R Observatory: Metrics for biofetchR version 0.1.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

biofetchR

0.1.2Package record

Download, Clean, Classify, Enrich and Export Biodiversity Occurrence Data

0packages depend

1.2Kdownloads / year

14.4%test coverage

13/13flavors OK

Overview

About

Maintained by Darren StuartCRAN page ↗

Downloads, imports, cleans, classifies, enriches and exports biodiversity occurrence data, with an emphasis on reproducible Global Biodiversity Information Facility (GBIF) https://api.gbif.org/v1/ workflows. The package supports batch occurrence downloads, taxonomic standardisation, coordinate cleaning, optional spatial thinning, spatial attribution and structured export of processed occurrence records and audit outputs. Terrestrial and freshwater workflows can join records to administrative units, protected areas, freshwater ecoregions, basins, rivers, lakes, reservoirs, wetlands and other contextual spatial overlays. Marine workflows support offshore and coastal records through joins to Marine Regions https://www.marineregions.org/ style layers, Exclusive Economic Zone (EEZ) units, marine ecoregions, Large Marine Ecosystems and user-supplied marine overlays. The package also supports native-range and invasive-status evidence workflows using the World Register of Marine Species (WoRMS) https://www.marinespecies.org/, evidence derived from Standardising and Integrating Alien Species (SInAS) https://zenodo.org/records/21933976, and Global Register of Introduced and Invasive Species (GRIIS) https://griis.org/ style species-country records. These tools are intended for biodiversity, macroecological and invasion-biology analyses where occurrence records need to be processed consistently, transparently and reproducibly.

Changes in 0.1.2

Bug fixes

Standardised failure handling for explicitly requested terrestrial and freshwater vector overlays. TEOW, FEOW, HydroLAKES, HydroRIVERS, HydroBASINS, Natural Earth urban and administrative layers, RESOLVE ecoregions, WDPA and Ramsar resources now use the pipeline's common auditable overlay-loading pathway.
When strict_overlay_loading = TRUE, failures while loading, validating or preparing these requested overlays are recorded in gbif_summary.csv and stop the pipeline before avoidable GBIF download submission.
Existing fail-soft behaviour is retained when strict_overlay_loading = FALSE: overlay failures are recorded explicitly while downstream processing may continue where possible.

Show all changes in 0.1.2Hide the rest of the changes in 0.1.2

Added regression tests covering strict and fail-soft overlay-loading behaviour, including verification that strict failures occur before the GBIF downloader is reached.
Updated the package-managed Standardising and Integrating Alien Species (SInAS) default from dataset 3.1.1 to dataset 3.2 (Zenodo record 21933976; DOI 10.5281/zenodo.21933976), while retaining SInAS 3.1.1 as an explicitly selectable legacy release.
Updated SInAS resource resolution and native-origin workflows for the 3.2 file layout, including SInAS_3.2.csv, All_Config_Files_v3.2.zip and All_Output_Files_v3.2.zip.
Fixed command-line curl downloads on Windows when cache or destination paths contain spaces or standalone hyphens, and corrected success detection when system2() captures curl output in quiet mode.

From NEWS.md in the release

Install

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

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

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

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-biofetchr

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-biofetchR

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: 8.3 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK7 OK2026-07-22

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.2

READMEYes · 3,767 wordsVignettesYes · 5 · dynamicNEWSYes · 67% structured · mentions 0.1.2Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 86 (1 internal)includes a package overview page
Examples that run: 39%20 run in a plain check (3 of them under a condition) · 31 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 60%
Documented parameters: 99%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (5)

How these are measured

Downloads

1.2K

CRAN downloads in the past year

Rank #8,620 · ~3/day · ~101/mo

Releases R versions

Daily download trend is not available in this view yet.

37730 days

1.1K90 days

1.2K1 year

Compare downloads with other packages →

Also on38 r2u

How downloads are counted

Dependencies

Declared dependencies

30 external dependencies (excludes base and recommended)

Installing biofetchR adds 103 packages (57 with compiled code, 80 MB of source tarballs). Heaviest: stringi 11 MB, sf 9.3 MB, ggplot2 6.0 MB.

Depends (1)

R >= 4.1.0

Imports (13)

cli CoordinateCleaner countrycode curl dplyr geodata jsonlite mregions2 readr rgbif rlang sf tibble

LinkingTo (0)

none

Suggests (17)

geosphere ggplot2 httr knitr lwgeom mapme.biodiversity osmdata readxl remotes rmarkdown rnaturalearth stringi stringr terra testthat tidyr worrms

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (1)

Darren Stuart

Author, Maintainer since 0.1.0 (2026)

Releases (3)

Pick two releases to compare their code metrics.

0.1.2Latest
record
2026-09-26 · current release · diff ↗
0.1.1
record
2026-08-19 · diff ↗
0.1.0
record
2026-07-21
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-07-21
Total releases: 3 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Download size: 3.0 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("biofetchR")

Format

Stuart, D. (2026). biofetchR: Download, Clean, Classify, Enrich and Export Biodiversity Occurrence Data (Version 0.1.2) [Computer software]. https://doi.org/10.32614/CRAN.package.biofetchR

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 biofetchR version 0.1.2 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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