[R] Error message with nmds

[Jari Oksanen]

On Tue, 2006-05-16 at 13:25 -0700, Jonathan Hughes wrote:
> 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?

Jonathan, this is a FAQ in the proper sense of the word: this is
frequently asked. Last thread was on April, 2006. See

https://stat.ethz.ch/pipermail/r-help/2006-April/092598.html

and answers. You may also use RSiteSearch with keyword "isoMDS" to find
other (and older) threads.

cheers, jari oksanen
-- 
Jari Oksanen -- Dept Biology, Univ Oulu, 90014 Oulu, Finland
email jari.oksanen at oulu.fi, homepage http://cc.oulu.fi/~jarioksa/