forcis: An R client to access the FORCIS database

[ahasverus]

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: TBD
Reviewers: TBD

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

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 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()

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 forcis (v0.1.0)

git hash: e80b91c5

• ✔️ 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.

Package License: GPL (>= 2)

---

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	105
internal	forcis	66
internal	graphics	3
imports	utils	56
imports	sf	12
imports	vroom	10
imports	jsonlite	3
imports	dplyr	NA
imports	ggplot2	NA
imports	rlang	NA
imports	tidyr	NA
suggests	fs	NA
suggests	knitr	NA
suggests	rmarkdown	NA
suggests	testthat	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

file.path (11), c (7), which (7), data.frame (6), for (6), seq_len (6), suppressWarnings (6), length (5), list.files (5), rbind (5), unique (5), as.numeric (4), colnames (3), tryCatch (3), url (3), drop (2), file (2), format (2), lapply (2), months (2), paste0 (2), strsplit (2), unlist (2), as.Date (1), gsub (1), nrow (1), options (1), readline (1), readLines (1), which.max (1)

forcis

get_species_names (11), data_to_sf (5), species_list (5), get_available_versions (3), get_metadata (3), cpr_north_filename (2), cpr_south_filename (2), get_current_version (2), get_latest_version (2), add_data_type (1), check_field_in_data (1), check_if_character (1), check_if_df (1), check_if_path_exists (1), check_if_valid_taxonomy (1), check_required_columns (1), check_unique_taxonomy (1), check_version (1), compute_abundances (1), compute_concentrations (1), compute_frequencies (1), convert_to_long_format (1), crs_robinson (1), data_types (1), date_format (1), download_file (1), download_forcis_db (1), filter_by_bbox (1), filter_by_month (1), filter_by_ocean (1), filter_by_polygon (1), filter_by_species (1), filter_by_year (1), geom_basemap (1), get_data_type (1), get_required_columns (1), get_version_metadata (1), plankton_net_filename (1), pump_filename (1), sediment_trap_filename (1)

utils

data (55), download.file (1)

sf

st_intersects (6), st_bbox (3), st_crs (2), st_as_sf (1)

vroom

vroom (10)

graphics

polygon (3)

jsonlite

read_json (3)

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 33 files) and
• 5 authors
• 6 vignettes
• no internal data file
• 8 imported packages
• 31 exported functions (median 27 lines of code)
• 81 non-exported functions in R (median 16 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	33	90.1
files_vignettes	6	96.8
files_tests	35	98.0
loc_R	1549	76.5
loc_vignettes	418	71.2
loc_tests	1200	86.4
num_vignettes	6	97.7	TRUE
n_fns_r	112	77.5
n_fns_r_exported	31	78.2
n_fns_r_not_exported	81	77.6
n_fns_per_file_r	2	31.7
num_params_per_fn	2	8.2
loc_per_fn_r	19	57.7
loc_per_fn_r_exp	27	58.8
loc_per_fn_r_not_exp	16	53.2
rel_whitespace_R	48	92.5
rel_whitespace_vignettes	68	89.5
rel_whitespace_tests	55	95.6	TRUE
doclines_per_fn_exp	38	46.8
doclines_per_fn_not_exp	0	0.0	TRUE
fn_call_network_size	157	84.7

---

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
11082922089	pages build and deployment	success	702763	164	2024-09-28
11082912111	pkgdown	success	e80b91	199	2024-09-28
11082809930	R CMD Check	success	e80b91	198	2024-09-28
11082809923	Test coverage	success	e80b91	94	2024-09-28
11082912112	Update CITATION.cff	success	e80b91	23	2024-09-28

---

3b. goodpractice results

R CMD check with rcmdcheck

R CMD check generated the following check_fail:

1. no_import_package_as_a_whole

Test coverage with covr

Package coverage: 97.38

Cyclocomplexity with cyclocomp

No functions have cyclocomplexity >= 15

Static code analyses with lintr

lintr found the following 7 potential issues:

message	number of times
Avoid changing the working directory, or restore it in on.exit	2
Avoid library() and require() calls in packages	5

---

Package Versions

package	version
pkgstats	0.1.6.17
pkgcheck	0.1.2.58

---

Editor-in-Chief Instructions:

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