[R] vegan metaMDS question

[Gavin Simpson]

On Wed, 2009-05-27 at 11:31 -0400, stephen sefick wrote:
> The design decision in metaMDS says that it uses:
> 
> Minchin, P.R. (1987) An evaluation of relative robustness of
> techniques for ecological ordinations. Vegetatio 71, 145-156.
> 
> This is the paper that I found by the same name.  Is this the correct reference?
> 
> Minchin, Peter R.1987. An Evaluation of the Relative Robustness  of
> Techniques for Ecological Ordination. Vegetatio. Vol. 69, No. 1/3:
> 89-107.

Yes, I suspect so - the other volume/pages refers to another paper of
Peter Minchin's. Jari has now fixed this in the sources and the change
will be made in the next version of Vegan released to CRAN. Thanks for
pointing this out.

> 
> In this paper the double standardization (wisconsin()) is used then a
> centering by species is preformed.  The centering by species isn't
> incorporated in the metaMDS methodology, is it?

No it isn't.

>   Is there a reason for
> this, or am I missing something?

Yes - the only mention of centring by species is in reference to PCA. If
you centre species data, you'd have negative numbers, which can't be
handled in most dissimilarity coefficients and hence doesn't make sense
for nMDS. If I've overlooked something in that paper let me know and
I'll take a closer look.

I forwarded your email to Jari Oksanen, who wrote the metaMDS code in
vegan. If he has anything more to add, I'm sure he'll reply to you
directly.

Why did you send this to R-Help and me? This is a specific
package-related question which should go to the maintainer (Jari). We
also have a forum for asking such questions on the vegan R-Forge pages.
There is no need to bother this list with such questions.

HTH

G

> best regards,
> 
-- 
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