[R-sig-eco] Quantifying functional trait diversity through Gower distance and pcoa

[chris mcowen]

Dear List,

I am relatively new to this area of ecology and R, coming from a
phylogenetic background. I am looking to quantify functional trait
diversity in in order to plot global functional trait diversity
hotspots. My trait data are categorical and all indicies of functional
diversity require continuous data.

My approach was to generate a distance matrix based on the Gower
method - i have done this with vegdist- and then i was planning on
running a pcoa on these to generate the continuous data to use in the
calculation of functional diversity indicies.

I have two questions:-

First, does this make sense, i appreciate i will loose information this way.

Second, I have looked at vegan but can not see a way to run a pcoa on
the output from a vegdist analysis, is this possible and once again
does this make sense?

Any help would be greatly appreciated,

Chris