[R] Specifying medoids in PAM?

[David Finlayson]

Thanks for your help, that worked.

David

On 6/8/05, Martin Maechler <maechler at stat.math.ethz.ch> wrote:
> >>>>> "MM" == Martin Maechler <maechler at stat.math.ethz.ch>
> >>>>>     on Wed, 8 Jun 2005 18:57:55 +0200 writes:
> 
> >>>>> "David" == David Finlayson <david.p.finlayson at gmail.com>
> >>>>>     on Wed, 8 Jun 2005 09:24:54 -0700 writes:
> 
>     David> Sorry, I wasn't trying to submit a bug report just yet.
> 
>     MM> the posting guide asks you to provide reproducible examples, in
>     MM> any case, not just for bug reports ...
>     MM> {and strictly speaking, you still haven't provided one, since
>     MM> it's a bit painful to read in your table below -- because of the
>     MM> extra row names ... but here I'm nit picking a bit }
> 
>     David> I wanted to see if I was using the command correctly.
> 
>     MM> Yes, you were.
> 
> 
>     >>> pam(stats.table, metric="euclidean", stand=TRUE, medoids=c(1,3,20,2,5), k=5)
> 
>     David> This command crashes RGUI.exe and windows sends an error report to
>     David> Microsoft. It also crashes if I first subtract the NA rows from
>     David> stats.table.
> 
>     MM> I can confirm to get segmentation faults using this example data
>     MM> with k=5 ,  so effectively, it seems you've uncovered a bug in pam().
>     MM> I will investigate and patch eventually.
> 
> I found and fixed the bug:
> Some part of the C code was assuming that the indices in
> 'medoids' were sorted (increasingly).
> 
> I.e., for the moment you can easily work around the problem by
> using
>    pam(stats.table, ...., medoids=c(1,2,3,5,20), k=5)
> instead of
>    pam(stats.table, ...., medoids=c(1,3,20,2,5), k=5)
> 
> 
> The next version of the cluster package which allows to specify
> the "fuzzyness exponent" in fanny()  will have this problem
> fixed.
> 
> Martin Maechler,
> ETH Zurich
> 


-- 
David Finlayson
Marine Geology & Geophysics
School of Oceanography
Box 357940
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USA

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