opticskxi

1.2.2

OPTICS K-Xi Density-Based Clustering

1packages depend

7.7Kdownloads / year

93.1%test coverage

11/13checks pass

Overview

About

Maintained by Thomas CharlonFirst published 2019-07-195 releasesCRAN page ↗GitLab ↗

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/.

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.

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).

Health

CRAN checks

2NOTE11OK

Failing flavors

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

Slowest check: 5.7 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.22

93.1%

Coverage · measured lines

88%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-07-11
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-15
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-10
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 95%
Return-value docs: 95%
References docs: 0%

Downloads

7.7K

CRAN downloads in the past year

Rank #7,186 · ~21/day · ~640/mo

Releases R versions

Daily download trend is not available in this view yet.

23830 days

1.5K90 days

7.7K1 year

Compare downloads with other packages →

Also on133 r2u38 autocran

Repository

GitLab ↗ thomaschln/opticskxi

Repository practices

Upstream repositoryBeta

Repository gitlab.com/thomaschln/opticskxi is linked, but repository-practices checks have not run for it yet. Checks are GitHub-only for now.

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

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

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

kgraph

Code & Tests

Code Composition

R 1,374 (48%)Rd 816 (28%)Vignettes 601 (21%)Other 78 (3%)

Code characteristics

Cyclomatic complexity: 2.0 median / 10 max
Test cases: 13 / 0.22 per code line

Test coverage

Line coverage

93%

Expression

91.1%

Tests / Examples

93.1% / 73% ex

Functions

41 21 exported

Complexity

2.6 avg / 10 max

Call network

41 nodes / 28 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

41 functions

Function	Cyclo	Coverage
norm_inprod exp	1	0%
stddev_mean exp	2	0%
inprod	2	0%
dist_matrix exp	2	75%
get_best_kxi exp	4	75%
normalize exp	4	80%

Datasets

Bundled datasets · 3

Name	Class	Rows × Cols	Also ships in
crohn	data.frame	387 × 212	in 3 packages
hla	data.frame	271 × 8	in 2 packages
multishapes	data.frame	1,100 × 3	in 2 packages

People & History

People (1)

Maintainer (1)

Thomas Charlon

Author, Maintainer

Authors (1)

Thomas Charlon

Author, Maintainer

Package Timeline

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

1.2.2Latest
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
2025-03-09 · diff ↗
1.2.0
2025-02-26 · diff ↗
1.1.0
2024-12-09 · diff ↗
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
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: 2.5 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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