#> authors:
#> - family-names: Doe
#> given-names: John
#> - family-names: Sánchez Fernández
#> given-names: Gregorio
#> email: fake@email2.com
#> alias: Chiquito de la Calzada
#> city: Malaga
#> country: ES
#> orcid: https://orcid.org/0000-0000-0000-0001
#> repository: https://github.com/ropensci/cffr
#> url: https://ropensci.org/
#> references:
#> - type: manual
#> title: 'R: A Language and Environment for Statistical Computing'
#> authors:
#> - name: R Core Team
#> institution:
#> name: R Foundation for Statistical Computing
#> address: Vienna, Austria
#> year: '2024'
#> url: https://www.R-project.org/
#> - type: book
#> title: This is a book
#> authors:
#> - family-names: Lee
#> given-names: Lisa
#> year: '1980'
#> publisher:
#> name: McGraw Hill
#> volume: '2'And finally we can read our created CITATION.cff file
using cff_read():
reading <- cff_read(tmp)
reading
#> cff-version: 1.2.0
#> message: If you use this software, please cite it using these metadata.
#> title: Modifying a 'cff' object
#> version: 0.0.1
#> authors:
#> - family-names: Doe
#> given-names: John
#> - family-names: Sánchez Fernández
#> given-names: Gregorio
#> email: fake@email2.com
#> alias: Chiquito de la Calzada
#> city: Malaga
#> country: ES
#> orcid: https://orcid.org/0000-0000-0000-0001
#> repository: https://github.com/ropensci/cffr
#> url: https://ropensci.org/
#> references:
#> - type: manual
#> title: 'R: A Language and Environment for Statistical Computing'
#> authors:
#> - name: R Core Team
#> institution:
#> name: R Foundation for Statistical Computing
#> address: Vienna, Austria
#> year: '2024'
#> url: https://www.R-project.org/
#> - type: book
#> title: This is a book
#> authors:
#> - family-names: Lee
#> given-names: Lisa
#> year: '1980'
#> publisher:
#> name: McGraw Hill
#> volume: '2'Note that cff_write() also has the keys
param, so the workflow can be simplified as:
allkeys <- list(
"url" = "https://ropensci.org/",
"version" = "0.0.1",
"repository" = "https://github.com/ropensci/cffr",
# If the field is already present, it would be overridden
title = "Modifying a 'cff' object",
authors = newauthors,
references = refs_cff
)
tmp2 <- tempfile(fileext = ".cff")
res <- cff_write(cff(), outfile = tmp2, keys = allkeys)
#> ✔ 'C:\Users\diego\AppData\Local\Temp\RtmpygP3mt\file1ed87e2f2e2.cff' generated
#> ══ Validating cff ══════════════════════════════════════════════════════════════
#> ✔ Congratulations! 'C:\Users\diego\AppData\Local\Temp\RtmpygP3mt\file1ed87e2f2e2.cff' is valid
res
#> cff-version: 1.2.0
#> message: If you use this software, please cite it using these metadata.
#> title: Modifying a 'cff' object
#> version: 0.0.1
#> authors:
#> - family-names: Doe
#> given-names: John
#> - family-names: Sánchez Fernández
#> given-names: Gregorio
#> email: fake@email2.com
#> alias: Chiquito de la Calzada
#> city: Malaga
#> country: ES
#> orcid: https://orcid.org/0000-0000-0000-0001
#> repository: https://github.com/ropensci/cffr
#> url: https://ropensci.org/
#> references:
#> - type: manual
#> title: 'R: A Language and Environment for Statistical Computing'
#> authors:
#> - name: R Core Team
#> institution:
#> name: R Foundation for Statistical Computing
#> address: Vienna, Austria
#> year: '2024'
#> url: https://www.R-project.org/
#> - type: book
#> title: This is a book
#> authors:
#> - family-names: Lee
#> given-names: Lisa
#> year: '1980'
#> publisher:
#> name: McGraw Hill
#> volume: '2'