[Scipy-tickets] [SciPy] #1272: Some hierarchical clustering methods not working for proximity matrices

SciPy Trac scipy-tickets@scipy....
Tue Sep 7 13:32:44 CDT 2010


#1272: Some hierarchical clustering methods not working for proximity matrices
---------------------------+------------------------------------------------
 Reporter:  cassio         |       Owner:  somebody
     Type:  defect         |      Status:  new     
 Priority:  normal         |   Milestone:  0.9.0   
Component:  scipy.cluster  |     Version:  0.7.0   
 Keywords:                 |  
---------------------------+------------------------------------------------
 The following methods: ward, centroid, median, in the package
 scipy.cluster.hierarchy are not working on a proximity matrix.

 Suppose I have 5 objects and a condensed distance matrix of 10 pairwise
 distances, when I try to run any of the above methods I get:

 ValueError: Valid methods when the raw observations are omitted are
 'single', 'complete', 'weighted', and 'average'.

 I don't understand why I cannot use ward, centroid or median only
 providing the proximity matrix, as those algorithms clearly allow for this
 (relational methods).

 In R I can use the hclust command and generate the hierarchies for ward,
 centroid and median.

 Sample code to generate the problem:

 from pylab import *
 from numpy import *
 from scipy.cluster.hierarchy import *

 y = random_sample(10)
 Z = ward(y)

-- 
Ticket URL: <http://projects.scipy.org/scipy/ticket/1272>
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