R Observatory: Metrics for densityClust version 0.3.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

densityClust

0.3.3

Clustering by Fast Search and Find of Density Peaks

1packages depend

31Kdownloads / year

0.0%test coverage

13/13checks pass

Overview

About

Maintained by Thomas Lin PedersenFirst published 2014-07-216 releasesCRAN page ↗GitHub ↗

An improved implementation (based on k-nearest neighbors) of the density peak clustering algorithm, originally described by Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle large datasets (> 100,000 samples) very efficiently. It was initially implemented by Thomas Lin Pedersen, with inputs from Sean Hughes and later improved by Xiaojie Qiu to handle large datasets with kNNs.

Install

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

install.packages("densityClust", 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("thomasp85/densityClust")

Development version from thomasp85/densityClust. 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-densityclust

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-densityClust

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-densityClust

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

Health

CRAN checks

13OK

Slowest check: 2.8 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.18

0.0%

Coverage · measured lines

100%

Documentation · exports

7

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
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 298 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 97%
Return-value docs: 75%
References docs: 44%

Downloads

31K

CRAN downloads in the past year

Rank #3,606 · ~85/day · ~2.6K/mo

Releases R versions

Daily download trend is not available in this view yet.

75230 days

2.7K90 days

31K1 year

Compare downloads with other packages →

Also on395 r2u24 autocran5.5K conda_forge206 bioconda

Repository

GitHub ↗ thomasp85/densityclust

164Stars

66Forks

4Open issues

0Open PRs

2Releases

57Commits

5Contributors

57 commits · Last activity 2024-01-29 · 0% stars, 30d

Stars over time

2025-07-17 · 1552026-07-18 · 164

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/thomasp85/densityclust on 2026-08-16.

Continuous integration (1)

GitHub Actions

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Coverage (1)

Codecov

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

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (7)

FNN ggplot2 ggrepelgrDevicesgridExtra RColorBrewer Rtsne

LinkingTo (1)

cpp11

Suggests (2)

covr testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

FCPS

Code & Tests

People & History

People (3)

Maintainer (1)

Thomas Lin Pedersen

Author, Maintainer

Authors (3)

Thomas Lin Pedersen

Author, Maintainer

Sean Hughes

Author · added in 0.2.1

Xiaojie Qiu

Author · added in 0.3

Package Timeline

6 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
0.3.3Latest
2024-01-29 · current release · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
0.3.2
2022-03-06 · diff ↗
0.3.1
2022-02-21 · diff ↗
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
0.3
2017-10-24 · diff ↗
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
0.2.1
2016-02-06 · diff ↗

Show 3 earlier events

R
R 3.2.0 released · 2015-04-16
0.1-1
2014-07-21
R
R 3.1.0 released · 2014-04-10

Package metadata

First published: 2014-07-21
Total releases: 6 / 12 yrs
License: GPL (>= 2) OSI
Download size: 89 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("densityClust")

Format

Pedersen, T. L., Hughes, S., & Qiu, X. (2024). densityClust: Clustering by Fast Search and Find of Density Peaks (Version 0.3.3) [Computer software]. https://doi.org/10.32614/CRAN.package.densityClust

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 densityClust version 0.3.3 [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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