Hi Katie, This is probably a bit late given the date of your post, but I was having similar problems with my own work and thought I'd respond anyway. I'm not sure that the script you've written here will fit 3D vectors for your 3D nmds. I tried it and it doesn't seem to work for me - it only gives 2D for the vectors. I found this: nmds3d <- metaMDS(varespec, k = 3, distance = 'bray', autotransform = FALSE) # run nmds with 3 dimensions nmds3d$stress # stress drops fit3d <- envfit(nmds3d, varechem[ ,1:4], choices = 1:3) # fit environmental vectors to 3d space ordirgl(nmds3d, envfit = fit3d) # dynamic 3D graph
at http://en.wikibooks.org/wiki/R_Programming/Ordination ordirgl (in package rgl) gives a very nifty interactive 3d plot, or ordiplot3d is a static version. I hope this is useful. Kind regards, Briony -- View this message in context: http://r.789695.n4.nabble.com/metaMDS-and-envfit-Help-reading-output-tp3513052p3798043.html Sent from the R help mailing list archive at Nabble.com. ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
