emodnet.wcs, Access EMODnet Web Coverage Service data through R

[maelle]

Submitting Author Name: Maëlle Salmon
Submitting Author Github Handle: @maelle
Repository: https://github.com/EMODnet/emodnet.wcs
Version submitted: 0.0.2
Submission type: Standard
Editor: TBD
Reviewers: TBD

Archive: TBD
Version accepted: TBD
Language: en

---

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

Package: emodnet.wcs
Title: Access EMODnet Web Coverage Service data through R
Version: 0.0.2.9000
Authors@R: c(
    person("Anna", "Krystalli", , "annakrystalli@googlemail.com", role = "aut",
           comment = c(ORCID = "0000-0002-2378-4915")),
    person("Salvador", "Fernández-Bejarano", , "salvador.fernandez@vliz.be", role = "aut",
           comment = c(ORCID = "0000-0003-0535-7677")),
    person("European Marine Observation Data Network (EMODnet) Biology project", "European Commission's Directorate - General for Maritime Affairs and Fisheries (DG MARE)", , "bio@emodnet.eu", role = "cph"),
    person("VLIZ (VLAAMS INSTITUUT VOOR DE ZEE)", , , "info@vliz.be", role = "fnd",
           comment = c(ROR = "0496vr396")),
    person("Pepijn", "de Vries", , "pepijn.devries@outlook.com", role = "ctb",
           comment = c(ORCID = "0000-0002-7961-6646")),
    person("Maëlle", "Salmon", , "maelle.salmon@gmail.com", role = c("cre", "aut"),
           comment = c(ORCID = "0000-0002-2815-0399"))
  )
Description: Access and interrogate EMODnet Web Coverage Service data
    through R.
License: MIT + file LICENSE
URL: https://github.com/EMODnet/emodnet.wcs,
    https://emodnet.github.io/emodnet.wcs/
BugReports: https://github.com/EMODnet/emodnet.wcs/issues
Depends: 
    R (>= 4.1.0)
Imports: 
    checkmate,
    cli,
    curl,
    glue,
    httr2,
    memoise,
    ows4R (>= 0.5-1),
    purrr,
    rlang,
    sf,
    terra,
    tibble
Suggests: 
    covr,
    fs,
    huxtable,
    knitr,
    rmarkdown,
    roxygen2,
    testthat (>= 3.0.0),
    vcr (>= 2.0.0),
    webmockr,
    withr
VignetteBuilder: 
    knitr
Remotes: 
    eblondel/ows4R
Config/testthat/edition: 3
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
Config/roxygen2/version: 8.1.0.9000

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
  • translation
  • rOpenSci internal tools

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

The package allow interrogation of and access to EMODnet’s, European Marine Observation and Data Network, geographic raster data.

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

The target audience of the package are EMODnet users that might need programmatic access to EMODnet's geographic raster data.
The package allows to include EMODnet vector data into scientific pipelines without needing to manually explore and download data.
It allows to access data about bathymetry, biology, human activities and seabed habitats.

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

Not to our knowledge. As indicated when we submitted emodnet.wfs, three packages allow to access EMODnet data in a complementary way: emodnet.wfs (vector data), emodnet.wcs (raster data), rerddap. The README of emodnet.wcs features a section comparing the three packages.

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

NA

• 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.

Use of Generative AI

• Generative AI tools were used to produce some of the material in this submission.

If so, please describe usage, and include links to any relevant aspects of your repository. See our blog post for background. (Explicit advice is not yet included in our Dev Guide; we are hoping to update very soon, and ask your cooperation and transparency in the meantime.)

I checked the Git log, and really don't remember using an LLM for the development of this package. I am however open to reviews complemented/helped by LLMs!

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]

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---

Matches are generated by the 'pkgmatch' package, based on inverse-term frequencies; see the main function documentation for details.

[ropensci-review-bot]

Checks for emodnet.wcs (v0.0.2.9000)

git hash: 834c9ca4

• ✔️ Package name is available
• ✔️ 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.
• ✔️ Repository has a website
• ✔️ Package has continuous integration checks.
• ✔️ Package coverage is 91.1%.
• ✖️ Not all authors have ORCID IDs
• ✔️ R CMD check found no errors.
• ✔️ R CMD check found no warnings.
• 👀 Some goodpractice linters failed.

Important: All failing checks above must be addressed prior to proceeding

(Checks marked with 👀 may be optionally addressed.)

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	70
internal	emodnet.wcs	68
internal	graphics	5
internal	MASS	2
internal	utils	1
imports	purrr	39
imports	memoise	4
imports	cli	2
imports	ows4R	2
imports	sf	2
imports	checkmate	1
imports	curl	1
imports	httr2	1
imports	rlang	1
imports	tibble	1
imports	glue	NA
imports	terra	NA
suggests	covr	NA
suggests	fs	NA
suggests	huxtable	NA
suggests	knitr	NA
suggests	rmarkdown	NA
suggests	roxygen2	NA
suggests	testthat	NA
suggests	vcr	NA
suggests	webmockr	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.

base

summary (18), c (11), parent.frame (4), format (3), is.null (3), list (2), names (2), strsplit (2), tryCatch (2), unlist (2), as.integer (1), attr (1), call (1), endsWith (1), inherits (1), length (1), message (1), ncol (1), nrow (1), range (1), seq_along (1), sprintf (1), startsWith (1), sub (1), suppressWarnings (1), trimws (1), try (1), unique (1), url (1), version (1), which (1)

emodnet.wcs

emdn_get_coverage_summaries (4), emdn_get_dimensions_info (4), get_service_name (3), emdn_get_band_descriptions (2), emdn_get_band_nil_values (2), emdn_get_coverage_dim_coefs (2), emdn_get_coverage_function (2), emdn_get_coverage_ids (2), emdn_get_resolution (2), emdn_has_dimension (2), extract_coverage_resp (2), get_service_url (2), check_coverages (1), check_one_present (1), check_service (1), check_service_name (1), check_wcs (1), check_wcs_version (1), cli_alert_info (1), cli_alert_success (1), cli_alert_warning (1), cli_rule (1), conc_band_uom (1), conc_bbox (1), conc_constraint (1), conc_nil_value (1), conc_resolution (1), conv_band_nil_value (1), conv_nil_to_na (1), create_client (1), default_crs (1), emdn_get_band_constraints (1), emdn_get_band_uom (1), emdn_get_bbox (1), emdn_get_coverage (1), emdn_get_coverage_summaries_all (1), emdn_get_dimension_types (1), emdn_get_dimensions_n (1), emdn_get_dimensions_names (1), emdn_get_grid_size (1), emdn_get_temporal_extent (1), emdn_get_vertical_extent (1), emdn_get_WGS84bbox (1), emdn_init_wcs_client (1), error_wrap (1), extr_bbox_crs (1), get_capabilities (1), get_cov_coefs (1), has_internet (1), kebabcase (1), request_service (1)

purrr

map_chr (29), map (5), map_int (2), map_dbl (1), map_if (1), map_lgl (1)

graphics

text (3), lines (2)

memoise

memoise (4)

cli

cli_warn (2)

MASS

band (2)

ows4R

OWSUtils$toBBOX (1), WCSClient$new (1)

sf

st_as_sfc (1), st_bbox (1)

checkmate

assert_character (1)

curl

nslookup (1)

httr2

req_url_query (1)

rlang

caller_env (1)

tibble

tibble (1)

utils

URLencode (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 (5% in 10 files) and YAML (95% in 5 files)
• 3 authors
• 1 vignette
• no internal data file
• 12 imported packages
• 26 exported functions (median 6 lines of code)
• 40 non-exported functions in R (median 5 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	10	75.3
files_vignettes	5	97.5
files_tests	8	93.5
loc_R	1113	85.1
loc_vignettes	438	75.5
loc_tests	503	80.0
num_vignettes	1	71.9
n_fns_r	66	89.9
n_fns_r_exported	26	85.7
n_fns_r_not_exported	40	92.4
n_fns_per_file_r	7	90.7
num_params_per_fn	1	50.2
loc_per_fn_r	6	53.9
loc_per_fn_r_exp	6	55.9
loc_per_fn_r_not_exp	5	63.7
doclines_per_fn_exp	168	96.9	TRUE
doclines_per_fn_not_exp	0	0.0	TRUE
fn_call_network_size	147	89.8

---

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
34598060885	pkgcheck	failure	834c9c	99	2026-09-11
34598060892	pkgdown.yaml	success	834c9c	218	2026-09-11
34598060818	R-CMD-check.yaml	success	834c9c	238	2026-09-11
34598060875	test-coverage.yaml	success	834c9c	231	2026-09-11

---

3b. goodpractice results

Test coverage with covr

Package coverage: 91.14

Cyclocomplexity with cyclocomp

The following function have cyclocomplexity >= 15:

function	cyclocomplexity
emdn_get_coverage	15

Static code analyses with lintr

lintr found the following 83 potential issues:

message	number of times
Avoid implicit assignments in function calls.	3
Don't nest pipes inside other calls.	18
expect_named(x, n) is better than expect_identical(names(x), n)	1
Lines should not be more than 80 characters.	57
Use "EPSG:" with fixed = TRUE here.	1
Use expect_identical(x, y) by default; resort to expect_equal() only when needed, e.g.	3

Other goodpractice checks

✖️ All internal functions are used
✖️ Documented functions have @export, @noRd, or @rdname
✖️ @inheritParams/@inheritDotParams reference known functions
✖️ All URLs are reachable
✖️ No URLs redirect to a different location

---

Package Versions

package	version
pkgstats	0.2.4
pkgcheck	0.2.0.22

---

Editor-in-Chief Instructions:

Processing may not proceed until the items marked with ✖️ have been resolved.

This package has some noteworthy properties, see 'Package Statistics' details above.

[maelle]

Reg ORCID, see ropensci-review-tools/pkgcheck#413