[R-sig-eco] returning site and species coordinates in NMDS using vegan

[Gavin Simpson]

On Tue, 2011-09-20 at 18:17 -0300, Victor L. Landeiro wrote:
> Hi Lauren,
> 
> site.scores<-scores(mds.result, display="sites")
> species.scores<-scores(mds.result, display="species")

I wanted to write that you can do this in a single call; but you can't.
You should be able to, so I'll take a look at scores.metaMDS and improve
it to work more like scores.cca for example.

G

> 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 at 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
> >
> >        [[alternative HTML version deleted]]
> >
> > _______________________________________________
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> > R-sig-ecology at r-project.org
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> >
> 
> 
> 

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