R Observatory: Metrics for bdc version 1.1.6

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

bdc

1.1.6Package record

Biodiversity Data Cleaning

0packages dependsuggested by 1

5.4Kdownloads / year

32.7%test coverage

13/13flavors OK

Overview

About

Maintained by Bruno RibeiroCRAN page ↗GitHub ↗Website ↗Issues ↗

It brings together several aspects of biodiversity data-cleaning in one place. 'bdc' is organized in thematic modules related to different biodiversity dimensions, including 1) Merge datasets: standardization and integration of different datasets; 2) pre-filter: flagging and removal of invalid or non-interpretable information, followed by data amendments; 3) taxonomy: cleaning, parsing, and harmonization of scientific names from several taxonomic groups against taxonomic databases locally stored through the application of exact and partial matching algorithms; 4) space: flagging of erroneous, suspect, and low-precision geographic coordinates; and 5) time: flagging and, whenever possible, correction of inconsistent collection date. In addition, it contains features to visualize, document, and report data quality – which is essential for making data quality assessment transparent and reproducible. The reference for the methodology is Ribeiro and colleagues (2022) doi:10.1111/2041-210X.13868.

Changes in 1.1.6

reword-countries.txt and country_names.txt were updated and fixed (by @sjevelazco; 274).
Migrated from {qs} to {qs2} package. Updated bdc_standardize_datasets() to use qs2::qs_save() and qs2::qs_read() instead of qs::qsave() and qs::qread(). The format option has been changed from "qs" to "qs2" and file extensions from .qs to .qs2.

From NEWS.md in the release

Install

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

install.packages("bdc", 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("brunobrr/bdc")

Development version from brunobrr/bdc. 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-bdc

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-bdc

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-bdc

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: 8.9 min · r-release-macos-x86_64

Status changes

OK13 OK2026-09-29
ERROR12 OK, 1 ERROR2026-09-04
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09

Show 8 earlier changesHide 8 earlier changes

ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-24
ERROR12 OK, 1 ERROR2026-05-17
OK13 OK2026-05-15
ERROR12 OK, 1 ERROR2026-05-13
OK13 OK2026-05-02
ERROR11 OK, 1 ERROR2026-04-25
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.6

READMEYes · 887 wordsVignettes· In the repository, left out of the releaseNEWSYes · 100% structured · mentions 1.1.6Citation fileNoWebsiteYes · pkgdown

The repository also keeps web-only articles.

Help pages: 23 (1 internal)
Examples that run: 55%12 run in a plain check · 2 only when donttest examples are enabled (R CMD check --as-cran) · 8 never run
Exported functions with examples: 96%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

5.4K

CRAN downloads in the past year

Rank #6,095 · ~15/day · ~447/mo

Releases R versions

Daily download trend is not available in this view yet.

56330 days

1.4K90 days

5.4K1 year

Compare downloads with other packages →

Also on110 r2u33 autocran

How downloads are counted

Repository

brunobrr/bdc ↗Account: brunobrr

25Stars

10Forks

5Open issues

0Open PRs

7Releases

1,349Commits

9Commit identities

bdcworkflowbiodiversity-data

License file reads as GPL-3.0 · 1,349 commits · Last activity 2026-10-16 · 0% stars, 30d · Default branch at 1.2.0, ahead of CRAN 1.1.6 (checked 2026-10-18)

Responsiveness

How these are sampled

PRs merged (all time): 97%
Median days to close, 50 most recently updated closed issues: 1
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-01-03 · 242026-08-22 · 25

How these are measured

PracticesBeta

11 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/brunobrr/bdc on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-10-16 · The repository has a site deploy workflow

pkgdown site last built 2026-10-16

Coverage (1)

Coverage reporting (Codecov)

Reproducibility and dev environment (1)

Makefile

Show all practicesHide 2 practices

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

AI coding toolsBeta

This repository shows signs of AI coding tools.

Claude Codefirst seen 2026-10-15
Named in .Rbuildignore: CLAUDE.md
Pull request it wrote: opened by a project member
Commits: at least 101 crediting it in the message

Models named in its commits

Claude Opus 5.5101 commits · Oct 2026

Some of these counts are a minimum, because the search stopped before the oldest commits.

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

39 external dependencies (excludes base and recommended)

Installing bdc adds 109 packages (58 with compiled code, 103 MB of source tarballs). Heaviest: stringi 11 MB, sf 9.3 MB, ggplot2 6.0 MB.

Depends (0)

none

Imports (21)

CoordinateCleaner doParallel dplyr DT foreach fs ggplot2 here magrittr purrr qs2 readr rgnparser rnaturalearth sf stringdist stringi stringr taxadb tibble tidyselect

LinkingTo (0)

none

Suggests (18)

contentid covr cowplot DBI duckdb knitr maps markdown rappdirs raster remotes rlang rmarkdown rnaturalearthdata sp rvest xml2 testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Suggested by 1

Suggests, most downloaded first

BeeBDC

How these are counted

Code & Tests

Datasets

People & History

People (7)

Bruno Ribeiro

Author, Maintainer since 1.0.0 (2022)

Karlo Guidoni-Martins

Author

Author

Author

Author

Contributor

Contributor

Releases (7)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
unarchivedReturned to CRAN
2026-01-24
1.1.6Latest
record
2026-01-24 · current release · diff ↗
archivedRemoved from CRAN
2026-01-17
requires archived package 'qs'
R
R 4.5.0 released · 2025-04-11
1.1.5
record
2024-12-17 · diff ↗
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
1.1.4
record
2023-03-13 · diff ↗
1.1.2
record
2022-08-18 · diff ↗
unarchivedReturned to CRAN
2022-05-27
1.1.1
record
2022-05-27 · diff ↗
archivedRemoved from CRAN
2022-05-23
check problems were not corrected in time
1.1.0
record
2022-04-22 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.0.0
record
2022-03-01

Show 1 earlier eventHide 1 earlier event

R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2022-03-01
Total releases: 7 / 4 yrs
License: GPL (>= 3) OSI
Download size: 646 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("bdc")

Format

Ribeiro, B., Bachman, S., Guidoni-Martins, K., Jardim, L., Loyola, R., Tessarolo, G., & Velazco, S. (2026). bdc: Biodiversity Data Cleaning (Version 1.1.6) [Computer software]. https://doi.org/10.32614/CRAN.package.bdc

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 bdc version 1.1.6 [Data set]. HJJB, LLC. Data release v2026-10-20. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-20, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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