R Observatory: Metrics for rgbif version 3.9.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

rgbif

3.9.0Package record

Interface to the Global Biodiversity Information Facility API

12packages dependsuggested by 16

123.2Kdownloads / year

58.5%test coverage

13/13flavors OK

Overview

About

Maintained by John WallerCRAN page ↗GitHub ↗Website ↗Issues ↗Declared funder: rOpenSci

A programmatic interface to the Web Service methods provided by the Global Biodiversity Information Facility (GBIF; https://www.gbif.org/developer/summary). GBIF is a database of species occurrence records from sources all over the globe. rgbif includes functions for searching for taxonomic names, retrieving information on data providers, getting species occurrence records, getting counts of occurrence records, and using the GBIF tile map service to make rasters summarizing huge amounts of data.

Changes in 3.9.0

BREAKING CHANGES

**Default taxonomy changed from GBIF Backbone to COL (Catalogue of Life) Extended Release** (#895)

Migration Guide

The following functions now use COL Extended Release (checklistKey = "7ddf754f-d193-4cc9-b351-99906754a03b") as the default taxonomy:

name_backbone() - Returns COL XR alpha-numeric taxon keys (e.g., "Q2M4") instead of numeric GBIF Backbone keys
name_backbone_checklist() - Matches names against COL XR by default
occ_search() - Searches using COL XR taxonomy
occ_download() - Creates downloads with COL XR taxonomy
occ_download_prep() - Prepares downloads with COL XR taxonomy
map_fetch() - Fetches maps using COL XR taxonomy
mvt_fetch() - Fetches map vector tiles using COL XR taxonomy

DEPRECATED

Show all changes in 3.9.0Hide the rest of the changes in 3.9.0

The following functions are deprecated because they use the GBIF Backbone taxonomy, and will not work with COL XR keys.

name_lookup() - use rcol::col_search() instead
name_suggest() - use rcol::col_suggest() instead
name_usage() - use rcol::col_usage() instead
name_issues() - use rcol::col_usage() to parse and examine name issues

Additionally:

elevation() - deprecated because it relies on a non-GBIF web service (GeoNames) and will be removed in a future version (#473)

NEW FEATURE

New functions for improved API coverage:

gbif_to_col() - Convert GBIF Backbone numeric taxon keys to COL Extended Release alpha-numeric keys. Returns the full API response including usage details, classification hierarchy, and match diagnostics.
occ_term() - Get occurrence term definitions from GBIF API (#857)
occ_download_countries() - Get country breakdown for occurrence downloads (#876)
occ_download_user_count() - Count downloads by user with optional status and date filtering (#875)
occ_download_organizations() - Get organization breakdown for occurrence downloads (#877)

MINOR IMPROVEMENTS

occ_search() now returns classifications as a named list of tibbles, with one tibble per checklistKey (taxonomy source). Each tibble contains one row per occurrence with taxonomic ranks pivoted into camelCase columns (checklistKey, kingdomName, kingdomKey, phylumName, phylumKey, className, classKey, etc.). This structure makes it easy to work with occurrences from different taxonomies separately while keeping the checklistKey information with the data. Known checklists (COL, backbone) are shown with friendly names, while unknown checklists use their UUID.
occ_search() now detects numeric taxonomic keys (taxonKey, speciesKey, kingdomKey, etc.) and automatically switches to the GBIF Backbone taxonomy checklistKey with a warning message. These numeric keys are legacy identifiers from the GBIF Backbone taxonomy. Users are advised to migrate to COL XR identifiers using gbif_to_col().
occ_download() and occ_download_prep() now detect numeric taxonomic keys in predicates and automatically inject the GBIF Backbone checklistKey at the predicate level with a warning message. This ensures existing code using numeric keys continues to work correctly.
occ_download() and occ_download_prep() now support checklistKey parameter at both the root level (as a top-level argument) and within predicates using pred(). This allows users to specify which taxonomy source to use for occurrence downloads (#841).
name_usage() now warns when datasetKey parameter is ignored. When a key is provided, the GBIF API ignores the datasetKey parameter and returns data based solely on the key. A warning is now issued to alert users of this behavior (#899).

API COVERAGE IMPROVEMENTS

Added missing parameters to improve GBIF API coverage:

dataset_search(), dataset_export(), and dataset_suggest() - Added category parameter (#845)
dataset_search() - Added continent, taxonKey, recordCount, modifiedDate, createdDate, contactUserId, contactEmail parameters (#859)
dataset_export() - Added missing parameters for complete API coverage (#862)
dataset_suggest() - Added missing parameters (#870)
occ_search() and occ_count() - Added nucleotide sequence filtering parameters: isSequenced, isInCluster, hasSequenceLink, sequenceLength, gcContent, targetGene (#851)
institution_search() - Added missing filter parameters (#882)
collection_search() - Added missing API filters (#884)
collection_export() - Added missing parameters and fixed dataset_export CI test stability (#889)
institution_export() - Added missing parameters (#891)
organizations() - Added missing API parameters: isEndorsed, networkKey, machineTagNamespace, machineTagName, machineTagValue, identifierType, identifier, modified, created (#894)

BUG FIXES

Fixed ORCID and ROR syntax in DESCRIPTION file (#897)
Replaced deleted taxon key (3119195) with valid key (5231190) in test fixtures (#843)

From NEWS.md in the release

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("rgbif", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("ropensci/rgbif")

Development version from ropensci/rgbif. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-rgbif

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-rgbif

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-rgbif

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 3.9 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-10-15
NOTE11 OK, 2 NOTE2026-07-16
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 3.9.0

README· In the repository, left out of the releaseVignettes· In the repository, left out of the releaseNEWSYes · 33% structured · mentions 3.9.0Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 108 (28 internal)includes a package overview page
Examples that run: 4%3 run in a plain check · 72 never run · 2 hold no code
Exported functions with examples: 93%
Documented parameters: 88%
Return-value docs: 70%
Help pages citing references: 28%

How these are measured

Downloads

123.2K

CRAN downloads in the past year

Rank #1,231 · ~337/day · ~10.3K/mo

Releases R versions

Daily download trend is not available in this view yet.

10.1K30 days

26.1K90 days

123.2K1 year

Compare downloads with other packages →

Also on874 r2u8 autocran5.9K conda_forge1.1K bioconda241 c2d4u

How downloads are counted

Repository

ropensci/rgbif ↗Organization: ropensci

184Stars

55Forks

41Open issues

0Open PRs

56Releases

2,148Commits

26Commit identities

gbifapidatabiodiversityspeciesrstatsrspocc

2,148 commits · Last activity 2026-10-13 · +1.1% stars, 30d · Default branch at 3.9.0.1, ahead of CRAN 3.9.0 (checked 2026-10-21)

Responsiveness

How these are sampled

PRs merged (all time): 92%
Median days to close, 50 most recently updated closed issues: 2
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2026-07-14 · 1772026-10-21 · 184

How these are measured

PracticesBeta

14 development-tooling and community-health practices detected across 8 families in the upstream repository

Checks run against github.com/ropensci/rgbif on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows

Governance and community (4)

Code of conduct (inherited from ropensci)Contributing guideIssue templatesPR template

Docs source (2)

pkgdown

GitHub Pages site last deployed 2019-10-15

Coverage (1)

Coverage reporting

Show all practicesHide 4 practices

Reproducibility and dev environment (1)

Makefile

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Research and citation (1)

codemeta.json

Git structural (1)

.gitattributes

How this is detected·Detection ruleset v4 (2026-10-20)

AI coding toolsBeta

This repository shows signs of AI coding tools.

GitHub Copilotfirst seen 2025-12-11
Pull request: opened by its own account
Commits: 16 by its own account · at least 16 crediting it in the message

Review tools

Copilot code review
Commits: at least 1 accepting its review suggestions

Counts are commits, not lines of code. Commits by a tool's accounts count once across all of its accounts. Commits crediting it are the largest count among its credit lines, a minimum.How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

21 external dependencies (excludes base and recommended)

Installing rgbif adds 42 packages (24 with compiled code, 38 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (0)

none

Imports (12)

xml2 ggplot2 crul data.table whisker magrittr jsonlite oai tibble lazyeval R6stats

LinkingTo (0)

none

Suggests (10)

testthat png terra magick protolite sf vcr (>= 2.0.0)knitr rmarkdown bit64

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

12direct

10indirect

Imports 12

Suggested by 16

Show all 28 packagesHide all 28 packages

Depends, Imports or LinkingTo, most downloaded first

spocc CoordinateCleaner occCite peruocc intSDM gatoRs arakno biofetchR RuHere gbif.range datamuseum spidR

Suggests, most downloaded first

rangeModelMetadata wallace taxify downscale geoflow tidysdm caretSDM biomes redlist KnowBR pigauto ohvbd aptg EcoCleanR b3gbi VasGBIF

How these are counted

Code & Tests

People & History

People (9)

John Waller

Author, Maintainer since 3.7.0 (2022) · added in 3.7.0

Scott Chamberlain

Author

Damiano Oldoni

Author · added in 1.0.0

Vijay Barve

Contributor · added in 0.1.5

Peter Desmet

Contributor · added in 1.2.0

Laurens Geffert

Contributor · added in 1.0.0

Dan Mcglinn

Contributor · added in 0.4.0

Karthik Ram

Contributor

rOpenSci

Funder · added in 3.1.0

Previously maintained by Scott Chamberlain (0.0.1 to 3.6.0).

Listed in earlier versions (1)

Carl Boettiger

no longer listed · 0.0.1 to 0.6.2

Releases (64)

Pick two releases to compare their code metrics.

3.9.0Latest
record
2026-10-05 · current release · diff ↗ ·
added 5 exports
gbif_to_col, occ_download_countries, occ_download_organizations, occ_download_user_count, occ_term
R
R 4.6.0 released · 2026-04-24
3.8.5
record
2026-03-20 · diff ↗ ·
added 6 exports
occ_download_stats, occ_download_stats_dataset, occ_download_stats_dataset_records, occ_download_stats_export, occ_download_stats_source, occ_download_stats_user_country
3.8.4
record
2025-11-13 · diff ↗
3.8.3
record
2025-09-04 · diff ↗ ·
added 13 exports
collection_export, collection_search, installation_comment, installation_contact, installation_dataset, installation_endpoint, installation_identifier, installation_machinetag, installation_search, installation_tag, institution_export, institution_search, lit_export
3.8.2
record
2025-06-12 · diff ↗ ·
added 1 export
occ_download_doi
R
R 4.5.0 released · 2025-04-11
3.8.1
record
2024-09-27 · diff ↗ ·
added 3 exports
occ_download_sql, occ_download_sql_prep, occ_download_sql_validate
3.8.0
record
2024-05-23 · diff ↗ ·
added 1 export
occ_download_describe
R
R 4.4.0 released · 2024-04-24
3.7.9
record
2024-01-11 · diff ↗ ·
added 15 exports
dataset, dataset_comment, dataset_constituents, dataset_contact, dataset_doi, dataset_duplicate, dataset_endpoint, dataset_export, dataset_get, dataset_identifier, dataset_machinetag, dataset_networks, dataset_noendpoint, dataset_process, dataset_tag
3.7.8
record
2023-09-11 · diff ↗ ·
added 1 export
pred_default
R
R 4.3.0 released · 2023-04-21
3.7.7
record
2023-04-03 · diff ↗
3.7.6
record
2023-03-23 · diff ↗ ·
added 6 exports
lit_count, lit_search, occ_count_basis_of_record, occ_count_country, occ_count_pub_country, occ_count_year
3.7.5
record
2023-01-05 · diff ↗

Show 64 earlier eventsHide 64 earlier events

3.7.4
record
2022-12-06 · diff ↗
3.7.3
record
2022-09-03 · diff ↗ ·
added 5 exports
dataset_gridded, gbif_geocode, name_parse, network, network_constituents
R
R 4.2.0 released · 2022-04-22
3.7.2
record
2022-04-11 · diff ↗
3.7.1
record
2022-03-16 · diff ↗
3.7.0
record
2022-02-08 · diff ↗ ·
added 4 exports
derived_dataset, derived_dataset_prep, name_backbone_checklist, pred_isnull
3.6.0
record
2021-06-02 · diff ↗
R
R 4.1.0 released · 2021-05-18
3.5.2
record
2021-01-27 · diff ↗
3.5.0
record
2021-01-13 · diff ↗
3.4.2
record
2021-01-06 · diff ↗
3.4.0
record
2020-12-03 · diff ↗
3.3.0
record
2020-09-08 · diff ↗
3.2.0
record
2020-07-23 · diff ↗
3.1.0
record
2020-06-30 · diff ↗
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
R
R 3.2.0 released · 2015-04-16
R
R 3.1.0 released · 2014-04-10
3.0.3
record
2014-02-16 · diff ↗
3.0.2
record
2013-07-18 · diff ↗ ·
removed 1 export
gbifmap

added 13 exports
blanktheme, colClasses, commas_to_periods, country_codes, gbifdata, gbifmap_dens, gbifmap_list, is.gbifdens, is.gbiflist, occurrencelist_many, parseresults, stylegeojson, togeojson
3.0.0
record
2020-06-23 · diff ↗ ·
added 3 exports
name_backbone_verbose, occ_download_cached, occ_get_verbatim
R
R 3.0.0 released · 2013-04-03
2.15.3
record
2013-03-01 · diff ↗
R
R 2.15.0 released · 2012-03-30
2.15.0
record
2012-03-21 · diff ↗
2.3
record
2020-05-28 · diff ↗
2.2.0
record
2020-03-09 · diff ↗
2.1.0
record
2020-02-13 · diff ↗
2.0.0
record
2020-01-31 · diff ↗ ·
added 13 exports
occ_download_wait, pred, pred_and, pred_gt, pred_gte, pred_in, pred_like, pred_lt, pred_lte, pred_not, pred_notnull, pred_or, pred_within
1.4.0
record
2019-10-30 · diff ↗ ·
removed 1 export
occ_issues_lookup

added 2 exports
gbif_issues_lookup, mvt_fetch
1.3.0
record
2019-05-08 · diff ↗
1.2.0
record
2019-02-26 · diff ↗
1.1.0
record
2018-10-20 · diff ↗ ·
added 1 export
name_issues
1.0.2
record
2018-07-06 · diff ↗
1.0.0
record
2018-07-03 · diff ↗ ·
removed 1 export
gbifmap

added 5 exports
DownReq, GbifQueue, map_fetch, occ_download_prep, occ_download_queue
0.9.9
record
2017-11-12 · diff ↗ ·
added 2 exports
occ_download_dataset_activity, occ_download_datasets
0.9.8
record
2017-04-19 · diff ↗ ·
removed 1 export
read_wkt
0.9.7
record
2017-01-21 · diff ↗ ·
removed 1 export
type_sum
0.9.6
record
2016-12-06 · diff ↗
0.9.5
record
2016-10-06 · diff ↗ ·
added 2 exports
occ_facet, occ_spellcheck
0.9.4
record
2016-06-29 · diff ↗
0.9.3
record
2016-03-29 · diff ↗ ·
added 1 export
wkt_parse
0.9.2
record
2016-02-02 · diff ↗ ·
removed 7 exports
commas_to_periods, datasetparser, gbif_capwords, gbifparser, gbifparser_verbatim, namelkupparser, parseresults

added 1 export
occ_data
0.9.0
record
2015-11-25 · diff ↗ ·
added 7 exports
gbif_citation, gbif_oai_get_records, gbif_oai_identify, gbif_oai_list_identifiers, gbif_oai_list_metadataformats, gbif_oai_list_records, gbif_oai_list_sets
0.8.9
record
2015-10-07 · diff ↗
0.8.8
record
2015-07-24 · diff ↗
0.8.6
record
2015-07-03 · diff ↗ ·
added 8 exports
as.download, occ_download, occ_download_cancel, occ_download_cancel_staged, occ_download_get, occ_download_import, occ_download_list, occ_download_meta
0.8.4
record
2015-06-08 · diff ↗ ·
removed 1 export
ldfast

added 3 exports
enumeration, enumeration_country, read_wkt
0.8.0
record
2015-03-09 · diff ↗
0.7.7
record
2014-11-07 · diff ↗ ·
removed 25 exports
create_gist, density_spplist, densitylist, gbifdata, gbifmap_dens, gbifmap_list, gbifxmlToDataFrame, get_credentials, gist, is.gbifdens, is.gbiflist, is.gbiflist_na, occurrencecount, occurrencedensity, occurrenceget, occurrencelist, occurrencelist_all, occurrencelist_many, providers, resources, stylegeojson, taxoncount, taxonget, taxonsearch, togeojson

added 5 exports
%>%, gbif_issues, gbif_names, occ_issues, occ_issues_lookup
0.7.0
record
2014-07-31 · diff ↗ ·
added 4 exports
gbif_bbox2wkt, gbif_photos, gbif_wkt2bbox, type_sum
0.6.2
record
2014-04-24 · diff ↗
0.6.0
record
2014-04-17 · diff ↗ ·
added 1 export
check_wkt
0.5.0
record
2014-02-16 · diff ↗ ·
removed 1 export
country_codes

added 4 exports
count_facet, elevation, installations, rgb_country_codes
0.4.0
record
2013-11-20 · diff ↗ ·
removed 2 exports
capwords, colClasses

added 28 exports
create_gist, dataset_metrics, dataset_search, dataset_suggest, datasetparser, datasets, gbif_capwords, gbifmap, gbifparser, gbifparser_verbatim, get_credentials, gist, is.gbiflist_na, ldfast, name_backbone, name_lookup, name_suggest, name_usage, namelkupparser, nodes, occ_count, occ_get, occ_metadata, occ_search, occurrencelist_all, organizations, parsenames, suggestfields
0.3.0
record
2013-07-19 · diff ↗
0.2.0
record
2013-03-01 · diff ↗ ·
added 1 export
gbifxmlToDataFrame
0.1.5
record
2012-12-04 · diff ↗ ·
removed 1 export
gbifdatause

added 6 exports
capwords, density_spplist, densitylist, gbifmap, occurrencecount, taxonget
0.0.1
record
2012-03-21
R
R 2.14.0 released · 2011-10-31

Package metadata

First published: 2012-03-21
Total releases: 64 / 14 yrs
License: MIT + file LICENSE OSI · relicensed from CC0 in 0.7.0
Download size: 5.0 MB

Appears in task views

Paleontology Analysis of Spatial Data

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("rgbif")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for rgbif version 3.9.0 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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