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

[dougwyu]

Hi Jari,

Thanks.  That's what i thought, but i was confused by this:  I changed metaMDS 
function in vegan so that it easily accepts unifrac distances

I thought it was something to do with formatting or a special unifrac output 
file or something.

doug

On 23 Apr 2012, at 12:36, Jari Oksanen wrote:

 
 On 23/04/2012, at 04:19 AM, dougwyu wrote:
 
 
 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
 
 
 Would you please point us to any documentation for importing unifrac 
 distance matrices into vegan?  (nothing specific about unifrac turns up in 
 the vegan documentation)
 
 I was about to do this and was under the impression that i could treat 
 unifrac matrices like any other distance matrix.  
 
 Doug,
 
 It is not about vegan but about R: vegan uses R dissimilarity/distance 
 structures (that inherit from class dist). Once you got it into R it is in 
 vegan, and there is nothing specific to vegan. 
 
 Cheers, Jari Oksanen
 -- 
 Jari Oksanen, Dept Biology, Univ Oulu, 90014 Finland
 jari.oksa...@oulu.fi, Ph. +358 400 408593, http://cc.oulu.fi/~jarioksa
 
 
 

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

[Jari Oksanen]

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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