R Observatory: Metrics for densityClust version 0.3.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

densityClust

0.3.3Package record

Clustering by Fast Search and Find of Density Peaks

0packages dependsuggested by 1

22.2Kdownloads / year

0.0%test coverage

13/13flavors OK

Overview

About

Maintained by Thomas Lin PedersenCRAN page ↗GitHub ↗Issues ↗

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.

Changes in 0.3.3

Upkeep
Move from Rcpp to cpp11

From NEWS.md in the release

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. 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-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). 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

Additional issues

rchk

CRAN check page ↗

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

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.3.3

READMEYes · 298 wordsVignettesNoNEWSYes · 100% structured · mentions 0.3.3Citation fileNo

Help pages: 9 (1 internal)includes a package overview page
Examples that run: 100%7 run in a plain check
Exported functions with examples: 75%
Documented parameters: 97%
Return-value docs: 75%
Help pages citing references: 44%

How these are measured

Downloads

22.2K

CRAN downloads in the past year

Rank #3,751 · ~61/day · ~1.8K/mo

Releases R versions

Daily download trend is not available in this view yet.

83330 days

2.5K90 days

22.2K1 year

Compare downloads with other packages →

Also on485 r2u16 autocran5.5K conda_forge224 bioconda

How downloads are counted

Repository

thomasp85/densityclust ↗Account: thomasp85

164Stars

66Forks

4Open issues

0Open PRs

2Releases

57Commits

5Commit identities

57 commits · Last activity 2024-01-29 · 0% stars, 30d · Default branch at 0.3.3.9000, ahead of CRAN 0.3.3 (checked 2026-10-11)

Responsiveness

How these are sampled

PRs merged (all time): 56%
Median days to close, 50 most recently updated closed issues: 58
Median days to close, 50 most recently updated closed PRs: 192

Stars over time

2025-10-01 · 1602026-07-18 · 164

How these are measured

PracticesBeta

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

Checks run against github.com/thomasp85/densityclust on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Governance and community (1)

Code of conduct

Docs source (1)

README.Rmd

Coverage (1)

Coverage reporting (Codecov)

Show all practicesHide 1 practice

CRAN release process (1)

cran-comments.md

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Installing densityClust adds 22 packages (11 with compiled code, 16 MB of source tarballs). Heaviest: ggplot2 6.0 MB, Rcpp 1.8 MB, isoband 1.5 MB.

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

0direct

0indirect

Suggested by 1

Suggests, most downloaded first

FCPS

How these are counted

Code & Tests

People & History

People (3)

Thomas Lin Pedersen

Author, Maintainer since 0.1-1 (2014)

Sean Hughes

Author · added in 0.2.1

Xiaojie Qiu

Author · added in 0.3

Releases (6)

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
0.3.3Latest
record
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
record
2022-03-06 · diff ↗
0.3.1
record
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
record
2017-10-24 · diff ↗ ·
added 2 exports
plotDensityClust, plotTSNE
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
0.2.1
record
2016-02-06 · diff ↗

Show 3 earlier eventsHide 3 earlier events

R
R 3.2.0 released · 2015-04-16
0.1-1
record
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

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 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 densityClust version 0.3.3 [Data set]. HJJB, LLC. Data release v2026-10-17. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-17, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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