[R] Fwd: MDS problems [ajtee@ajtee.uklinux.net]

Adam Tee adam at ajtee.uklinux.net
Sat Mar 27 13:25:32 CET 2004

On 03/26/04 14:07:30, Jari Oksanen wrote:
> The error message is clear: You have some identical sites so that
> theirdistance is zero. I think the canonical solution is to remove  
> the duplicate cases from the data before calculating the  
> dissimilarities. If your data frame is called X:
> Xuniq <- unique(X)
> x.dist <- dist(Xuniq)
> (or, as a one-liner: x.dist <- dist(unique(X))

One of the difficulties is that it is significant that some of the data  
is identical as I am comparing musical sequences. The above does not  
work as I am not dealing with the raw data. I am using my own  
dissimilarity measure output by a separate program.  The reason for  
using MDS is to visualise the data based on the developed dissimilarity  

Would it be better to use PCA ??


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