opticskxi: OPTICS K-Xi Density-Based Clustering

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/>.

Version:	1.2.1
Depends:	R (≥ 3.5.0)
Imports:	ggplot2, magrittr, Matrix, rlang
Suggests:	amap, dbscan, cowplot, fastICA, fpc, ggrepel, grid, grDevices, gtable, knitr, parallel, plyr, reshape2, testthat
Published:	2025-03-09
DOI:	10.32614/CRAN.package.opticskxi
Author:	Thomas Charlon [aut, cre]
Maintainer:	Thomas Charlon <charlon at protonmail.com>
BugReports:	https://gitlab.com/thomaschln/opticskxi/-/issues
License:	GPL-3
URL:	https://gitlab.com/thomaschln/opticskxi
NeedsCompilation:	no
Materials:	NEWS
CRAN checks:	opticskxi results

Documentation:

Reference manual:	opticskxi.html , opticskxi.pdf
Vignettes:	Ensemble Metrics And Models For Density-Based Clustering (source, R code) OPTICS K-Xi Density-Based Clustering (source, R code)

Downloads:

Package source:	opticskxi_1.2.1.tar.gz
Windows binaries:	r-devel: opticskxi_1.2.1.zip, r-release: opticskxi_1.2.1.zip, r-oldrel: opticskxi_1.2.1.zip
macOS binaries:	r-release (arm64): opticskxi_1.2.1.tgz, r-oldrel (arm64): opticskxi_1.2.1.tgz, r-release (x86_64): opticskxi_1.2.1.tgz, r-oldrel (x86_64): opticskxi_1.2.1.tgz
Old sources:	opticskxi archive

Reverse dependencies:

Reverse imports:

kgraph

Linking:

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