R Observatory: Metrics for clustur version 0.1.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

clustur

0.1.4

Clustering

1packages depend

6.6Kdownloads / year

92.9%test coverage

13/13checks pass

Overview

About

Maintained by Patrick SchlossFirst published 2024-11-145 releasesCRAN page ↗GitHub ↗

A tool that implements the clustering algorithms from 'mothur' (Schloss PD et al. (2009) doi:10.1128/AEM.01541-09). 'clustur' make use of the cluster() and make.shared() command from 'mothur'. Our cluster() function has five different algorithms implemented: 'OptiClust', 'furthest', 'nearest', 'average', and 'weighted'. 'OptiClust' is an optimized clustering method for Operational Taxonomic Units, and you can learn more here, (Westcott SL, Schloss PD (2017) doi:10.1128/mspheredirect.00073-17). The make.shared() command is always applied at the end of the clustering command. This functionality allows us to generate and create clustering and abundance data efficiently.

Install

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

install.packages("clustur", 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("SchlossLab/clustur")

Development version from SchlossLab/clustur. 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-clustur

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-clustur

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-clustur

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

Health

CRAN checks

13OK

Slowest check: 9.7 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 12.38

92.9%

Coverage · measured lines

100%

Documentation · exports

4

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
OK2026-05-02
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 1 earlier snapshots

NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 181 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

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

Downloads

6.6K

CRAN downloads in the past year

Rank #5,751 · ~18/day · ~548/mo

Releases R versions

Daily download trend is not available in this view yet.

22530 days

1.4K90 days

6.6K1 year

Compare downloads with other packages →

Also on440 r2u19 autocran

Repository

GitHub ↗ schlosslab/clustur

2Stars

0Forks

2Open issues

0Open PRs

4Releases

47Commits

2Contributors

License GPL-3.0 · 47 commits · Last activity 2026-08-17 · 0% stars, 30d

Stars over time

2025-02-05 · 12026-07-07 · 2

Repository practices

Upstream repositoryBeta

5 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/schlosslab/clustur on 2026-08-16.

Continuous integration (1)

GitHub Actions

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Lint, format, editor (2)

lintrRStudio project

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

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (4)

MatrixmethodsRcpputils

LinkingTo (2)

Rcpp testthat

Suggests (4)

knitr rmarkdown testthat xml2

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

mums2

Code & Tests

People & History

People (3)

Maintainer (1)

Patrick Schloss

Author, Maintainer, Copyright holder

Authors (3)

Patrick Schloss

Author, Maintainer, Copyright holder

Gregory Johnson

Author

Sarah Westcott

Author

Copyright holders (1)

Patrick Schloss

Author, Maintainer, Copyright holder

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
0.1.4Latest
2026-01-08 · current release · diff ↗
0.1.3
2025-04-21 · diff ↗
0.1.2
2025-04-14 · diff ↗
R
R 4.5.0 released · 2025-04-11
0.1.1
2024-11-25 · diff ↗
0.1.0
2024-11-14
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-11-14
Total releases: 5 / 2 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.5.0
Download size: 237 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("clustur")

Format

Schloss, P., Johnson, G., & Westcott, S. (2026). clustur: Clustering (Version 0.1.4) [Computer software]. https://doi.org/10.32614/CRAN.package.clustur

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 clustur version 0.1.4 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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