Re: [R] Error message with nmds

From: Jari Oksanen <jarioksa_at_sun3.oulu.fi>
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

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/

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Received on Wed May 17 16:21:51 2006

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