Hi Lauren,

site.scores<-scores(mds.result, display="sites")
species.scores<-scores(mds.result, display="species")

Note that your result from metaMDS function should be based on "raw data"
not on "distance matrices". If your input to metaMDS function is a distance
matrix you will not be able to recover species scores.

victor



On Tue, Sep 20, 2011 at 5:54 PM, L Quinn <lquinn@hotmail.com> wrote:

>
> Hi,
> I am running a simple NMDS as outlined by Jari Oksanen in vegantutor, e.g.
> spp.dist<-vegdist(spp)spp.mds<-metaMDS(spp,trace=FALSE)spp.mds
> I am able to plot the results (species nicely overlaying sites) using
> plot(spp.mds,display="species",type="t",family="sans",font=2,xlim=c(-0.4,0.4),ylim=c(-0.4,0.4))#
> and points(env.mds,display="sites")
> However, try as I might, I am not able to make this figure look pretty
> enough in R to satisfy journal editors/reviewers. I want to redraw the
> results in Excel, but I don't know how to extract species and site
> coordinates from spp.mds. I see that I can do this using isoMDS in MASS, but
> I'd prefer to use vegan. Perhaps I'm missing something obvious, but I
> haven't been able to find it anywhere so far. How does one go about
> extracting those coordinates?
> Thanks in advance.
> Lauren
>
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-- 
victor
_______________________________

Victor Lemes Landeiro
http://ppbio.inpa.gov.br/Port/public/disciplinas2/introducaor/document_view
fones
(62)85764316(Oi); (62)81702517(Tim)

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