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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