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forcis: An R client to access the FORCIS database #660

Open ahasverus opened 2 days ago

ahasverus commented 2 days ago

Submitting Author Name: Nicolas Casajus Submitting Author Github Handle: !--author1-->@ahasverus<!--end-author1-- 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

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

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).

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.

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.

Not applicable.

Pre-submission inquiry: #655 Editor: @adamhsparks

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.

This package:

Publication options

MEE Options - [x] The package is novel and will be of interest to the broad readership of the journal. - [x] The manuscript describing the package is no longer than 3000 words. - [x] 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](http://besjournals.onlinelibrary.wiley.com/hub/journal/10.1111/(ISSN)2041-210X/journal-resources/policy-on-publishing-code.html)) - (*Scope: Do consider MEE's [Aims and Scope](http://besjournals.onlinelibrary.wiley.com/hub/journal/10.1111/(ISSN)2041-210X/aims-and-scope/read-full-aims-and-scope.html) 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

ropensci-review-bot commented 2 days ago

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ropensci-review-bot commented 2 days ago

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Editor check started

:wave:

ropensci-review-bot commented 2 days ago

Checks for forcis (v0.1.0)

git hash: e80b91c5

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()', 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](https://docs.ropensci.org/pkgcheck/reference/checks_to_markdown.html) 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 [![R-CMD-check.yaml](https://github.com/FRBCesab/forcis/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/FRBCesab/forcis/actions) [![pkgdown.yaml](https://github.com/FRBCesab/forcis/actions/workflows/pkgdown.yaml/badge.svg)](https://github.com/FRBCesab/forcis/actions) **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](https://r-lib.github.io/rcmdcheck/) R CMD check generated the following check_fail: 1. no_import_package_as_a_whole #### Test coverage with [covr](https://covr.r-lib.org/) Package coverage: 97.38 #### Cyclocomplexity with [cyclocomp](https://github.com/MangoTheCat/cyclocomp) No functions have cyclocomplexity >= 15 #### Static code analyses with [lintr](https://github.com/jimhester/lintr) [lintr](https://github.com/jimhester/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