returning site and species coordinates in NMDS using vegan
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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