Re: [R] Clustering algorithms don't find obvious clusters

From: Dave Roberts <dvrbts_at_ecology.msu.montana.edu>
Date: Fri, 11 Jun 2010 12:57:24 -0700

Henrik,

     The clustering algorithms you refer to (and almost all others) expect the matrix to be symmetric. They do not seek a graph-theoretic solution, but rather proximity in geometric or topological space.

     How did you convert y9oru matrix to a dissimilarity?

Dave Roberts

Henrik Aldberg wrote:
> I have a directed graph which is represented as a matrix on the form
>
>
> 0 4 0 1
>
> 6 0 0 0
>
> 0 1 0 5
>
> 0 0 4 0
>
>
> Each row correspond to an author (A, B, C, D) and the values says how many
> times this author have cited the other authors. Hence the first row says
> that author A have cited author B four times and author D one time. Thus the
> matrix represents two groups of authors: (A,B) and (C,D) who cites each
> other. But there is also a weak link between the groups. In reality this
> matrix is much bigger and very sparce but it still consists of distinct
> groups of authors.
>
>
> My problem is that when I cluster the matrix using pam, clara or agnes the
> algorithms does not find the obvious clusters. I have tried to turn it into
> a dissimilarity matrix before clustering but that did not help either.
>
>
> The layout of the clustering is not that important to me, my primary
> interest is the to get the right nodes into the right clusters.
>
>
>
> Sincerely
>
>
> Henrik
>
> [[alternative HTML version deleted]]
>
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-



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https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Received on Fri 11 Jun 2010 - 21:11:01 GMT

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