[R] Error message with nmds

Jonathan Hughes jhughes at ess.washington.edu
Tue May 16 22:25:21 CEST 2006

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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