[SciPy-User] cluster.hierarchy.fcluster: Choosing value for threshold t?

Pundurs Mark (Nokia-LC/Chicago) mark.pundurs@nokia....
Wed Apr 25 12:39:52 CDT 2012

I have ~8000 observations of 1-D data (not a standard use case for cluster.hierarchy, I suspect). I send the output of linkage to fcluster; if I choose a t of 1.5, the output array has only one unique value, and if I choose t=0.5, the output array has as many unique values as does the input data. I can see from dendrogram that there are intermediate levels of clustering; apart from trial and error, how do I find a t that returns such a clustering?

(Does the vertical axis of the dendrogram have anything to do with fcluster's t argument? In the dendrogram, clusters split at integer values of the vertical component.)

Mark Pundurs
Data Analyst - Traffic
Location & Commerce

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