R help - Oct 2012 - In vegan package: running adonis (or similar) on a distance matrix

Hi,
Using Vegan package I was wondering if there's a way to use a distance 
matrix as an input for adonis (or any of the other similar hypothesis 
testing functions) instead of the usual species by sample table.
Working in the field of microbial ecology, what I'm trying to do is to 
overcome the problem of having to use discrete units such as species or 
OTUs, which are problematic in microbial ecology (if not outright 
theoretically false).
What I have instead is a phylometric distance matrix between all my 
samples based on a phylogenetic tree.

Some people have apparently made such a python implementation 
<http://qiime.org/scripts/compare_categories.html>, but I'd rather use
R.

Thanks in advance,
Roey

Roey Angel <angel <at> mpi-marburg.mpg.de> writes:
> 
> Hi,
> Using Vegan package I was wondering if there's a way to use a distance 
> matrix as an input for adonis (or any of the other similar hypothesis 
> testing functions) instead of the usual species by sample table.
> Working in the field of microbial ecology, what I'm trying to do is to 
> overcome the problem of having to use discrete units such as species or 
> OTUs, which are problematic in microbial ecology (if not outright 
> theoretically false).
> What I have instead is a phylometric distance matrix between all my 
> samples based on a phylogenetic tree.
> 
Dear Roye Angel,

According to the documentation, this can be done. See description of the first
argument ('formula') in ?adonis. Your distances (dissmilarities) must be
in
standard R form and inherit from class "dist". If they are in some
other form,
you should change them to "dist" class. This may succeed with command
as.dist().

Cheers, Jari Oksanen

Dear Jari Oksanen,
Many thanks for your reply; adonis() does seem to accept a distance 
matrix as an input.
Regarding the documentation, what got me confused is that 'data' is 
described as; "the data frame from which A, B, and C would be drawn." 
but of course this refers only to the design of the experiment and not 
the response variable. Perhaps it might be useful to redefine it as 
'design' or 'explanatory variables' etc.

Roey

-- 
Dr. Roey Angel

Max-Planck-Institute for Terrestrial Microbiology
Karl-von-Frisch-Strasse 10
D-35043 Marburg, Germany

Office: +49-(0)6421178832
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