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

[Jari Oksanen]

Chris,

Here some random exegeses:

You should be aware that functional diversity seems to be dangerous field
where you cannot do the right thing: there are different schools of thought,
and you can always get a "wrong referee" what ever you do. Be warned. The
major difference seems to be between tree-based and ordination-based
(distance based) approaches. Some other, perhaps even more dangerous fields,
are distance decay (Mantel) vs. variation partition (RDA) where you will be
shot down by a "wrong referee" what ever you do. Even after you change your
manuscript following one referee, the other referee burns you because you
did so. Beta diversity is still one dangerous example that is hot to touch.
You better read the literature very carefully.

I find it curious that the same things have been invented in a bit different
disguise in several fields of ecology s.lat. Aquatic and marine ecologists
have taxonomic diversity which seems to be exactly the same thing except it
uses taxonomy instead of traits. Mycologists and microbiologist have
phylogenetic diversity since they don't have traits and don't know the
"species", but they only have OTUs, sequences and phylogenies. Terrestrial,
aquatic and microbial ecologists do not read the same journals and so they
reinvent parallel variants of similar things and use different words and
names.  

Finally, if you make your traits into distances (dissimilarities), it is
best to see what Marti Anderson tells you to do with them. She has ideas for
full space analysis of differences (like adonis in vegan), for full space
analysis of dispersion (like betadisper in vegan), and for reduced space
analysis (like db-RDA as in capscale in vegan). All these use the geometry
of PCoA/ classic MDS/ metric MDS, although this is not always visible to the
surface:. The full space analyses by Marti Anderson even handle the
imaginary dimensions (associated with negative eigenvalues in metric MDS)
within the function which may be very hard to handle with explicit PCoA.

Cheers, Jari Oksanen