R Observatory: Metrics for ClassifyITS version 1.0.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ClassifyITS

1.0.2

Fungal Assignment Pipeline

0packages depend

1.7Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Quinn MoonFirst published 2026-04-092 releasesCRAN page ↗

Fungi are ubiquitous in Earth's wonderfully diverse ecosystems. The 'ClassifyITS' package aids in the taxonomic classification of environmental internal transcribed spacer (ITS) short-read barcoding data. Unlike previous methods, it employs taxon-specific e-value and percent identity cutoffs at each taxonomic rank from kingdom to species. The package takes a conservative approach and outputs both graphics and user-friendly files to help users manually inspect fungal operational taxonomic units (OTUs) that fail classification at relevant levels (e.g., Phylum). 'ClassifyITS' is based on taxonomic cutoff criteria from "The Global Soil Mycobiome consortium dataset for boosting fungal diversity research" (Fungal Diversity, Tedersoo, 2021, doi:10.1007/s13225-021-00493-7) and "Best practices in metabarcoding of fungi: From experimental design to results" (Molecular Ecology, Tedersoo, 2022, doi:10.1111/mec.16460).

Install

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

install.packages("ClassifyITS", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

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-classifyits

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-ClassifyITS

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-ClassifyITS

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

Health

CRAN checks

13OK

Slowest check: 1.9 min · r-oldrel-macos-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

6

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-10
5 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 745 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

1.7K

CRAN downloads in the past year

Rank #9,977 · ~5/day · ~139/mo

Releases R versions

Daily download trend is not available in this view yet.

15530 days

95790 days

1.7K1 year

Compare downloads with other packages →

Also on46 r2u20 autocran

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (6)

ggplot2 gridExtragridreshape2 data.table seqinr

LinkingTo (0)

none

Suggests (3)

formatR knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Maintainer (1)

Quinn Moon

Author, Maintainer

Authors (1)

Quinn Moon

Author, Maintainer

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.0.2Latest
2026-04-23 · current release · diff ↗
0.1.0
2026-04-09
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2026-04-09
Total releases: 2 / 1 yrs
License: GPL-3 OSI
Download size: 139 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("ClassifyITS")

Format

Quinn Moon. (2026). ClassifyITS: Fungal Assignment Pipeline (Version 1.0.2) [Computer software]. https://doi.org/10.32614/CRAN.package.ClassifyITS

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 ClassifyITS version 1.0.2 [Data set]. HJJB, LLC. Data release v2026-08-16. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-16, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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