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

[Gavin Simpson]

On Tue, 2011-09-20 at 20:54 +0000, 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

Why don't you tell use what you want to do to produce a plot that will
meet the reviewers/editors requirements? That way we can help you with R
code to do the plot as I am 100% certain you won't be able to do a
better job with Excel.

Yes, I am that confident! I've published umpteen papers using vegan
plots, that with a bit of crafting haven't had any problems getting past
reviewers/editors of the ecological/environmental journals I have
published in.

G

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