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: @salvafern
Other Package Authors Github handles: (comma separated, delete if none) @lottepohl
Repository: https://github.com/lifewatch/mregions2
Version submitted:
Submission type: Standard
Editor: @jooolia
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 = "[email protected]",
         comment = c(ORCID = "0000-0003-0535-7677", github = "salvafern")),
  person(given = "Lotte",family = "Pohl", role = "aut",
         email = "[email protected]",
         comment = c(ORCID = "0000-0002-7607-7018", github = "whaleshark99")),
  person("LifeWatch Belgium", role = "fnd", comment = "https://lifewatch.be")
  )
Maintainer: Salvador Fernandez-Bejarano <[email protected]>
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.):
  • 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 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: ropensci-archive/mregions#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.

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

Technical checks

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.

Publication options

• 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:

MEE Options

• 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)

Code of conduct

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

[ropensci-review-bot]

Thanks for submitting to rOpenSci, our editors and @ropensci-review-bot will reply soon. Type @ropensci-review-bot help for help.

[ropensci-review-bot]

🚀

Editor check started

👋

[ropensci-review-bot]

Checks for mregions2 (v1.0.0)

git hash: 9ed0de6d

• ✔️ 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 91.5%.
• ✔️ R CMD check found no errors.
• ✔️ R CMD check found no warnings.

Package License: MIT + file LICENSE

---

1. Package Dependencies

Details of Package Dependency Usage (click to open)

The table below tallies all function calls to all packages ('ncalls'), both internal (r-base + recommended, along with the package itself), and external (imported and suggested packages). 'NA' values indicate packages to which no identified calls to R functions could be found. Note that these results are generated by an automated code-tagging system which may not be entirely accurate.

type	package	ncalls
internal	base	176
internal	mregions2	121
internal	stats	24
imports	magrittr	200
imports	httr2	51
imports	checkmate	45
imports	methods	19
imports	glue	18
imports	sf	14
imports	cli	7
imports	memoise	5
imports	utils	3
imports	dplyr	3
imports	ISOcodes	2
imports	digest	2
imports	rdflib	1
imports	xml2	1
imports	wrapr	NA
imports	curl	NA
suggests	leaflet	10
suggests	ows4R	NA
suggests	httptest2	NA
suggests	jsonlite	NA
suggests	knitr	NA
suggests	leaflet.extras2	NA
suggests	mapview	NA
suggests	mregions	NA
suggests	rmarkdown	NA
suggests	testthat	NA
suggests	wk	NA
suggests	purrr	NA
suggests	withr	NA
linking_to	NA	NA

Click below for tallies of functions used in each package. Locations of each call within this package may be generated locally by running 's <- pkgstats::pkgstats(<path/to/repo>)', and examining the 'external_calls' table.

magrittr

%>% (200)

base

c (28), url (11), source (9), tolower (9), for (8), list (8), names (8), subset (8), all (7), as.character (7), unique (7), file.path (5), options (5), paste0 (5), data.frame (4), format (4), length (4), seq_along (4), gsub (3), if (3), version (3), class (2), dim (2), is.null (2), lapply (2), nrow (2), tempdir (2), as.integer (1), by (1), difftime (1), file.info (1), getOption (1), ifelse (1), is.na (1), readLines (1), rm (1), sort (1), substitute (1), Sys.getenv (1), unlist (1), with (1)

mregions2

mrp_view (14), is_error (11), marineregions.org (9), base_map (3), gaz_records_by_name_at (3), gaz_rest_sources (3), get_records_by_lat_long_at (3), get_records_by_type_at (3), get_source_at (3), gaz_rest_geometries (2), gaz_rest_record_by_mrgid (2), gaz_rest_records_by_lat_long (2), gaz_rest_records_by_names (2), gaz_rest_source_by_sourceid (2), gaz_rest_types (2), gaz_search.sfg (2), add_labels (1), assert_deps (1), assert_internet (1), assert_mrgid_exists (1), assert_only_one_filter (1), assert_placetype (1), assert_service (1), assert_typeid (1), c_rdf (1), cache_max_time (1), check_if_missing (1), check_server_warning (1), gaz_add_geometry (1), gaz_geometry (1), gaz_geometry.mr_df (1), gaz_geometry.numeric (1), gaz_relations (1), gaz_relations.mr_df (1), gaz_relations.numeric (1), gaz_rest_geometry (1), gaz_rest_names_by_mrgid (1), gaz_rest_records_by_name (1), gaz_rest_records_by_source (1), gaz_rest_records_by_type (1), gaz_rest_relations_by_mrgid (1), gaz_rest_wmses (1), gaz_search (1), gaz_search_by_source (1), gaz_search_by_source.character (1), gaz_search_by_source.numeric (1), gaz_search_by_type (1), gaz_search_by_type.character (1), gaz_search_by_type.numeric (1), gaz_search.character (1), gaz_search.numeric (1), gaz_search.sf (1), gaz_search.sfc (1), geom_perform (1), is_internet_down (1), is_test (1), mr_memoise (1), mrp_get (1), mrp_get_sanity_check (1), mrp_view_cds (1), mrp_view_eca_reg13_nox (1), mrp_view_eca_reg14_sox_pm (1), mrp_view_ecoregions (1), mrp_view_ecs (1), mrp_view_ecs_boundaries (1), mrp_view_eez (1), mrp_view_eez_12nm (1), mrp_view_eez_24nm (1), mrp_view_eez_archipelagic_waters (1), mrp_view_eez_boundaries (1), mrp_view_eez_iho (1)

httr2

req_headers (12), req_error (11), resp_check_status (8), resp_status (5), req_url_query (4), request (3), url_parse (3), url_build (2), resp_body_string (1), resp_is_error (1), resp_status_desc (1)

checkmate

assert_character (15), assert_integerish (15), assert_int (4), assert_logical (4), assert_numeric (3), assert_data_frame (2), assert_double (2)

stats

offset (18), filter (5), df (1)

methods

coerce (18), is (1)

glue

glue (18)

sf

st_read (3), st_as_sfc (2), st_bbox (2), st_crs (2), st_point (2), st_sfc (2), st_coordinates (1)

leaflet

tileOptions (3), leafletCRS (2), leafletOptions (2), addTiles (1), leaflet (1), WMSTileOptions (1)

cli

cli_abort (7)

memoise

memoise (5)

dplyr

right_join (2), bind_rows (1)

utils

unzip (3)

digest

digest (2)

ISOcodes

ISO_639_2$Alpha_2 (1), ISO_639_2$Name (1)

rdflib

rdf_serialize (1)

xml2

xml_attr (1)

NOTE: Some imported packages appear to have no associated function calls; please ensure with author that these 'Imports' are listed appropriately.

---

2. Statistical Properties

This package features some noteworthy statistical properties which may need to be clarified by a handling editor prior to progressing.

Details of statistical properties (click to open)

The package has:

• code in R (100% in 12 files) and
• 2 authors
• 3 vignettes
• 1 internal data file
• 16 imported packages
• 59 exported functions (median 3 lines of code)
• 123 non-exported functions in R (median 6 lines of code)

---

Statistical properties of package structure as distributional percentiles in relation to all current CRAN packages
The following terminology is used:

• loc = "Lines of Code"
• fn = "function"
• exp/not_exp = exported / not exported

All parameters are explained as tooltips in the locally-rendered HTML version of this report generated by the checks_to_markdown() function

The final measure (fn_call_network_size) is the total number of calls between functions (in R), or more abstract relationships between code objects in other languages. Values are flagged as "noteworthy" when they lie in the upper or lower 5th percentile.

measure	value	percentile	noteworthy
files_R	12	65.5
files_vignettes	3	92.4
files_tests	43	99.0
loc_R	1104	70.7
loc_vignettes	391	71.7
loc_tests	1807	93.2
num_vignettes	3	94.2
data_size_total	7328	69.2
data_size_median	7328	77.0
n_fns_r	182	88.4
n_fns_r_exported	59	90.2
n_fns_r_not_exported	123	87.4
n_fns_per_file_r	10	87.7
num_params_per_fn	2	11.9
loc_per_fn_r	5	8.1
loc_per_fn_r_exp	3	1.5	TRUE
loc_per_fn_r_not_exp	6	13.8
rel_whitespace_R	35	85.0
rel_whitespace_vignettes	55	86.2
rel_whitespace_tests	12	86.1
doclines_per_fn_exp	55	68.4
doclines_per_fn_not_exp	0	0.0	TRUE
fn_call_network_size	100	79.2

---

2a. Network visualisation

Click to see the interactive network visualisation of calls between objects in package

---

3. goodpractice and other checks

Details of goodpractice checks (click to open)

3a. Continuous Integration Badges

GitHub Workflow Results

id	name	conclusion	sha	run_number	date
4809625294	pages build and deployment	success	c80782	33	2023-04-26
4807668829	pkgcheck	success	9ed0de	82	2023-04-26
4809552258	pkgdown	success	9ed0de	49	2023-04-26
4807666863	R-CMD-check	success	9ed0de	31	2023-04-26
4807668826	R-CMD-check-schedule	success	9ed0de	122	2023-04-26
4807666847	test-coverage	success	9ed0de	30	2023-04-26

---

3b. goodpractice results

R CMD check with rcmdcheck

R CMD check generated the following note:

1. checking data for non-ASCII characters ... NOTE
   Note: found 1 marked UTF-8 string

R CMD check generated the following check_fail:

1. rcmdcheck_non_ascii_characters_in_data

Test coverage with covr

Package coverage: 91.54

Cyclocomplexity with cyclocomp

The following functions have cyclocomplexity >= 15:

function	cyclocomplexity
gaz_rest_records_by_name	19
gaz_add_geometry	15

Static code analyses with lintr

lintr found the following 403 potential issues:

message	number of times
Avoid library() and require() calls in packages	11
Lines should not be more than 80 characters.	392

---

Package Versions

package	version
pkgstats	0.1.3.4
pkgcheck	0.1.1.23

---

Editor-in-Chief Instructions:

This package is in top shape and may be passed on to a handling editor

[maurolepore]

Thanks @salvafern for this submission and for pointing to ropensci-archive/mregions#62.

How can we leave a record that the maintainer of mregions is OK with the decision of submitting mregions2? Maybe you can point me to an GH-issue comment?

[salvafern]

Hi @maurolepore, thanks for checking out! 🚀

I am actually the current maintainer of mregions (ropensci-archive/mregions@e5fb45b). Before me were @LennertSchepers and @sckott (ropensci-archive/mregions@dd7b6e4).

Since we had this public conversation on ropensci-archive/mregions#62, and also got the idea of a new package from @maelle (see ropensci-archive/mregions#62 (comment)), I think we are all on the same page about submitting mregions2. But if there is any objection from Lennert or Scott I'm happy to discuss of course 😃

[sckott]

No objection from me

[LennertSchepers]

No objection from me, @salvafern is in our team so we discussed the whole process in detail.

[LennertSchepers]

Worth noting if you need written approval: we are also the Marine Regions data system developers/maintainers/owners (see e.g. https://marineregions.org/editors.php)

[maurolepore]

Thanks @salvafern and everyone else for your support.
I'll stat searching for a handling editor.

[maelle]

@ropensci-review-bot assign @jooolia as editor

[ropensci-review-bot]

Assigned! @jooolia is now the editor

[jooolia]

Editor checks:

• Documentation: The package has sufficient documentation available online (README, pkgdown docs) to allow for an assessment of functionality and scope without installing the package. In particular,

  • Is the case for the package well made?
  • Is the reference index page clear (grouped by topic if necessary)?
  • Are vignettes readable, sufficiently detailed and not just perfunctory?

• Fit: The package meets criteria for fit and overlap.

• Installation instructions: Are installation instructions clear enough for human users?

• Tests: If the package has some interactivity / HTTP / plot production etc. are the tests using state-of-the-art tooling?

  • Yes httptest2

• Contributing information: Is the documentation for contribution clear enough e.g. tokens for tests, playgrounds?

  • .github/CONTRIBUTING.md exists, but only gives detail to email one of the authors and to abide by the Code of Conduct rules. I think this could be improved with resources contained here: https://devguide.ropensci.org/collaboration.html?q=contribu#contributing-guide

• License: The package has a CRAN or OSI accepted license.

• Project management: Are the issue and PR trackers in a good shape, e.g. are there outstanding bugs, is it clear when feature requests are meant to be tackled?
  Github action checks are kept open as issues, one for each branch.

---

Editor comments

Dear @salvafern and @whaleshark99,

Thanks for your submission. Overall the package is in great shape. The only thing that I would note would that it would be even better with more information on how to contribute to the package. Feel free to let me know if there is a reason that additional info should not be added. I will start looking for reviewers.

Cheers, Julia

---

[jooolia]

@ropensci-review-bot seeking reviewers

[ropensci-review-bot]

Please add this badge to the README of your package repository:

[![Status at rOpenSci Software Peer Review](https://badges.ropensci.org/590_status.svg)](https://github.com/ropensci/software-review/issues/590)

Furthermore, if your package does not have a NEWS.md file yet, please create one to capture the changes made during the review process. See https://devguide.ropensci.org/releasing.html#news

[jooolia]

Hello, I am still actively looking for reviewers. Thanks, Julia

[Kattuvan]

@jooolia I accept your invitation to review it. This is my first attempt to review a package.
Do you have a Test Case to look for bugs.
Do I have to get a data frame to test all those 30 functions/methods

[Kattuvan]

@jooolia I found the guidelines https://devguide.ropensci.org/reviewerguide.html
I am sorry for my earlier mail

[jooolia]

@ropensci-review-bot assign @Kattuvan as reviewer

[ropensci-review-bot]

@Kattuvan added to the reviewers list. Review due date is 2023-06-20. Thanks @Kattuvan for accepting to review! Please refer to our reviewer guide.

rOpenSci’s community is our best asset. We aim for reviews to be open, non-adversarial, and focused on improving software quality. Be respectful and kind! See our reviewers guide and code of conduct for more.

[ropensci-review-bot]

@Kattuvan: If you haven't done so, please fill this form for us to update our reviewers records.

[jooolia]

Thanks @Kattuvan for agreeing to review! Glad that you found the guide. :)

[jooolia]

@ropensci-review-bot assign @sheilasaia as reviewer

[ropensci-review-bot]

@sheilasaia added to the reviewers list. Review due date is 2023-06-21. Thanks @sheilasaia for accepting to review! Please refer to our reviewer guide.

rOpenSci’s community is our best asset. We aim for reviews to be open, non-adversarial, and focused on improving software quality. Be respectful and kind! See our reviewers guide and code of conduct for more.

[jooolia]

Hello @salvafern, sorry for the delay in my handling. I missed these updates. :(
Thank you for all of the work!

[jooolia]

Hi @Kattuvan,
Do you feel that the changes and updates have addressed your concerns?
Thanks, Julia

[salvafern]

Hi @jooolia, did you receive any message from @Kattuvan ? Any chance to move this submission forward?
Best, Salva

[Kattuvan]

Hi,Please move the submission to the next level. Regards,Murali On Thursday, February 22, 2024 at 08:44:27 a.m. EST, salvafern ***@***.***> wrote: Hi @jooolia, did you receive any message from @Kattuvan ? Any chance to move this submission forward? Best, Salva — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: ***@***.***>

[salvafern]

Hi @jooolia , please let me know if there is anything else I can do on my side to move this submission forward.
Best, Salva

[jooolia]

Dear Salva, Sorry for the delay. I will get back to you at the latest by March 10th. Thank you for your patience. Cheers, Julia Le lun. 4 mars 2024, 16:02, salvafern ***@***.***> a écrit :

…

Hi @jooolia <https://github.com/jooolia> , please let me know if there is anything else I can do on my side to move this submission forward. Best, Salva — Reply to this email directly, view it on GitHub <#590 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAOPZSXTJENIDT2YUMMWATDYWSEIBAVCNFSM6AAAAAAXMQPDZCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNZWG44DGOBRGI> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[jooolia]

Dear @salvafern,
Things are looking good, although the comments about the CI have not fully been addressed in my view. I had a quick look, but the logs are too old (more than three months) to be viewed. Could you try re-running the Github Actions for the pkg-check and R-CMD-check so that we can help troubleshoot what is happening here?

Thanks!

[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 ropensci/mregions2#21 and ropensci/rdflib#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! 😁

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• Fix any links in badges for CI and coverage to point to the new repository URL.
• Increment the package version to reflect the changes you made during review. In NEWS.md, add a heading for the new version and one bullet for each user-facing change, and each developer-facing change that you think is relevant.
• We're starting to roll out software metadata files to all rOpenSci packages via the Codemeta initiative, see https://docs.ropensci.org/codemetar/ for how to include it in your package, after installing the package - should be easy as running codemetar::write_codemeta() in the root of your package.
• You can add this installation method to your package README install.packages("<package-name>", repos = "https://ropensci.r-universe.dev") thanks to R-universe.

Should you want to acknowledge your reviewers in your package DESCRIPTION, you can do so by making them "rev"-type contributors in the Authors@R field (with their consent).

Welcome aboard! We'd love to host a post about your package - either a short introduction to it with an example for a technical audience or a longer post with some narrative about its development or something you learned, and an example of its use for a broader readership. If you are interested, consult the blog guide, and tag @ropensci/blog-editors in your reply. They will get in touch about timing and can answer any questions.

We maintain an online book with our best practice and tips, this chapter starts the 3d section that's about guidance for after onboarding (with advice on releases, package marketing, GitHub grooming); the guide also feature CRAN gotchas. Please tell us what could be improved.

Last but not least, you can volunteer as a reviewer via filling a short form.

[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