Re: st: Clustering with Sequence analysis/optimal matching

[brendan.halpin@ul.ie (Brendan Halpin)]

On Wed, Mar 21 2012, Stefan Weih wrote:

> Thanks for your comments, Brendan.
>
> However, as indicated in the correspondance earlier, I did use Ward's
> method. Also no typo involved. For the complete syntax on my clustering
> procedure, please see below:
>
> sqclusterdat
> clustermat wardslinkage SQdist, name(wards) add
> cluster tree wards, cutnumber(20)
> sqclusterdat, return


OK, that's fairly unambiguous. I'm puzzled. As far as I understand,
reversals (where after combining clusters i and j, the distance from
cluster k to the joint cluster is less than d(i,k) and/or d(j,k)) don't
happen with Ward's method. 

Could your distance matrix be defective? For instance, could it be
non-metric? Normally OM is guaranteed to generate metric distances, but
if the substitution matrix is not metric, the distances are not
guaranteed to be metric. That's a long shot, though -- I have no idea
whether non-metric distances will give Ward's method indigestion. 


Another thing that might be helpful would be to post the output from the
following:

. sqclusterdat
. clustermat wardslinkage SQdist, name(wards) add
. cluster query wards
. return list
. cluster tree wards, cutnumber(20)


Regards,

Brendan
-- 
Brendan Halpin,   Department of Sociology,   University of Limerick,   Ireland
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