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

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From: Adam Tee (adam@ajtee.uklinux.net)
Date: Sat 27 Mar 2004 - 23:25:32 EST


Message-id: <20040327122532.GA3719@ajtee>

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
measure.

Would it be better to use PCA ??

Adam

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