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>.
| Version: | 1.2.0 |
| Depends: | R (≥ 3.5.0) |
| Imports: | ggplot2, magrittr, rlang, text2vec |
| Suggests: | amap, dbscan, cowplot, fastICA, fpc, ggrepel, grid, grDevices, gtable, knitr, parallel, plyr, reshape2, testthat |
| Published: | 2025-02-26 |
| 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.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_1.2.0.tar.gz |
| Windows binaries: | r-devel: opticskxi_1.2.0.zip, r-release: opticskxi_1.1.0.zip, r-oldrel: opticskxi_1.2.0.zip |
| macOS binaries: | r-devel (arm64): opticskxi_1.2.0.tgz, r-release (arm64): opticskxi_1.2.0.tgz, r-oldrel (arm64): opticskxi_1.2.0.tgz, r-devel (x86_64): opticskxi_1.2.0.tgz, r-release (x86_64): opticskxi_1.2.0.tgz, r-oldrel (x86_64): opticskxi_1.2.0.tgz |
| Old sources: | opticskxi archive |
Linking:
Please use the canonical form https://CRAN.R-project.org/package=opticskxi to link to this page.