OptCirClust

0.0.4

Circular, Periodic, or Framed Data Clustering: Fast, Optimal, and Reproducible

1packages depend

2.8Kdownloads / year

61.3%test coverage

10/13checks pass

Overview

About

Maintained by Joe SongFirst published 2020-12-094 releasesCRAN page ↗

Fast, optimal, and reproducible clustering algorithms for circular, periodic, or framed data. The algorithms introduced here are based on a core algorithm for optimal framed clustering the authors have developed (Debnath & Song 2021) doi:10.1109/TCBB.2021.3077573. The runtime of these algorithms is O(K N log^2 N), where K is the number of clusters and N is the number of circular data points. On a desktop computer using a single processor core, millions of data points can be grouped into a few clusters within seconds. One can apply the algorithms to characterize events along circular DNA molecules, circular RNA molecules, and circular genomes of bacteria, chloroplast, and mitochondria. One can also cluster climate data along any given longitude or latitude. Periodic data clustering can be formulated as circular clustering. The algorithms offer a general high-performance solution to circular, periodic, or framed data clustering.

Install

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

install.packages("OptCirClust", 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-optcirclust

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-OptCirClust

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-OptCirClust

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

Health

CRAN checks

3NOTE10OK

Failing flavors

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

Slowest check: 2.3 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.76

61.3%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

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
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 330 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 50%

Downloads

2.8K

CRAN downloads in the past year

Rank #14,612 · ~8/day · ~233/mo

Releases R versions

Daily download trend is not available in this view yet.

19530 days

71090 days

2.8K1 year

Compare downloads with other packages →

Also on412 r2u3 autocran25 c2d4u

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (7)

Ckmeans.1d.dpgraphicsplotrix Rcpp Rdpackstatsreshape2

LinkingTo (1)

Rcpp

Suggests (5)

ape ggplot2 knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

1indirect

CircularSilhouette

Code & Tests

People & History

People (2)

Maintainer (1)

Joe Song

Author, Maintainer

Authors (2)

Joe Song

Author, Maintainer

Tathagata Debnath

Author

Package Timeline

4 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
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
0.0.4Latest
2021-07-28 · current release · diff ↗
R
R 4.1.0 released · 2021-05-18
0.0.3
2020-12-18 · diff ↗
0.0.2
2020-12-15 · diff ↗
0.0.1
2020-12-09
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-12-09
Total releases: 4 / 6 yrs
License: LGPL (>= 3) OSI
Download size: 528 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

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