# Manipulating Citations with cffr

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:

- 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) 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.

## Creating a `CITATION.cff` file for my R package

With cffr creating a `CITATION.cff` file is quite straightforward. You just need to run `cff_write()`:

    library(cffr)

    cff_write()

    # You are done!

Under the hood, `cff_write()` performs the following tasks:

- It extracts the metadata using `cff_create()`.
- Optionally modifies it with `cff_modify()`.
- Writes a `CITATION.cff` file.
- Validates the result using `cff_validate()`.

Congratulations! Now you have a full `CITATION.cff` file for your R package.

## Modifying your `CITATION.cff` file

You 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.

### 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"                 "abstract"            "authors"
    #> [10] "preferred-citation"  "repository"          "repository-artifact"
    #> [13] "repository-code"     "url"                 "date-released"
    #> [16] "contact"             "keywords"            "references"
    #> [19] "commit"              "identifiers"         "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 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 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 valid

Now, 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 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/RtmpVJ2GjP/file2413808ea79.cff' generated
    #> ══ Validating cff ══════════════════════════════════════════════════════════════
    #> ✔ Congratulations! '/tmp/RtmpVJ2GjP/file2413808ea79.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)
    #> ✔ '/tmp/RtmpVJ2GjP/file2418293504.cff' generated
    #> ══ Validating cff ══════════════════════════════════════════════════════════════
    #> ✔ Congratulations! '/tmp/RtmpVJ2GjP/file2418293504.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'

## References

Druskat, Stephan. 2021. “Making Software Citation Easi(er) - The Citation File Format and Its Integrations.” https://doi.org/10.5281/zenodo.5529914.
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.