[R] metaMDS and envfit: Help reading output
brionynorton at gmail.com
Thu Sep 8 09:15:23 CEST 2011
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
ordirgl (in package rgl) gives a very nifty interactive 3d plot, or
ordiplot3d is a static version.
I hope this is useful.
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.
More information about the R-help