[R] Error message with nmds

From: Jonathan Hughes <jhughes_at_ess.washington.edu>
Date: Wed 17 May 2006 - 06:25:21 EST

I am trying to apply nmds to a data matrix but I receive the following error message:

Error in isoMDS(dis, y = y, k = k, maxit = maxit) :

        zero or negative distance between objects 5 and 7

The data are in a vegetation cover-class matrix (species in columns, plots in rows, classes 1-8 with lots of zero values) converted to a dissimilarity matrix (bray curtis).

I assumed that objects 5 and 7 refer to rows of my original data; and they do have the same species with the same cover classes. I deleted one of these rows but I received the same error message with a rerun of nmds. As it turns out, the new rows 5 and 7 are the same. How do I avoid this problem?

Any advice for this neophyte would be greatly appreciated. Thanks!

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