Fastcluster: Fast hierarchical, agglomerative clustering routines for R and Python

Abstract

The fastcluster package is a C++ library for hierarchical, agglomerative clustering. It provides a fast implementation of the most e_cient, current algorithms when the input is a dissimilarity index. Moreover, it features memory-saving routines for hierarchical clustering of vector data. It improves both asymptotic time complexity (in most cases)and practical performance (in all cases) compared to the existing implementations in standard software: several R packages, MATLAB, Mathematica, Python with SciPy. The fastcluster package presently has interfaces to R and Python. Part of the functionality is designed as a drop-in replacement for the methods hclust and flashClust in R and scipy.cluster.hierarchy.linkage in Python, so that existing programs can be e_ortlessly adapted for improved performance.