pearson correlation with axes of NMDS or capscale

Hi all,

In Primer/permanova+ it is possible to get the pearson correlation of a
species with the axes of NMDS or capscale. Is it possible to extract or
calculate these as well based on the output from metaMDS() or capscale
(), both from the vegan-package?

Wout,

Short answer: Yes.

A bit longer answer: you shouldn't do this for metaMDS (or NMDS in
general) since there the orientation of axes is random and axes do not
have a special meaning.

A longer answer or how to do this. You may paste the following to an R
window (explanations are commented):

### BEGIN R
## NMDS
library(vegan)
data(dune)
m <- metaMDS(dune)
cor(dune, scores(m, dis="si"))
## capscale, copying the previous method, but 4 axes
m <- capscale(dune ~ 1)
cor(dune, scores(m, dis="si", choices=1:4)
## capscale, the direct way re-using the previous result
scores(m, dis="sp", scaling=-2, const = sqrt(nrow(dune)-1)))
### END

That is, with appropriate scaling, capscale scores are the correlations
between species and axes.

Cheers, Jari Oksanen