R Observatory: Metrics for opticskxi version 1.2.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

opticskxi

1.2.2Package record

OPTICS K-Xi Density-Based Clustering

1packages depend

6.6Kdownloads / year

93.1%test coverage

11/13flavors OK

Overview

About

Maintained by Thomas CharlonCRAN page ↗GitLab ↗Issues ↗

Density-based clustering methods are well adapted to the clustering of high-dimensional data and enable the discovery of core groups of various shapes despite large amounts of noise. This package provides a novel density-based cluster extraction method, OPTICS k-Xi, and a framework to compare k-Xi models using distance-based metrics to investigate datasets with unknown number of clusters. The vignette first introduces density-based algorithms with simulated datasets, then presents and evaluates the k-Xi cluster extraction method. Finally, the models comparison framework is described and experimented on 2 genetic datasets to identify groups and their discriminating features. The k-Xi algorithm is a novel OPTICS cluster extraction method that specifies directly the number of clusters and does not require fine-tuning of the steepness parameter as the OPTICS Xi method. Combined with a framework that compares models with varying parameters, the OPTICS k-Xi method can identify groups in noisy datasets with unknown number of clusters. Results on summarized genetic data of 1,200 patients are in Charlon T. (2019) doi:10.13097/archive-ouverte/unige:161795. A short video tutorial can be found at https://www.youtube.com/watch?v=P2XAjqI5Lc4/.

Changes in 1.2.2

Fix tests

From NEWS.md in the release

Install

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

install.packages("opticskxi", 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("thomaschln/opticskxi")

Development version from thomaschln/opticskxi. 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-opticskxi

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-opticskxi

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-opticskxi

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

2NOTE11OK

Check messages

NOTERd contentsr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Rd files without \usage:
  ‘compound.Rd’ ‘exposition.Rd’ ‘pipe.Rd’
\arguments should not be documented without \usage.

CRAN check page ↗

Slowest check: 5.2 min · r-oldrel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTENow
NOTE12 OK, 1 NOTE2026-07-11
OK13 OK2026-06-15
ERROR12 OK, 1 ERROR2026-06-10
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.2.2

README· In the repository, left out of the releaseVignettesYes · 2 · dynamicNEWSYes · 100% structured · mentions 1.2.2Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 29
Examples that run: 100%9 run in a plain check
Exported functions with examples: 33%
Documented parameters: 95%
Return-value docs: 95%
Help pages citing references: 0%

Vignettes (2)

How these are measured

Downloads

6.6K

CRAN downloads in the past year

Rank #15,892 · ~18/day · ~547/mo

Releases R versions

Daily download trend is not available in this view yet.

30030 days

78590 days

6.6K1 year

Compare downloads with other packages →

Also on90 r2u1 autocran

How downloads are counted

Repository

gitlab.com/thomaschln/opticskxi ↗

0Stars

0Forks

0Open issues

0Open PRs

0Releases

38Commits

3Commit identities

License file reads as GPL-3.0 · 38 commits · Last activity 2026-06-10 · The default branch showed an older version (1.2.1) than CRAN on 2026-10-21

Responsiveness

not measured

How these are measured

PracticesBeta

3 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against gitlab.com/thomaschln/opticskxi on 2026-10-21.

Continuous integration (1)

GitLab CI

Reproducibility and dev environment (2)

MakefileDockerfile

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Installing opticskxi adds 18 packages (8 with compiled code, 14 MB of source tarballs). Heaviest: ggplot2 6.0 MB, isoband 1.5 MB, farver 1.2 MB.

Depends (1)

R >= 3.5.0

Imports (4)

ggplot2 magrittrMatrixrlang

LinkingTo (0)

none

Suggests (14)

amap dbscan cowplot fastICA fpc ggrepelgridgrDevicesgtable knitrparallelplyr reshape2 testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Depends, Imports or LinkingTo, most downloaded first

kgraph

How these are counted

Code & Tests

Datasets

People & History

People (1)

Thomas Charlon

Author, Maintainer since 0.1 (2019)

Releases (5)

Pick two releases to compare their code metrics.

1.2.2Latest
record
2026-06-10 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
1.2.1
record
2025-03-09 · diff ↗ ·
added 1 export
normalize
1.2.0
record
2025-02-26 · diff ↗ ·
removed 3 exports
print_table, psych_kxi_ensemble_models, psych_kxi_pipeline

added 5 exports
cosine_simi, dist_matrix, norm_inprod, print_vignette_table, stddev_mean
1.1.0
record
2024-12-09 · diff ↗ ·
added 4 exports
ensemble_metrics, ensemble_models, psych_kxi_ensemble_models, psych_kxi_pipeline
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
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
0.1
record
2019-07-19
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-07-19
Total releases: 5 / 7 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 661 KB / 4 files
Download size: 3.1 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("opticskxi")

Format

Charlon, T. (2026). opticskxi: OPTICS K-Xi Density-Based Clustering (Version 1.2.2) [Computer software]. https://doi.org/10.32614/CRAN.package.opticskxi

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 opticskxi version 1.2.2 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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