R Observatory: Metrics for taxonomizr version 0.11.1

Balamuta, James Joseph

taxonomizr

0.11.1

Functions to Work with NCBI Accessions and Taxonomy

1packages depend

10.4Kdownloads / year

99.4%test coverage

9/13checks pass

Overview

About

Maintained by Scott Sherrill-MixFirst published 2017-03-0913 releasesCRAN page ↗GitHub ↗

Functions for assigning taxonomy to NCBI accession numbers and taxon IDs based on NCBI's accession2taxid and taxdump files. This package allows the user to download NCBI data dumps and create a local database for fast and local taxonomic assignment.

Install

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

install.packages("taxonomizr", 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("sherrillmix/taxonomizr")

Development version from sherrillmix/taxonomizr. 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-taxonomizr

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

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-taxonomizr

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-taxonomizr

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

4NOTE9OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc
NOTE r-devel-linux-x86_64-fedora-gcc
NOTE r-devel-windows-x86_64

Slowest check: 2.6 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.69

99.4%

Coverage · measured lines

100%

Documentation · exports

4

Dependencies · direct

Check history

NOTE2026-07-16
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-11
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
WARNING2026-05-10
12 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE

Show 1 earlier snapshots

OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 2,453 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 80%
Documented parameters: 97%
Return-value docs: 100%
References docs: 30%

Downloads

10.4K

CRAN downloads in the past year

Rank #6,779 · ~29/day · ~870/mo

Releases R versions

Daily download trend is not available in this view yet.

36130 days

1.3K90 days

10.4K1 year

Compare downloads with other packages →

Also on430 r2u1 autocran4.8K conda_forge557 bioconda

Repository

GitHub ↗ sherrillmix/taxonomizr

82Stars

14Forks

0Open issues

0Open PRs

9Releases

311Commits

1Contributors

License GPL-2.0 · 311 commits · Last activity 2025-07-24 · 0% stars, 30d

Stars over time

2025-07-02 · 772026-07-07 · 82

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/sherrillmix/taxonomizr on 2026-08-03.

Continuous integration (1)

Travis CI

Docs source (1)

README.Rmd

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.0.0

Imports (4)

RSQLite R.utils data.table curl

LinkingTo (0)

none

Suggests (3)

testthat knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

DBTC

Code & Tests

People & History

People (1)

Maintainer (1)

Scott Sherrill-Mix

Author, Maintainer

Authors (1)

Scott Sherrill-Mix

Author, Maintainer

Package Timeline

13 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
0.11.1Latest
2025-03-13 · current release · diff ↗
0.10.8
2025-02-28 · diff ↗
0.10.7
2025-01-08 · diff ↗
R
R 4.4.0 released · 2024-04-24
0.10.6
2023-12-15 · diff ↗
R
R 4.3.0 released · 2023-04-21
0.10.2
2023-01-31 · diff ↗
0.9.3
2022-06-26 · diff ↗
0.9.2
2022-06-23 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
0.8.0
2021-05-07 · diff ↗
0.7.1
2021-04-23 · diff ↗
0.6.0
2021-02-09 · diff ↗

Show 8 earlier events

R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
0.5.3
2019-04-22 · diff ↗
0.5.1
2018-08-31 · diff ↗
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
0.2.2
2017-03-09
R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2017-03-09
Total releases: 13 / 9 yrs
License: GPL (>= 2) | file LICENSE OSI
Minimum R: ≥ 3.0.0
Download size: 84 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Start here. This is the citation for the package itself.

citation("taxonomizr")

CRAN DOI

https://doi.org/10.32614/CRAN.package.taxonomizr

BibTeX, derived from DESCRIPTION

@Manual{taxonomizr,
  title  = {taxonomizr: Functions to Work with NCBI Accessions and Taxonomy},
  author = {Sherrill-Mix, Scott},
  year   = {2025},
  note   = {R package version 0.11.1},
  doi    = {10.32614/CRAN.package.taxonomizr},
  url    = {https://CRAN.R-project.org/package=taxonomizr}
}

Derived from the package DESCRIPTION, not from a citation file the authors wrote. If they publish one later, prefer it.

This is the citation for the package. It is not a citation for the R Observatory.

Cite this page

Use this when the claim is about a measurement on this page.

BibTeX

@misc{robservatorytaxonomizr,
  author    = {Balamuta, James Joseph},
  title     = {{R} {Observatory}: Metrics for {taxonomizr} version 0.11.1},
  year      = {2026},
  publisher = {HJJB, LLC},
  url       = {https://r-observatory.thecoatlessprofessor.com/packages/taxonomizr},
  note      = {Data set. Data release v2026-08-05}
}

APA

Balamuta, J. J. (2026). R Observatory: Metrics for taxonomizr version 0.11.1 [Data set]. HJJB, LLC. Data release v2026-08-05. https://r-observatory.thecoatlessprofessor.com/packages/taxonomizr

RIS

TY  - DATA
AU  - Balamuta, James Joseph
TI  - R Observatory: Metrics for taxonomizr version 0.11.1
PY  - 2026
PB  - HJJB, LLC
N1  - Data release v2026-08-05
UR  - https://r-observatory.thecoatlessprofessor.com/packages/taxonomizr
ER  -

In prose

These package metrics were obtained from the R Observatory (Balamuta, 2026), data release v2026-08-05, https://r-observatory.thecoatlessprofessor.com/packages/taxonomizr.

Bound to data release v2026-08-05, which is what makes the numbers on this page reproducible. See how to cite.

Report a problem with this page →