[R-sig-eco] Unifrac distance matrix with dbRDA in Vegan

[John Erb-Downward]

Hi Migee, 
   I think the reason that you've not found a lot of info on it is that there is are not a lot of people doing this (or constrained ordinations generally in microbial ecology).  Unifrac is a fairly new method that has gotten a lot of traction in microbial ecology, but to the best of my knowledge there is no way of doing a constrained ordination in QIIME (which is the tool generally used for Unifrac analysis).  So as far as validation, I think you're in rather uncharted waters.  However, the PNAS paper "Bacterial community structures are unique and resilient in full-scale bioenergy systems" does an RDA with unifrac distances and Rob Knight is one of the authors on the paper.  Since he was one of the people who created the metric, I doubt he would have allowed the analysis if he thought it was invalid.  I have done what you are describing and it worked, but in all honesty I don't think that it is any better than a CCA.  
 
Good luck, 

-John

> 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.
> 
> If anybody have experience on using capscale with unifrac or know of
> any other packages that does this well would be great.
> 
> Thank you
> 
> Migee