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

Shakya, Migun microbeatic at gmail.com
Sat Apr 21 21:41:05 CEST 2012


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
>
>
>
>



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