Package: opticskxi
Title: OPTICS K-Xi Density-Based Clustering
Version: 1.2.1
Authors@R: person("Thomas", "Charlon", role = c("aut", "cre"), email = "charlon@protonmail.com", comment = c(ORCID = "0000-0001-7497-0470"))
Description: 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/>.
Imports: ggplot2, magrittr, Matrix, rlang
Depends: R (>= 3.5.0)
Suggests: amap, dbscan, cowplot, fastICA, fpc, ggrepel, grid,
        grDevices, gtable, knitr, parallel, plyr, reshape2, testthat
VignetteBuilder: knitr
License: GPL-3
Encoding: UTF-8
RoxygenNote: 7.3.2
URL: https://gitlab.com/thomaschln/opticskxi
BugReports: https://gitlab.com/thomaschln/opticskxi/-/issues
Repository: https://thomaschln.r-universe.dev
Date/Publication: 2026-06-10 12:31:26 UTC
RemoteUrl: https://gitlab.com/thomaschln/opticskxi
RemoteRef: HEAD
RemoteSha: e8e7e08ed6af6c9b1261593dba0af4dda976cd37
NeedsCompilation: no
Packaged: 2026-06-10 15:26:07 UTC; root
Author: Thomas Charlon [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-7497-0470>)
Maintainer: Thomas Charlon <charlon@protonmail.com>