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An R client to access the FORCIS database · Issue #660 · ropensci/software-review · GitHub

Date accepted: 2025-05-13

Submitting Author Name: Nicolas Casajus
Submitting Author Github Handle: @ahasverus
Other Package Authors Github handles: (comma separated, delete if none) @MatGreco90, @ChaabaneS, @xgiraud
Repository: https://github.com/frbcesab/forcis
Version submitted: 0.1.0
Submission type: Standard
Editor: @beatrizmilz
Reviewers: @sckott, @heyairf

Archive: TBD
Version accepted: TBD
Language: en

• Paste the full DESCRIPTION file inside a code block below:

Package: forcis
Type: Package
Title: An R Client to Access the FORCIS Database
Version: 0.1.0
Authors@R: c(
    person(given   = "Nicolas",
           family  = "Casajus",
           role    = c("aut", "cre", "cph"),
           email   = "nicolas.casajus@fondationbiodiversite.fr",
           comment = c(ORCID = "0000-0002-5537-5294")),
    person(given   = "Mattia",
           family  = "Greco",
           role    = "aut",
           email   = "mattia_greco@outlook.com",
           comment = c(ORCID = "0000-0003-2416-6235")),
    person(given   = "Sonia",
           family  = "Chaabane",
           role    = "aut",
           email   = "sonia.chaabane@gmail.com",
           comment = c(ORCID = "0000-0002-4653-8610")),
    person(given   = "Xavier",
           family  = "Giraud",
           role    = "aut",
           email   = "giraud@cerege.fr",
           comment = c(ORCID = "0000-0001-5067-8176")),
    person(given   = "Thibault",
           family  = "de Garidel-Thoron",
           role    = "aut",
           email   = "garidel@cerege.fr",
           comment = c(ORCID = "0000-0001-8983-9571")),
    person(given   = "Khalil",
           family  = "Hammami",
           role    = "ctb",
           email   = "khalil.hammami@enetcom.usf.tn"))
Description: Provides an interface to the FORCIS database 
    (<https://zenodo.org/doi/10.5281/zenodo.7390791>) on global foraminifera
    distribution. This package allows to download and to handle FORCIS data.
    It is part of the FRB-CESAB working group FORCIS.
    <https://www.fondationbiodiversite.fr/en/the-frb-in-action/programs-and-projects/le-cesab/forcis/>.
URL: https://frbcesab.github.io/forcis
BugReports: https://github.com/FRBCesab/forcis/issues
License: GPL (>= 2)
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
VignetteBuilder: knitr
Depends: 
    R (>= 2.10)
Imports: 
    dplyr,
    ggplot2,
    jsonlite,
    rlang,
    sf,
    tidyr,
    utils,
    vroom
Suggests: 
    fs,
    knitr,
    rmarkdown,
    testthat (>= 3.0.0),
    withr
Config/testthat/edition: 3

• Please indicate which category or categories from our package fit policies this package falls under: (Please check an appropriate box below. If you are unsure, we suggest you make a pre-submission inquiry.):

  • data retrieval
  • data extraction
  • data munging
  • data deposition
  • data validation and testing
  • workflow automation
  • version control
  • citation management and bibliometrics
  • scientific software wrappers
  • field and lab reproducibility tools
  • database software bindings
  • geospatial data
  • text analysis

• Explain how and why the package falls under these categories (briefly, 1-2 sentences):

This package is designed to download the FORCIS data files hosted on Zenodo. It includes functions to download (data retrieval), select, filter, reshape, and visualize data (data munging).

• Who is the target audience and what are scientific applications of this package?

This package should be of interest to scientists working on Foraminifera species distribution and interested in the FORCIS database (spatial analyses, time series analyses, etc.). The package have been developed to facilitate the data wrangling to avoid some pitfalls and to easily get data ready to be analyzed/visualized.

• Are there other R packages that accomplish the same thing? If so, how does yours differ or meet our criteria for best-in-category?

No other package exists to handle the FORCIS database. Note that we are authors of the database and already published a Data paper describing the database.

• (If applicable) Does your package comply with our guidance around Ethics, Data Privacy and Human Subjects Research?

Not applicable.

• If you made a pre-submission inquiry, please paste the link to the corresponding issue, forum post, or other discussion, or @tag the editor you contacted.

Pre-submission inquiry: #655
Editor: @adamhsparks

• Explain reasons for any pkgcheck items which your package is unable to pass.

The function pkgcheck::pkgcheck() returns the following report:

── forcis 0.1.0 ────────────────────────────────────────────

✔ Package name is available
✔ has a 'codemeta.json' file.
✔ has a 'contributing' file.
✔ uses 'roxygen2'.
✔ 'DESCRIPTION' has a URL field.
✔ 'DESCRIPTION' has a BugReports field.
✔ Package has at least one HTML vignette
✔ All functions have examples.
✔ Package has continuous integration checks.
✔ Package coverage is 97.4%.
✔ R CMD check found no errors.
✔ R CMD check found no warnings.

ℹ Current status:
✔ This package may be submitted.

The package goodpractice returns warnings:

• Write unit tests: some functions are difficult to test (HTTP requests)
• Avoid calling setwd(): this function is used in unit tests in combination with withr::defer()

Confirm each of the following by checking the box.

• I have read the rOpenSci packaging guide.
• I have read the author guide and I expect to maintain this package for at least 2 years or to find a replacement.

This package:

• does not violate the Terms of Service of any service it interacts with.
• has a CRAN and OSI accepted license.
• contains a README with instructions for installing the development version.
• includes documentation with examples for all functions, created with roxygen2.
• contains a vignette with examples of its essential functions and uses.
• has a test suite.
• has continuous integration, including reporting of test coverage.

• Do you intend for this package to go on CRAN?

• Do you intend for this package to go on Bioconductor?

• Do you wish to submit an Applications Article about your package to Methods in Ecology and Evolution? If so:

• The package is novel and will be of interest to the broad readership of the journal.
• The manuscript describing the package is no longer than 3000 words.
• You intend to archive the code for the package in a long-term repository which meets the requirements of the journal (see MEE's Policy on Publishing Code)
• (Scope: Do consider MEE's Aims and Scope for your manuscript. We make no guarantee that your manuscript will be within MEE scope.)
• (Although not required, we strongly recommend having a full manuscript prepared when you submit here.)
• (Please do not submit your package separately to Methods in Ecology and Evolution)

• I agree to abide by rOpenSci's Code of Conduct during the review process and in maintaining my package should it be accepted.

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