mdendro
Extended Agglomerative Hierarchical Clustering in R
Index
Description
R package mdendro enables the calculation of agglomerative hierarchical clustering (AHC), extending the standard functionalities in several ways:
- Native handling of both similarity and dissimilarity (distances) matrices.
- Calculation of pair-group dendrograms and variable-group multidendrograms [1].
- Implementation of the most common AHC methods in both weighted and unweighted forms: single linkage, complete linkage, average linkage (UPGMA and WPGMA), centroid (UPGMC and WPGMC), and Ward.
- Implementation of two additional parametric families of methods: versatile linkage [2], and beta flexible. Versatile linkage leads naturally to the definition of two additional methods: harmonic linkage, and geometric linkage.
- Calculation of the cophenetic (or ultrametric) matrix.
- Calculation of five descriptors of the final dendrogram: cophenetic correlation coefficient, space distortion ratio, agglomerative coefficient, chaining coefficient, and tree balance.
- Plots of the descriptors for the parametric methods.
All this functionality is obtained with two functions: linkage, and descplot. Function linkage may be considered as a replacement for functions hclust (in package stats) and agnes (in package cluster). To enhance usability and interoperability, the linkage class includes several methods for plotting, summarizing information, and class conversion.
Usage
To use mdendro, check first the documentation at GitHub:
- Full documentation, including description, installation, tutorial, rationale and reference manual: documentation at GitHub
- CRAN: The Comprehensive R Archive Network mdendro page
- Source code: GitHub sergio-gomez / mdendro
- Archived: zenodo with DOI:10.5281/zenodo.4849734
Alternatively, you may use MultiDendrograms, an application with graphical user interface, or the Hierarchical_Clustering program in Radatools.
References
| [1] |
Solving Non-uniqueness in Agglomerative Hierarchical Clustering Using Multidendrograms
Alberto Fernández and Sergio Gómez Journal of Classification 25 (2008) 43-65 (view) (pdf) (doi) (Springer Nature) |
| [2] |
Versatile linkage: a family of space-conserving strategies for agglomerative hierarchical clustering
Alberto Fernández and Sergio Gómez Journal of Classification 37 (2020) 584-597 (view) (pdf) (doi) (Springer Nature) |
Authors
Alberto Fernández:
-
Dept. Enginyeria Química, Universitat Rovira i Virgili, Tarragona, Spain
(email) (ORCID) (Google Scholar) (GitHub)
Sergio Gómez: