Published by the Foundation for Open Access Statistics Editors-in-chief: Bettina Grün, Torsten Hothorn, Rebecca Killick, Edzer Pebesma, Achim Zeileis    ISSN 1548-7660; CODEN JSSOBK
Authors: Guy Brock, Vasyl Pihur, Susmita Datta, Somnath Datta
Title: clValid: An R Package for Cluster Validation
Abstract: The R package clValid contains functions for validating the results of a clustering analysis. There are three main types of cluster validation measures available, "internal", "stability", and "biological". The user can choose from nine clustering algorithms in existing R packages, including hierarchical, K-means, self-organizing maps (SOM), and model-based clustering. In addition, we provide a function to perform the self-organizing tree algorithm (SOTA) method of clustering. Any combination of validation measures and clustering methods can be requested in a single function call. This allows the user to simultaneously evaluate several clustering algorithms while varying the number of clusters, to help determine the most appropriate method and number of clusters for the dataset of interest. Additionally, the package can automatically make use of the biological information contained in the Gene Ontology (GO) database to calculate the biological validation measures, via the annotation packages available in Bioconductor. The function returns an object of S4 class "clValid", which has summary, plot, print, and additional methods which allow the user to display the optimal validation scores and extract clustering results.

Page views:: 34375. Submitted: 2007-04-03. Published: 2008-03-18.
Paper: clValid: An R Package for Cluster Validation     Download PDF (Downloads: 38638)
clValid_0.5-6.tar.gz: R source package Download (Downloads: 1533; 284KB) v25i04.R: example code from the paper Download (Downloads: 1472; 1KB)

DOI: 10.18637/jss.v025.i04

This work is licensed under the licenses
Paper: Creative Commons Attribution 3.0 Unported License
Code: GNU General Public License (at least one of version 2 or version 3) or a GPL-compatible license.