R Observatory: Metrics for taxizedb version 0.3.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

taxizedb

0.3.2Package record

Offline Access to Taxonomic Databases

0packages depend

4.4Kdownloads / year

58.8%test coverage

13/13flavors OK

Overview

About

Maintained by Tamás StirlingCRAN page ↗GitHub ↗Website ↗Issues ↗

Download taxonomic databases, convert them into 'SQLite' format, and query them locally for fast, reliable, and reproducible access to taxonomic data.

Changes in 0.3.2

MINOR IMPROVEMENTS

For certain databases, the db_download_*() function downloaded a preprocessed SQLite database from the cloud, where it was updated automatically e.g. daily. However, cloud access occasionally broke. To provide robust functionaility. db_download_*() was updated to download raw data and convert it to SQLite locally, on demand, for all databases. (#81)

BUG FIXES

Replaced readr::read_tsv_chunked with vroom::vroom() to avoid memory limitation for checks on macOS. (#89)

DEFUNCT

TPL is no longer available so db_download_tpl() will fail. However, if the database was downloaded earlier, it can still be queried using taxizedb functions. (#87)

From NEWS.md in the release

Install

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

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

Development version from ropensci/taxizedb. 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-taxizedb

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-taxizedb

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-taxizedb

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: 1.7 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
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 0.3.2

README· In the repository, left out of the releaseVignettes· In the repository, left out of the releaseNEWSYes · 33% structured · mentions 0.3.2Citation fileYes · computed when R runs itWebsiteYes · pkgdown

Help pages: 14includes a package overview page
Examples that run: 0%12 never run
Exported functions with examples: 85%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

4.4K

CRAN downloads in the past year

Rank #8,169 · ~12/day · ~367/mo

Releases R versions

Daily download trend is not available in this view yet.

34630 days

1.1K90 days

4.4K1 year

Compare downloads with other packages →

Also on164 r2u3 autocran1.3K conda_forge

How downloads are counted

Repository

ropensci/taxizedb ↗Organization: ropensci

35Stars

8Forks

16Open issues

1Open PRs

8Releases

320Commits

9Commit identities

taxonomytaxonomic-databasesitisrstatstaxizerr-package

320 commits · Last activity 2025-06-17 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 90%
Median days to close, 50 most recently updated closed issues: 26
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-10-21 · 332026-07-07 · 35

How these are measured

PracticesBeta

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

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

Continuous integration (3)

GitHub ActionsR CMD check workflowCircleCI

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

Governance and community (4)

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

Docs source (2)

README.Rmd

GitHub Pages site last deployed 2021-05-03

Reproducibility and dev environment (1)

Makefile

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

13 external dependencies (excludes base and recommended)

Installing taxizedb adds 41 packages (23 with compiled code, 27 MB of source tarballs). Heaviest: stringi 11 MB, RSQLite 4.2 MB, vctrs 1.0 MB.

Depends (1)

R >= 4.1

Imports (11)

curl DBI RSQLite dplyr (>= 0.7.0)tibble rlang readr dbplyr magrittr hoardr vroom

LinkingTo (0)

none

Suggests (2)

taxize testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (3)

Tamás Stirling

Contributor, Maintainer since 0.3.1 (2023) · added in 0.3.1

Zebulun Arendsee

Author · added in 0.2.0

Scott Chamberlain

Author

Previously maintained by Scott Chamberlain (0.1.0 to 0.3.0).

Releases (7)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
unarchivedReturned to CRAN
2025-06-18
0.3.2Latest
record
2025-06-18 · current release · diff ↗ ·
removed 1 export
%>%
R
R 4.5.0 released · 2025-04-11
archivedRemoved from CRAN
2024-08-31
policy violation Spamming personal email address of team member in HTML
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
0.3.1
record
2023-04-03 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
0.3.0
record
2021-01-15 · diff ↗ ·
added 1 export
taxa_at
0.2.2
record
2020-08-26 · diff ↗
0.2.0
record
2020-08-13 · diff ↗ ·
added 15 exports
children, classification, db_download_ncbi, db_download_wfo, db_download_wikidata, db_load_ncbi, db_load_wikidata, db_path, downstream, name2taxid, src_ncbi, src_wfo, src_wikidata, taxid2name, taxid2rank
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

Show 3 earlier eventsHide 3 earlier events

0.1.4
record
2017-06-21 · diff ↗
0.1.0
record
2017-05-04
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-05-04
Total releases: 7 / 9 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1
Download size: 37 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("taxizedb")

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 taxizedb version 0.3.2 [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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