R Observatory: Metrics for taxa version 0.4.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

taxa

0.4.4

Classes for Storing and Manipulating Taxonomic Data

0packages dependsuggested by 1

6.2Kdownloads / year

70.5%test coverage

13/13flavors OK

Overview

About

Maintained by Zachary FosterCRAN page ↗GitHub ↗Website ↗Issues ↗

Provides classes for storing and manipulating taxonomic data. Most of the classes can be treated like base R vectors (e.g. can be used in tables as columns and can be named). Vectorized classes can store taxon names and authorities, taxon IDs from databases, taxon ranks, and other types of information. More complex classes are provided to store taxonomic trees and user-defined data associated with them.

Changes in 0.4.4

Fixing minor CRAN check issues.

From NEWS.md in the release

Install

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

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

Development version from ropensci/taxa. 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-taxa

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-taxa

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-taxa

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: 2.2 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.4.4

READMEYes · 226 wordsVignettesNoNEWSYes · 33% structured · mentions 0.4.4Citation fileYes · software entry onlyWebsiteYes · pkgdown

Help pages: 95 (51 internal)
Examples that run: 100%38 run in a plain check
Exported functions with examples: 79%
Documented parameters: 100%
Return-value docs: 16%
Help pages citing references: 0%

How these are measured

Downloads

6.2K

CRAN downloads in the past year

Rank #7,126 · ~17/day · ~520/mo

Releases R versions

Daily download trend is not available in this view yet.

42230 days

1.2K90 days

6.2K1 year

Compare downloads with other packages →

Also on146 r2u4 autocran1.6K conda_forge346 bioconda132 c2d4u

How downloads are counted

Repository

ropensci/taxa ↗Organization: ropensci

51Stars

12Forks

56Open issues

0Open PRs

10Releases

648Commits

9Commit identities

taxonomytaxondata-cleaningrstatsrr-package

648 commits · Last activity 2025-07-28 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 3
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-06-29 · 492026-07-07 · 51

How these are measured

PracticesBeta

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

Checks run against github.com/ropensci/taxa on 2026-10-11.

Continuous integration (2)

GitHub ActionsTravis CI (config file)

Governance and community (4)

Code of conductContributing guideIssue templatesPR template

Docs source (1)

README.Rmd

Coverage (1)

Coverage reporting (Codecov)

Show all practicesHide 3 practices

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Installing taxa adds 19 packages (10 with compiled code, 18 MB of source tarballs). Heaviest: stringi 11 MB, viridisLite 1.2 MB, vctrs 1.0 MB.

Depends (2)

R >= 3.0.2vctrs

Imports (11)

dplyr magrittr tibble rlang stringr crayonutilspillarmethodsviridisLite cli

LinkingTo (0)

none

Suggests (3)

roxygen2 testthat rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Suggested by 1

Suggests, most downloaded first

taxlist

How these are counted

Code & Tests

People & History

People (2)

Zachary Foster

Author, Maintainer since 0.2.1 (2018)

Scott Chamberlain

Author

Previously maintained by Scott Chamberlain (0.1.0 to 0.2.0).

Releases (12)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.4.4Latest
record
2025-07-28 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
0.4.3
record
2024-02-20 · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
0.4.2
record
2022-04-12 · diff ↗
0.4.1
record
2022-03-11 · diff ↗
0.4.0
record
2021-07-13 · diff ↗ ·
removed 56 exports
all_names, arrange_obs, arrange_taxa, branches, classifications, database_list, extract_tax_data, filter_obs, filter_taxa, get_data, get_data_frame, get_dataset, hierarchies, hierarchy, id_classifications, ids, is_branch, leaves_apply, lookup_tax_data, map_data, map_data_, mutate_obs, n_leaves_1, n_obs, n_obs_1, n_subtaxa_1, n_supertaxa_1, nms, obs, obs_apply and 26 more

added 30 exports
%in%, tax_auth<-, tax_author<-, tax_cite<-, tax_date<-, tax_db<-, tax_id<-, tax_name<-, tax_rank<-, as_data_frame, as_taxon, classification, db_ref, is_classification, is_taxon, is_taxon_authority, is_taxon_db, is_taxon_id, is_taxon_rank, is_taxonomy, tax_auth, tax_author, tax_cite, tax_date, tax_db, tax_id, tax_name, tax_rank, taxon_authority, taxon_db
R
R 4.1.0 released · 2021-05-18
0.3.4
record
2020-04-29 · diff ↗
R
R 4.0.0 released · 2020-04-24
0.3.3
record
2020-02-25 · diff ↗
R
R 3.6.0 released · 2019-04-26
0.3.2
record
2019-01-02 · diff ↗ ·
added 1 export
parse_edge_list

Show 6 earlier eventsHide 6 earlier events

0.3.1
record
2018-08-09 · diff ↗ ·
added 3 exports
get_dataset, print_tree, taxonomy_table
0.2.1
record
2018-05-03 · diff ↗ ·
added 6 exports
leaves_apply, n_leaves, n_leaves_1, taxon_ids, taxon_names, taxon_ranks
R
R 3.5.0 released · 2018-04-23
0.2.0
record
2017-12-19 · diff ↗ ·
removed 1 export
name_classifications

added 8 exports
branches, classifications, get_data_frame, internodes, is_internode, map_data_, n_supertaxa_1, remove_redundant_names
0.1.0
record
2017-07-16
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-07-16
Total releases: 12 / 9 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.0.2
Download size: 100 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("taxa")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.12688/f1000research.14013.1.

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 taxa version 0.4.4 [Data set]. HJJB, LLC. Data release v2026-10-17. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-17, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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