Unifrac distance matrix with dbRDA in Vegan
Hi Jari, I think I was concerned by the limited publication using the method. But, I think after going through few papers esp the PNAS paper "Bacterial community structures are unique and resilient in full-scale bioenergy systems", I am more confident in the method as it gives similar result to CCA. I am still struggling on its advantage over CCA though, except for evolutionary relationship between communites given by the Unifrac itself. Thanks Migee
On 4/21/12 1:30 PM, "Jari Oksanen" <jari.oksanen at oulu.fi> wrote:
On 20/04/2012, at 17:29 PM, Migun Shakya wrote:
Hi all,
There has been few publications in microbial ecology recently
that have successfully used UniFrac distance matrix with dbRDA, but i
have failed to find the clear idea on tools or R package that they
have used. I know there is a capscale function in vegan that does
dbRDA or CAP (Constrained Analysis of Principal Coordinates). I used
this function to analyze my data with unifrac distance, but I am
concerned as I couldnt find anything validating the use of unifrac
distance metrics with capscale function of vegan.
Migee, What do you think is a validation? As to dbRDA (capscale) or NMDS, these should should be valid with any dissimilarity measure, and unifrac distance is a dissimilarity measure. Sounds like perfectly valid to me. By the way, I changed metaMDS function in vegan so that it easily accepts unifrac distances a couple of years ago after I was in a workshop with Susan Letcher, and she suggested I do this. Cheers, Jari Oksanen -- Jari Oksanen, Dept Biology, Univ Oulu, 90014 Finland