Message-ID: <328DB489-6B56-4237-92AC-B97E7A96DDDB@gmail.com>
Date: 2011-09-21T00:07:50Z
From: Cliff Beall
Subject: returning site and species coordinates in NMDS using vegan
In-Reply-To: <BAY169-W98AAEA11D2716E96F7B59ACE0A0@phx.gbl>
The site coordinates are in spp.mds$points and the species coordinates are in spp.mds$species
I have used those to make bubble plots, scaling the size of points by species abundance. I got the idea from PRIMER and extended it with R.
I use the R graphics though, I think they are very flexible.
On Sep 20, 2011, at 4:54 PM, L Quinn 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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