---
title: "From R to CFF"
subtitle: "Crosswalk"
description: >
  A comprehensive description of the internal mappings performed by
  the cffr package.
author: Diego Hernangómez
bibliography: REFERENCES.bib
link-citations: true
toc: true
vignette: >
  %\VignetteIndexEntry{From R to CFF}
  %\VignetteEngine{quarto::html}
  %\VignetteEncoding{UTF-8}
tbl-cap-location: bottom
knitr:
  opts_chunk:
    collapse: true
    comment: "#>"
    code-fold: true
    code-summary: "**Example**"
---

```{r}
#| include: false
library(cffr)
```

The goal of this vignette is to provide an explicit map between the metadata
fields used by **cffr** and each valid key in the [Citation File Format schema
version
1.2.0](https://github.com/citation-file-format/citation-file-format/blob/main/schema-guide.md#valid-keys).

## Summary {#summary}

We summarize here the fields that **cffr** can coerce and the original source of
information for each of them. The details for each key are presented in the next
section of the document. The assessment of fields is based on the [Guide to
Citation File Format schema version
1.2.0](https://github.com/citation-file-format/citation-file-format/blob/main/schema-guide.md#valid-keys)
[@druskat_citation_2021].

```{r}
#| label: tbl-summary
#| echo: false
#| tbl-cap: "cffr and R packages: Conversion table"
keys <- cff_schema_keys(sorted = TRUE)
origin <- vector(length = length(keys))
origin[keys == "cff-version"] <- "argument on function"
origin[keys == "type"] <- "Fixed value: 'software'"
origin[keys == "identifiers"] <- "DESCRIPTION/CITATION files"
origin[keys == "references"] <- "DESCRIPTION/CITATION files"

origin[
  keys %in%
    c(
      "message",
      "title",
      "version",
      "authors",
      "abstract",
      "repository",
      "repository-code",
      "url",
      "date-released",
      "contact",
      "keywords",
      "license",
      "commit"
    )
] <- "DESCRIPTION file"

origin[
  keys %in%
    c(
      "doi",
      "preferred-citation"
    )
] <- "CITATION file"

origin[origin == "FALSE"] <- "Ignored by cffr"

df <- data.frame(
  key = paste0("<a href='#", keys, "'>", keys, "</a>"),
  source = origin
)

knitr::kable(df, escape = FALSE)
```

## Details

### abstract

This key is extracted from the `"Description"` field of the `DESCRIPTION` file.

```{r}
#| label: abstract
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)

cat(pkg$get("Description"))
```

Back to @tbl-summary.

### authors

This key is coerced from the `"Authors"` or `"Authors@R"` field of the
`DESCRIPTION` file. By default, persons with the role `"aut"` or `"cre"` are
considered, however this can be modified via the `authors_roles` argument.

```{r}
#| label: authors
# An example DESCRIPTION
path <- system.file("examples/DESCRIPTION_many_persons", package = "cffr")
pkg <- desc::desc(path)

# See persons listed
pkg$get_authors()

# Default behaviour, use authors and creators (maintainers)
cff_obj <- cff_create(path)
cff_obj$authors

# Use now Copyright holders and maintainers
cff_obj_alt <- cff_create(path, authors_roles = c("cre", "cph"))
cff_obj_alt$authors
```

Back to @tbl-summary.

### cff-version

This key can be set via the arguments of the `cff_create()`/`cff_write()`
functions:

```{r}
#| label: cffversion
cff_objv110 <- cff_create("jsonlite", cff_version = "v1.1.0")

cat(cff_objv110$`cff-version`)
```

Back to @tbl-summary.

### commit

This key is extracted from the `"RemoteSha"` field of the `DESCRIPTION` file.
This is the case of packages installed using the
[r-universe](https://r-universe.dev/search) or packages such as **remotes** or
**pak**.

```{r}
#| label: commit
# An example DESCRIPTION
path <- system.file("examples/DESCRIPTION_r_universe", package = "cffr")
pkg <- desc::desc(path)

# See RemoteSha
pkg$get("RemoteSha")

cff_read(path)
```

Back to @tbl-summary.

### contact

This key is coerced from the `"Authors"` or `"Authors@R"` field of the
`DESCRIPTION` file. Only persons with the role `"cre"` (i.e., the maintainer(s))
are considered.

```{r}
#| label: contact
cff_obj <- cff_create("rmarkdown")
pkg <- desc::desc(file.path(find.package("rmarkdown"), "DESCRIPTION"))

cff_obj$contact

pkg$get_author()
```

Back to @tbl-summary.

### date-released

This key is extracted from the `DESCRIPTION` file following this logic:

- The `"Date"` field.
- If not present, `"Date/Publication"`. This field is present in packages built
  on **CRAN** and **Bioconductor**.
- If not present, `"Packaged"`, which is present in packages built by the
  [r-universe](https://r-universe.dev/search).

```{r}
#| label: date-released
# From an installed package

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

cat(pkg$get("Date/Publication"))

cat(cff_obj$`date-released`)

# 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)

pkgnodate <- desc::desc(tmp)
cffnodate <- cff_create(tmp)

# Won't appear
cat(cffnodate$`date-released`)

pkgnodate

# Adding a Date

desc::desc_set("Date", "1999-01-01", file = tmp)

cat(cff_create(tmp)$`date-released`)
```

Back to @tbl-summary.

### doi {#doi}

This key is coerced from the `"doi"` field of the
[preferred-citation](#preferred-citation) object. If not present and the package
is on **CRAN**, it is populated with the DOI provided by **CRAN** (e.g.
<https://doi.org/10.32614/CRAN.package.cffr>).

```{r}
#| label: doi
cff_doi <- cff_create("cffr")

cat(cff_doi$doi)

cat(cff_doi$`preferred-citation`$doi)
```

Back to @tbl-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](#url) or [repository-code](#repository-code).

- From the `CITATION` file, it includes all the DOIs not included in [doi](#doi)
  and the identifiers (if any) not included in the `"identifiers"` key of
  [preferred-citation](#preferred-citation).

- If the package is on **CRAN** and it has a `CITATION` file providing a doi,
  the doi provided by **CRAN** is added as well.

```{r}
#| label: identifiers
file <- system.file("examples/DESCRIPTION_many_urls", package = "cffr")

pkg <- desc::desc(file)

cat(pkg$get_urls())

cat(cff_create(file)$url)

cat(cff_create(file)$`repository-code`)

cff_create(file)$identifiers
```

Back to @tbl-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
```

```{r}
#| label: keyword
# A DESCRIPTION file without keywords
nokeywords <- system.file("examples/DESCRIPTION_basic", package = "cffr")
tmp2 <- tempfile("DESCRIPTION")

# Create a temporary file
file.copy(nokeywords, tmp2)

pkgnokeywords <- desc::desc(tmp2)
cffnokeywords <- cff_create(tmp2)

# Won't appear
cat(cffnokeywords$keywords)

pkgnokeywords

# Adding Keywords

desc::desc_set(
  "X-schema.org-keywords",
  "keyword1, keyword2, keyword3",
  file = tmp2
)

cat(cff_create(tmp2)$keywords)
```

Additionally, if the source code of the package is hosted on GitHub, **cffr**
can retrieve the topics of the repository via the [GitHub
API](https://docs.github.com/en/rest) and include those topics as keywords. This
option is controlled via the `gh_keywords` argument:

```{r}
#| label: ghkeyword
# Get cff object from jsonvalidate

jsonval <- cff_create("jsonvalidate")

# Keywords are retrieved from the GitHub repo

jsonval

# Check keywords
jsonval$keywords

# The repo
jsonval$`repository-code`
```

Back to @tbl-summary.

### license

This key is extracted from the `"License"` field of the `DESCRIPTION` file.

```{r}
#| label: license
cff_obj <- cff_create("yaml")

cat(cff_obj$license)

pkg <- desc::desc(file.path(find.package("yaml"), "DESCRIPTION"))

cat(pkg$get("License"))
```

Back to @tbl-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](https://github.com/citation-file-format/citation-file-format/blob/main/schema-guide.md#license-url).

> - **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](https://github.com/citation-file-format/citation-file-format/blob/main/schema-guide.md#definitionslicense-enum)).
>
> - **usage**:
>
>   ``` yaml
>   license-url: "https://obscure-licenses.com?id=1234"
>   ```

Back to @tbl-summary.

### message

This key is extracted from the `DESCRIPTION` field, specifically as:

```{r}
#| eval: false
#| code-fold: false
msg <- paste0(
  'To cite package "',
  "NAME_OF_THE_PACKAGE",
  '" in publications use:'
)
```

```{r}
#| label: message
cat(cff_create("jsonlite")$message)
```

Back to @tbl-summary.

### preferred-citation {#preferred-citation}

This key is extracted from the `CITATION` file. If several references are
provided, it selects the first citation as the `"preferred-citation"` and the
rest of them as [references](#references).

```{r}
#| label: preferred-citation
cffobj <- cff_create("rmarkdown")

cffobj$`preferred-citation`

citation("rmarkdown")[1]
```

Back to @tbl-summary.

### references {#references}

This key is extracted from the `CITATION` file if several references are
provided. The first citation is considered as the
[preferred-citation](#preferred-citation) and the rest of them as
`"references"`. It also extracts package dependencies and adds them to this
field using `citation(auto = TRUE)` on each dependency.

```{r}
#| label: references
cffobj <- cff_create("rmarkdown")

cffobj$references

citation("rmarkdown")[-1]
```

Back to @tbl-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 repository
(like **CRAN** or the [r-universe](https://r-universe.dev/search)). For packages
without this field on the `DESCRIPTION` (which is the typical case for an
in-development package), **cffr** tries to search the package on any of the
default repositories specified on `options("repos")`.

In the case of [Bioconductor](https://bioconductor.org/) packages, those are
identified if a
["biocViews"](https://contributions.bioconductor.org/description.html#biocviews)
is present on the `DESCRIPTION` file.

If **cffr** detects that the package is available on **CRAN**, it returns the
canonical URL form of the package (i.e.
<https://CRAN.R-project.org/package=jsonlite>).

```{r}
#| label: repository
# Installed package

inst <- cff_create("jsonlite")

cat(inst$repository)

# 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)

desc::desc(runiv)$get("Repository")

# 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)

# Change name
desc::desc_set("Package", "ggplot2", file = tmp)

cat(cff_create(tmp)[["repository"]])
```

Back to @tbl-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](https://github.com/citation-file-format/citation-file-format/blob/main/schema-guide.md#repository-artifact).

> - **description**: The URL of the work in a build artifact/binary repository
>   (when the work is software).
>
> - **usage**:
>
>   ``` yaml
>   repository-artifact: "https://search.maven.org/artifact/org.corpus-tools/cff-maven-plugin/0.4.0/maven-plugin"
>   ```

Back to @tbl-summary.

### repository-code {#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](https://github.com/).
- [GitLab](https://about.gitlab.com/).
- [R-Forge](https://r-forge.r-project.org/).
- [Bitbucket](https://bitbucket.org/).
- [Codeberg](https://codeberg.org/).

```{r}
#| label: repository-code
# Installed package on GitHub

cat(cff_create("jsonlite")$`repository-code`)

# GitLab

gitlab <- system.file("examples/DESCRIPTION_gitlab", package = "cffr")

cat(cff_create(gitlab)$`repository-code`)

# Codeberg
codeberg <- system.file("examples/DESCRIPTION_codeberg", package = "cffr")

cat(cff_create(codeberg)$`repository-code`)
```

Back to @tbl-summary.

### title

This key is extracted from the `"Description"` field of the `DESCRIPTION` file.

```{r}
#| eval: false
#| code-fold: false
title <- paste0("NAME_OF_THE_PACKAGE", ": ", "TITLE_OF_THE_PACKAGE")
```

```{r}
#| label: title
# Installed package

cat(cff_create("testthat")$title)
```

Back to @tbl-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](https://github.com/citation-file-format/citation-file-format/blob/main/schema-guide.md#type).

Back to @tbl-summary.

### url {#url}

This key is extracted from the `"BugReports"` or `"URL"` fields on the
`DESCRIPTION` file. It corresponds to the first URL that is different from
[repository-code](#repository-code).

```{r}
#| label: url
# Many urls
manyurls <- system.file("examples/DESCRIPTION_many_urls", package = "cffr")

cat(cff_create(manyurls)$url)

# Check

desc::desc(manyurls)
```

Back to @tbl-summary.

### version

This key is extracted from the `"Version"` field on the `DESCRIPTION` file.

```{r}
#| label: version
#| code-fold: false
# Should be (>= 3.0.0)
cat(cff_create("testthat")$version)
```

Back to @tbl-summary.

## References
