R Observatory: Metrics for yatah version 1.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

yatah

1.0.0Package record

Yet Another TAxonomy Handler

0packages depend

2.3Kdownloads / year

100.0%test coverage

13/13flavors OK

Overview

About

Maintained by Antoine BichatCRAN page ↗GitHub ↗Website ↗Issues ↗

Provides functions to manage taxonomy when lineages are described with strings and ranks separated with special patterns like "|*__" or ";*__".

Changes in 1.0.0

last_clade(), last_rank() and all_clades() are now deprecated in favor

of get_last_clade(), get_last_rank() and get_all_clades() (#11).

New functions get_clade() (#12) and is_at_least_rank().
New dataset all_ranks.

From NEWS.md in the release

Install

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

install.packages("yatah", 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("abichat/yatah")

Development version from abichat/yatah. 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-yatah

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-yatah

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-yatah

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: 1.5 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
WARNING12 OK, 1 WARNING2026-06-08
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.0

READMEYes · 223 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 1.0.0Citation fileNoWebsiteYes · pkgdown

Help pages: 20 (6 internal)includes a package overview page
Examples that run: 100%14 run in a plain check
Exported functions with examples: 92%
Documented parameters: 98%
Return-value docs: 92%
Help pages citing references: 0%

Vignettes (1)

Taxonomy of Gammaproteobacteria HTML

How these are measured

Downloads

2.3K

CRAN downloads in the past year

Rank #18,784 · ~6/day · ~192/mo

Releases R versions

Daily download trend is not available in this view yet.

23430 days

69690 days

2.3K1 year

Compare downloads with other packages →

Also on66 r2u3 autocran

How downloads are counted

Repository

abichat/yatah ↗Account: abichat

6Stars

1Forks

0Open issues

0Open PRs

2Releases

150Commits

3Commit identities

taxonomyclades

License file reads as GPL-3.0 · 150 commits · Last activity 2024-04-13

Responsiveness

How these are sampled

PRs merged (all time): 93%
Median days to close, 50 most recently updated closed issues: 13
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2019-06-14 · 62026-07-07 · 6

How these are measured

PracticesBeta

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

Checks run against github.com/abichat/yatah on 2026-10-21.

Continuous integration (4)

GitHub ActionsR CMD check workflowTravis CI (config file)AppVeyor

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

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2024-04-13 · The repository has a site deploy workflow

pkgdown site last built 2024-04-13

Coverage (1)

Coverage reporting (Codecov)

Reproducibility and dev environment (1)

data-raw/

Show all practicesHide 2 practices

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Installing yatah adds 12 packages (10 with compiled code, 18 MB of source tarballs). Heaviest: stringi 11 MB, Rcpp 1.8 MB, ape 1.4 MB.

Depends (1)

R >= 2.10

Imports (5)

ape lifecycle purrrstatsstringr

LinkingTo (0)

none

Suggests (5)

dplyr knitr rmarkdown spelling testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (1)

Antoine Bichat

Author, Maintainer since 0.0.1 (2019)

Releases (4)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.0.0Latest
record
2024-04-13 · current release · diff ↗ ·
added 5 exports
get_all_clades, get_clade, get_last_clade, get_last_rank, is_at_least_rank
R
R 4.3.0 released · 2023-04-21
0.2.1
record
2022-11-12 · diff ↗ ·
added 3 exports
trim_common, trim_rank, trim_void
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
0.1.0
record
2020-03-01 · diff ↗
0.0.1
record
2019-06-28
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-06-28
Total releases: 4 / 7 yrs
License: GPL-3 OSI
Minimum R: ≥ 2.10
Bundled data: 228 KB / 2 files
Download size: 411 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("yatah")

Format

Bichat, A. (2024). yatah: Yet Another TAxonomy Handler (Version 1.0.0) [Computer software]. https://doi.org/10.32614/CRAN.package.yatah

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 yatah version 1.0.0 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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