R Observatory: Metrics for genieclust version 1.3.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

genieclust

1.3.0

Genie: Fast and Robust Hierarchical Clustering

8packages depend

13.5Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Marek GagolewskiFirst published 2020-07-3012 releasesCRAN page ↗GitHub ↗

Genie is a robust hierarchical clustering algorithm (Gagolewski, Bartoszuk, Cena, 2016 DOI:10.1016/j.ins.2016.05.003). 'genieclust' is its faster, more capable implementation (Gagolewski, 2021 DOI:10.1016/j.softx.2021.100722). It enables clustering with respect to mutual reachability distances, allowing it to act as an alternative to 'HDBSCAN*' that can identify any number of clusters or their entire hierarchy. When combined with the 'deadwood' package, it can act as an outlier detector. Additional package features include the Gini and Bonferroni inequality indices, external cluster validity measures (e.g., the normalised clustering accuracy, the adjusted Rand index, the Fowlkes-Mallows index, and normalised mutual information), and internal cluster validity indices (e.g., the Calinski-Harabasz, Davies-Bouldin, Ball-Hall, Silhouette, and generalised Dunn indices). The 'Python' version of 'genieclust' is available via 'PyPI'.

Install

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

install.packages("genieclust", 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("gagolews/genieclust")

Development version from gagolews/genieclust. 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-genieclust

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-genieclust

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-genieclust

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

Health

CRAN checks

13OK

Slowest check: 2.9 min · r-devel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

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
OK2026-04-22
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 93%
Return-value docs: 100%
References docs: 80%

Downloads

13.5K

CRAN downloads in the past year

Rank #2,806 · ~37/day · ~1.1K/mo

Releases R versions

Daily download trend is not available in this view yet.

2.5K30 days

5.5K90 days

13.5K1 year

Compare downloads with other packages →

Also on5.6K r2u14 autocran5.1K conda_forge41 c2d4u

Repository

GitHub ↗ gagolews/genieclust

74Stars

12Forks

14Open issues

0Open PRs

18Releases

730Commits

4Contributors

clustering-algorithmcluster-analysispython3hdbscanpythonmachine-learning-algorithmsnmslibmlpack

730 commits · Last activity 2026-06-18 · +4.2% stars, 30d

Stars over time

2025-07-26 · 652026-08-09 · 74

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/gagolews/genieclust on 2026-08-16.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

Makefile

Research and citation (1)

CITATION.cff

Coverage (1)

Codecov

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

Dependencies

Declared dependencies

3 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (4)

Rcppstatsutilsdeadwood

LinkingTo (1)

Rcpp

Suggests (1)

datasets

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

8direct

1indirect

genie Kmedians RGMM STARRS evoFE modACDC mlr3cluster partition

Code & Tests

People & History

People (4)

Maintainer (1)

Marek Gagolewski

Author, Maintainer, Copyright holder

Authors (1)

Marek Gagolewski

Author, Maintainer, Copyright holder

Contributors (3)

Maciej Bartoszuk

Contributor

Anna Cena

Contributor

Peter M. Larsen

Contributor

Copyright holders (1)

Marek Gagolewski

Author, Maintainer, Copyright holder

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.3.0Latest
2026-02-23 · current release · diff ↗
1.2.0
2025-07-24 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.1.6
2024-08-22 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.1.5-2
2023-10-18 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.1.3
2023-01-17 · diff ↗
1.1.0
2022-09-05 · diff ↗
1.0.1
2022-08-08 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.0.0
2021-04-22 · diff ↗
0.9.8
2021-01-08 · diff ↗
0.9.7
2021-01-07 · diff ↗

Show 3 earlier events

0.9.4
2020-08-01 · diff ↗
0.9.3
2020-07-30
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-07-30
Total releases: 12 / 6 yrs
License: AGPL-3 OSI
Download size: 73 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Cluster Analysis & Finite Mixture Models

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("genieclust")

The authors publish a CITATION.cff, so they have said how they want this cited. Run citation() and use what it gives you.

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 genieclust version 1.3.0 [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.

Report a problem with this page →