[R-sig-eco] NMDS and envfit

[Gavin Simpson]

On Wed, 2013-05-15 at 14:42 +0300, adrien wrote:
> Hello,
> 
> for the function envfit in package vegan, the manual suggests that "The 
> function fits environmental vectors or factors onto an ordination" but 
> since there are scores for both sites and species, does envfit correlate 
> the environmental factors to the sites or to the species NMDS scores? Or 
> to both, at the same time? Or am I missing something?

There are really only site scores in nMDS, and anyway, all versions of
envfit would work on the site scores. So only the chosen axis scores are
used in the envfit process.

As for the species scores; metaMDS adds these as a convenience feature
if the species data is available to it. They are added as a weighted
average of the site scores and then possibly expanded. 

G

> thanks for any input on this!
> 
> adrien


-- 
Gavin Simpson, PhD                          [t] +1 306 337 8863
Adjunct Professor, Department of Biology    [f] +1 306 337 2410
Institute of Environmental Change & Society [e] gavin.simpson at uregina.ca
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University of Regina
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