mregions2: Access Data from Marineregions.org: The Marine Regions Gazetteer and the Marine Regions Data Products

[salvafern]

Date accepted: 2024-06-09

Submitting Author Name: Salvador Fernández Bejarano Submitting Author Github Handle: !--author1-->@salvafern<!--end-author1-- Other Package Authors Github handles: (comma separated, delete if none) !--author-others-->@lottepohl<!--end-author-others-- Repository: https://github.com/lifewatch/mregions2 Version submitted: Submission type: Standard Editor: !--editor-->@jooolia<!--end-editor-- Reviewers: @Kattuvan, @sheilasaia

Due date for @Kattuvan: 2023-06-20 Due date for @sheilasaia: 2023-06-21

Archive: TBD Version accepted: TBD Language: en

---

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

Package: mregions2
Type: Package
Title: Access Data from Marineregions.org: The Marine Regions Gazetteer and the Marine Regions Data Products
Version: 1.0.0
Authors@R: c(
  person(given = "Salvador", family = "Fernandez-Bejarano", role = c("aut", "cre"),
         email = "salvador.fernandez@vliz.be",
         comment = c(ORCID = "0000-0003-0535-7677", github = "salvafern")),
  person(given = "Lotte",family = "Pohl", role = "aut",
         email = "lotte.pohl@imbrsea.eu",
         comment = c(ORCID = "0000-0002-7607-7018", github = "whaleshark99")),
  person("LifeWatch Belgium", role = "fnd", comment = "https://lifewatch.be")
  )
Maintainer: Salvador Fernandez-Bejarano <salvador.fernandez@vliz.be>
Description: Explore and retrieve marine geo-spatial data from the Marine Regions Gazetteer and the Marine Regions Data Products, including the Maritime Boundaries.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Config/testthat/edition: 3
Imports: 
    checkmate,
    glue,
    httr2,
    magrittr,
    sf,
    utils,
    rdflib,
    ISOcodes,
    memoise,
    cli,
    dplyr,
    xml2,
    wrapr,
    methods,
    curl,
    digest
RoxygenNote: 7.2.0
URL: https://github.com/lifewatch/mregions2,
    https://lifewatch.github.io/mregions2/
BugReports: https://github.com/lifewatch/mregions2/issues
Suggests: 
    ows4R (>= 0.3),
    httptest2,
    jsonlite,
    knitr,
    leaflet,
    leaflet.extras2,
    mapview,
    mregions,
    rmarkdown,
    testthat,
    wk,
    purrr,
    withr
VignetteBuilder: knitr
Roxygen: list(markdown = TRUE)
Depends: 
    R (>= 2.10)

Scope

• 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.):
  • [x] 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
  • [x] geospatial data
  • [ ] text analysis
• Explain how and why the package falls under these categories (briefly, 1-2 sentences):

This package reads the Marine Regions Gazetteer and the Marine Regions Data Products via a REST API and OGC web services respectively. The data is mostly geospatial as it contains locations of marine places in the world.

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

The main purpose of Marine Regions is to serve as the geographical backbone of biodiversity databases such as WoRMS or EurOBIS, hence the main user will be scientists that want to geo-reference their research. But it can also be useful for industry, policy and law makers.

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

There is already a package to read Marine Regions. The need for this second package is explained in one of the package's articles: Why mregions2? . It was also discussed beforehand that a new package was the best approach: https://github.com/ropensci/mregions/pull/62 (Mostly to not break compatibility)

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

In general I think this does not apply. The only data being collected from users is the user-agent in all HTTP requests. This gets the environment variable HTTPUserAgent via getOption() in mr_user_agent

On the other hand, Marine Regions has sensitive data products such as the maritime boundaries. It is stated clearly on our disclaimer that the data has no legal value whatsoever.

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

Technical checks

Confirm each of the following by checking the box.

• [x] I have read the rOpenSci packaging guide.
• [x] 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:

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

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

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

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Code of conduct

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

[salvafern]

Hi @jooolia, apologies for the delay. The logs are fresh now: https://github.com/lifewatch/mregions2/actions/runs/8615096758/job/23609894330

I think the same issue continues: See https://github.com/lifewatch/mregions2/issues/21 and https://github.com/ropensci/rdflib/issues/47

Any ideas are highly appreciated!

[jooolia]

Thanks @salvafern for the reruns. I will have a look and get back to you (and it seems that rdflib has commented out the ubuntu tests for now). thanks, Julia

[jooolia]

Hi @salvafern , I have forked mregions2 and will look into the github actions tomorrow. thanks for your patience.

[salvafern]

That's great, thank you!

[jooolia]

Hi @salvafern, I have gotten R-CMD-check to run without errors, although it is a bit of a workaround at the moment. I will look into the yaml files tonight and update you then (or if all goes well submit a pull request) with what has worked and what we could imagine doing. Cheers, Julia

[jooolia]

Hi @salvafern I have opened a PR in the repo to your dev branch. Let me know what you think. I had to remove pkgcheck, but all three others I was able to get to work and pass. Cheers, Julia

[salvafern]

Hi @jooolia , I have merge your PR to the main branch. Seems to work fine now. Thanks a lot! Let me know what are the next steps.

[jooolia]

@ropensci-review-bot approve mregions2

[ropensci-review-bot]

Approved! Thanks @salvafern for submitting and @Kattuvan, @sheilasaia for your reviews! :grin:

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[salvafern]

@ropensci-review-bot invite me to ropensci/mregions2

[ropensci-review-bot]

Invitation sent!

[salvafern]

@ropensci-review-bot finalize transfer of mregions2

[ropensci-review-bot]

Transfer completed. The mregions2 team is now owner of the repository and the author has been invited to the team