R Observatory: Metrics for occCite version 0.6.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

occCite

0.6.3Package record

Querying and Managing Large Biodiversity Occurrence Datasets

0packages dependsuggested by 1

1.9Kdownloads / year

60.4%test coverage

13/13flavors OK

Overview

About

Maintained by Hannah L. OwensCRAN page ↗GitHub ↗Website ↗Issues ↗rOpenSci review: issue 407 ↗

Facilitates the gathering of biodiversity occurrence data from disparate sources. Metadata is managed throughout the process to facilitate reporting and enhanced ability to repeat analyses.

Changes in 0.6.3

Updated taxonRectification() to catch user-supplied full titles from the GNA and convert to short titles (leftover problem from major taxize update).
Updated example data downloads and GBIF-related functions to encompass new alphanumeric rgbif taxon keys in impeding update. These fixes are not breaking changes for packages that depend on occCite.

From NEWS.md in the release

Install

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

install.packages("occCite", 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/occCite")

Development version from ropensci/occCite. 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-occcite

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-occCite

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

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

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 3.5 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
ERROR12 OK, 1 ERROR2026-07-22
OK7 OK2026-06-30

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.6.3

README· In the repository, left out of the releaseVignettesYes · 2 · dynamicNEWSYes · 100% structured · mentions 0.6.3Citation fileYes · computed when R runs itWebsiteYes · pkgdown

Help pages: 16
Examples that run: 36%5 run in a plain check · 2 only when donttest examples are enabled (R CMD check --as-cran) · 7 never run
Exported functions with examples: 91%
Documented parameters: 100%
Return-value docs: 82%
Help pages citing references: 0%

Vignettes (2)

How these are measured

Downloads

1.9K

CRAN downloads in the past year

Rank #6,038 · ~5/day · ~155/mo

Releases R versions

Daily download trend is not available in this view yet.

51430 days

1.4K90 days

1.9K1 year

Compare downloads with other packages →

Also on81 r2u

How downloads are counted

Repository

ropensci/occcite ↗Organization: ropensci

24Stars

5Forks

13Open issues

0Open PRs

19Releases

550Commits

8Commit identities

biodiversity-informaticsbiodiversity-databiodiversity-standardscitationsmuseum-collectionsmuseum-metadatamuseum-collection-specimens

License file reads as GPL-3.0 · 550 commits · Last activity 2026-09-02 · 0% stars, 30d · Default branch at 0.6.3.9000, ahead of CRAN 0.6.3 (checked 2026-10-22) · Discussions: 2 posts

Responsiveness

How these are sampled

PRs merged (all time): 83%
Median days to close, 50 most recently updated closed issues: 4
Median days to close, 50 most recently updated closed PRs: 1

Stars over time

2025-02-10 · 232026-07-07 · 24

How these are measured

PracticesBeta

10 development-tooling and community-health practices detected across 7 families in the upstream repository

Checks run against github.com/ropensci/occcite on 2026-10-22.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Governance and community (2)

Code of conduct (inherited from ropensci)Contributing guide

Docs source (2)

pkgdown

GitHub Pages site last deployed 2026-09-02

Coverage (1)

Coverage reporting

Show all practicesHide 3 practices

CRAN release process (1)

cran-comments.md

Research and citation (1)

codemeta.json

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

26 external dependencies (excludes base and recommended)

Installing occCite adds 97 packages (54 with compiled code, 92 MB of source tarballs). Heaviest: stringi 11 MB, sf 9.3 MB, ggplot2 6.0 MB.

Depends (1)

R >= 3.5.0

Imports (19)

BIEN DBI RefManageR RColorBrewer RPostgreSQL bib2df curl dplyr ggplot2 htmltools leaflet lubridatemethodsrgbif rlangstatsstringr tidyr viridis

LinkingTo (0)

none

Suggests (9)

ape bit64 covr httr knitr remotes rmarkdown taxize (>= 0.10)testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Suggested by 1

Suggests, most downloaded first

wallace

How these are counted

Code & Tests

Datasets

People & History

People (7)

Hannah L. Owens

Author, Maintainer since 0.3.0 (2020)

Author

Author

Author

Author

Author

Reviewer · added in 0.5.2

Damiano reviewed the package (v. 0.5.2) for rOpenSci, see <https://github.com/ropensci/software-review/issues/407>

Releases (20)

Pick two releases to compare their code metrics.

0.6.3Latest
record
2026-09-01 · current release · diff ↗
unarchivedReturned to CRAN
2026-06-29
0.6.2
record
2026-06-29 · diff ↗
R
R 4.6.0 released · 2026-04-24
archivedRemoved from CRAN
2026-02-22
issues were not corrected in time
unarchivedReturned to CRAN
2025-09-29
0.6.1
record
2025-09-29 · diff ↗
archivedRemoved from CRAN
2025-09-09
requires archived package 'waffle'
0.6.0
record
2025-06-16 · diff ↗
R
R 4.5.0 released · 2025-04-11
0.5.9
record
2024-10-28 · diff ↗
0.5.8
record
2024-09-05 · diff ↗
0.5.7
record
2024-06-23 · diff ↗
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
0.5.6
record
2022-08-05 · diff ↗ ·
added 2 exports
GBIFLogin, occCiteData

Show 25 earlier eventsHide 25 earlier events

R
R 4.2.0 released · 2022-04-22
0.5.4
record
2022-03-21 · diff ↗
0.5.3
record
2022-03-16 · diff ↗
unarchivedReturned to CRAN
2022-03-04
0.5.2
record
2022-03-04 · diff ↗ ·
removed 1 export
tabulate.occResults
archivedRemoved from CRAN
2021-12-01
check problems were not corrected in time On Internet access, again
unarchivedReturned to CRAN
2021-11-01
0.5.1
record
2021-11-01 · diff ↗
archivedRemoved from CRAN
2021-10-22
policy violation On Internet access: site has broken CA trust chain
0.5.0
record
2021-10-13 · diff ↗
0.4.9
record
2021-07-23 · diff ↗
unarchivedReturned to CRAN
2021-06-11
0.4.8
record
2021-06-11 · diff ↗
archivedRemoved from CRAN
2021-05-23
policy violation on Internet access
R
R 4.1.0 released · 2021-05-18
0.4.7
record
2021-04-27 · diff ↗
unarchivedReturned to CRAN
2021-02-21
0.4.6
record
2021-02-21 · diff ↗
archivedRemoved from CRAN
2021-02-09
check problems were not corrected in time
unarchivedReturned to CRAN
2020-11-28
0.4.5
record
2020-11-28 · diff ↗ ·
removed 3 exports
BIENtableCleanup, map.occCite, sumFig.occCite

added 1 export
occCiteMap
archivedRemoved from CRAN
2020-11-04
check problems were not corrected in time
0.4.0
record
2020-10-21 · diff ↗
0.3.0
record
2020-10-06
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-10-06
Total releases: 20 / 6 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 48 KB / 1 file
Download size: 4.9 MB

Appears in task views

Paleontology

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("occCite")

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 occCite version 0.6.3 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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