Manipulating citations with cffr

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

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 increasingly used in the software citation ecosystem. GitHub, Zenodo and Zotero support 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:

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

Modifying your CITATION.cff file

You can customize a cff object (a custom cffr S3 class) using the coercion system provided in the package and the keys argument.

For demonstration, we create a cff object using cff() and then add or modify its contents.

Adding new keys

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 from 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 by passing 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 key 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) to objects that follow 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 = "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> (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: 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 ══════════════════════════════════════════════════════════════
#> ✔ This <cff> is valid.

Next, we 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'

The process is similar to the example with person: we 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
#>     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 result can be written with cff_write():

# Create a temporary output file.
tmp <- tempfile(fileext = ".cff")

see_res <- cff_write(finalobject, outfile = tmp)
#> ✔ 'C:\Users\diego\AppData\Local\Temp\Rtmpq8KzkA\file428039fa2f9f.cff' generated.
#> ══ Validating cff ══════════════════════════════════════════════════════════════
#> ✔ 'C:\Users\diego\AppData\Local\Temp\Rtmpq8KzkA\file428039fa2f9f.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
#>     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: 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
#>     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 key 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)
#> ✔ 'C:\Users\diego\AppData\Local\Temp\Rtmpq8KzkA\file428067ef3dd4.cff' generated.
#> ══ Validating cff ══════════════════════════════════════════════════════════════
#> ✔ 'C:\Users\diego\AppData\Local\Temp\Rtmpq8KzkA\file428067ef3dd4.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
#>     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.