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

Zoltan Botta-Dukat bdz at botanika.hu
Tue Nov 16 21:06:51 CET 2010

Dear Chris,

I'm not sure that You really have to create continuous "traits" by PCoA. 
You can simply calculate functional diversity from the distance matrix. 
If you have abundance data, I suggest calculating Rao's quadratic 
entropy (it is implemented for example in FD and ade4 packages). If only 
presence/absence data are available, you could find indices in Schmera 
et al. (2009).

Using PCoA is needed only if you want to apply detailed analysis 
proposed by Villéger et al. 2008. However, before do it, I suggest 
reading Podani's comments (Podani 2009).

Best wishes


Podani, J. 2009. Convex hulls, habitat filtering, and functional 
diversity: mathematical elegance versus ecological interpretability. 
Community Ecology 10(2): 244-250.

Schmera, D., T. Erős and J. Podani. 2009. A measure for assessing 
functional diversity in ecological communities. Aquatic Ecol. 43: 
157-167. DOI 10.1007/s10452-007-9152-9

2010.11.16. 16:08 keltezéssel, chris mcowen írta:
> 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
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