Re: [R] Error message with nmds

From: Jari Oksanen <>
Date: Wed 17 May 2006 - 15:48:50 EST

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

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, homepage

______________________________________________ mailing list
PLEASE do read the posting guide!
Received on Wed May 17 16:21:51 2006

Archive maintained by Robert King, hosted by the discipline of statistics at the University of Newcastle, Australia.
Archive generated by hypermail 2.1.8, at Wed 17 May 2006 - 18:10:10 EST.

Mailing list information is available at Please read the posting guide before posting to the list.