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80 lines
2.5 KiB
80 lines
2.5 KiB
6 years ago
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C++ interface to fast hierarchical clustering algorithms
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========================================================
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This is a simplified C++ interface to fast implementations of hierarchical
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clustering by Daniel Müllner. The original library with interfaces to R
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and Python is described in:
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Daniel Müllner: "fastcluster: Fast Hierarchical, Agglomerative Clustering
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Routines for R and Python." Journal of Statistical Software 53 (2013),
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no. 9, pp. 1–18, http://www.jstatsoft.org/v53/i09/
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Usage of the library
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--------------------
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For using the library, the following source files are needed:
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fastcluster_dm.cpp, fastcluster_R_dm.cpp
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original code by Daniel Müllner
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these are included by fastcluster.cpp via #include, and therefore
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need not be compiled to object code
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fastcluster.[h|cpp]
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simplified C++ interface
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fastcluster.cpp is the only file that must be compiled
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The library provides the clustering function *hclust_fast* for
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creating the dendrogram information in an encoding as used by the
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R function *hclust*. For a description of the parameters, see fastcluster.h.
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Its parameter *method* can be one of
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HCLUST_METHOD_SINGLE
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single link with the minimum spanning tree algorithm (Rohlf, 1973)
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HHCLUST_METHOD_COMPLETE
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complete link with the nearest-neighbor-chain algorithm (Murtagh, 1984)
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HCLUST_METHOD_AVERAGE
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complete link with the nearest-neighbor-chain algorithm (Murtagh, 1984)
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HCLUST_METHOD_MEDIAN
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median link with the generic algorithm (Müllner, 2011)
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For splitting the dendrogram into clusters, the two functions *cutree_k*
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and *cutree_cdist* are provided.
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Note that output parameters must be allocated beforehand, e.g.
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int* merge = new int[2*(npoints-1)];
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For a complete usage example, see lines 135-142 of demo.cpp.
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Demonstration program
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---------------------
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A simple demo is implemented in demo.cpp, which can be compiled and run with
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make
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./hclust-demo -m complete lines.csv
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It creates two clusters of line segments such that the segment angle between
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line segments of different clusters have a maximum (cosine) dissimilarity.
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For visualizing the result, plotresult.r can be used as follows
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(requires R <https://r-project.org> to be installed):
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./hclust-demo -m complete lines.csv | Rscript plotresult.r
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Authors & Copyright
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-------------------
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Daniel Müllner, 2011, <http://danifold.net>
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Christoph Dalitz, 2018, <http://www.hsnr.de/ipattern/>
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License
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-------
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This code is provided under a BSD-style license.
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See the file LICENSE for details.
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