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The fastcluster package: User’s manual Version 1.1.11

By Daniel Müllner


The fastcluster package is a C++ library for hierarchical, agglomerative clustering. It efficiently implements the seven most widely used clustering schemes: single, complete, average, weighted/mcquitty, Ward, centroid and median linkage. The library currently has interfaces to two languages: R and Python/SciPy. Part of the functionality is designed as drop-in replacement for existing routines: linkage in the SciPy package scipy.cluster.hierarchy, hclust in R’s stats package, and the flashClust package. Once the fastcluster library is loaded at the beginning of the code, every program that uses hierarchical clustering can benefit immediately and effortlessly from the performance gain. Moreover, there are memory-saving routines for clustering of vector data, which go beyond what the existing packages provide. This document describes the usage for the two interfaces for R and Python and is meant as the reference document for the end user. Installation instructions are given in the file INSTALL in the source distribution and are not repeated here. The sections about the two interfaces are independent and in consequence somewhat redundant, so that users who need a reference for one interface need to consult only one section. If you use the fastcluster package for scientific work, please cite it as

Topics: hclust.vector..................................... 5
Year: 2013
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