[R] metaMDS and envfit: Help reading output

[Briony]

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

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