Manipulating citations with cffr

cffr is designed for R package developers. The main goal of cffr is to create a CITATION.cff file using metadata from the following files:

  • Your DESCRIPTION file.
  • If available, the citation information located in inst/CITATION.

What is a CITATION.cff file?

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

This format is gaining popularity within the software citation ecosystem. GitHub, Zenodo and Zotero have fully supported this citation format (Druskat 2021).

GitHub support is of special interest:

GitHub citation support announcement
Nat Friedman (@natfriedman) July 27, 2021

See GitHub’s guide to CITATION files for more information.

Creating a CITATION.cff file for your R package

Creating a CITATION.cff file with cffr is straightforward. You only need to run cff_write():

library(cffr)

cff_write()

# Done.

Under the hood, cff_write() performs these tasks:

  • Extracts the metadata using cff_create().
  • Optionally modifies it with cff_modify().
  • Writes a CITATION.cff file.
  • Validates the result using cff_validate().

You now have a complete CITATION.cff file for your R package.

Modifying your CITATION.cff file

You can customize the cff object (a custom cffr class) using the coercion system provided in the package, as well as the keys argument.

We create a cff object using cff() (for demonstration only) and then add or modify its contents.

Adding new fields

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: John

The 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 add url, version and repository. We also overwrite the title key. We add these arguments 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 is 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 ══════════════════════════════════════════════════════════════
#> ✔ This <cff> is valid.

Persons and references

cffr 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 first add a new author. To do that, we need 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 = "[email protected]",
  comment = c(
    alias = "Chiquito de la Calzada",
    city = "Malaga",
    country = "ES",
    ORCID = "0000-0000-0000-0001"
  )
)

chiquito
#> [1] "Gregorio Sánchez Fernández <[email protected]> (alias: Chiquito de la Calzada, city: Malaga, country: ES, ORCID: <https://orcid.org/0000-0000-0000-0001>)"

# Convert to `cff`.
chiquito_cff <- as_cff_person(chiquito)
chiquito_cff
#> - family-names: Sánchez Fernández
#>   given-names: Gregorio
#>   email: [email protected]
#>   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: [email protected]
#>   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: [email protected]
#>   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 ══════════════════════════════════════════════════════════════
#> ✔ This <cff> is valid.

Now, we may want to add references to our data. In the following example, we 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"

# Automatic 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 (2026). _R: A Language and Environment for Statistical
#> Computing_. R Foundation for Statistical Computing, Vienna, Austria.
#> doi:10.32614/R.manuals <https://doi.org/10.32614/R.manuals>.
#> <https://www.R-project.org/>.
#> 
#> Lee L (1980). _This is a book_, volume 2. McGraw Hill.

# Convert 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
#>     website: https://ror.org/02zz1nj61
#>   institution:
#>     name: R Foundation for Statistical Computing
#>     website: https://ror.org/05qewa988
#>     address: Vienna, Austria
#>   year: '2026'
#>   doi: 10.32614/R.manuals
#>   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: [email protected]
#>   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
#>     website: https://ror.org/02zz1nj61
#>   institution:
#>     name: R Foundation for Statistical Computing
#>     website: https://ror.org/05qewa988
#>     address: Vienna, Austria
#>   year: '2026'
#>   doi: 10.32614/R.manuals
#>   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 ══════════════════════════════════════════════════════════════
#> ✔ This <cff> is valid.

Create your modified CITATION.cff file

The results can be written with cff_write():

# For example.
tmp <- tempfile(fileext = ".cff")

see_res <- cff_write(finalobject, outfile = tmp)
#> ✔ '/tmp/RtmpkD6Zyg/filed507d59723b.cff' generated.
#> ══ Validating cff ══════════════════════════════════════════════════════════════
#> ✔ '/tmp/RtmpkD6Zyg/filed507d59723b.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: [email protected]
#>   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
#>     website: https://ror.org/02zz1nj61
#>   institution:
#>     name: R Foundation for Statistical Computing
#>     website: https://ror.org/05qewa988
#>     address: Vienna, Austria
#>   year: '2026'
#>   doi: 10.32614/R.manuals
#>   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'

Finally, we can read the 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: [email protected]
#>   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
#>     website: https://ror.org/02zz1nj61
#>   institution:
#>     name: R Foundation for Statistical Computing
#>     website: https://ror.org/05qewa988
#>     address: Vienna, Austria
#>   year: '2026'
#>   doi: 10.32614/R.manuals
#>   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 argument, 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 is overridden.
  title = "Modifying a 'cff' object",
  authors = newauthors,
  references = refs_cff
)

tmp2 <- tempfile(fileext = ".cff")

res <- cff_write(cff(), outfile = tmp2, keys = allkeys)
#> ✔ '/tmp/RtmpkD6Zyg/filed5045723898.cff' generated.
#> ══ Validating cff ══════════════════════════════════════════════════════════════
#> ✔ '/tmp/RtmpkD6Zyg/filed5045723898.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: [email protected]
#>   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
#>     website: https://ror.org/02zz1nj61
#>   institution:
#>     name: R Foundation for Statistical Computing
#>     website: https://ror.org/05qewa988
#>     address: Vienna, Austria
#>   year: '2026'
#>   doi: 10.32614/R.manuals
#>   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'

References

Druskat, Stephan. 2021. Making Software Citation Easi(er) - The Citation File Format and Its Integrations. Version 1. https://doi.org/10.5281/zenodo.5529914.
Druskat, Stephan, Jurriaan H. Spaaks, Neil Chue Hong, et al. 2021. Citation File Format. https://doi.org/10.5281/zenodo.5171937.