[R] In vegan package: running adonis (or similar) on a distance matrix

[Jari Oksanen]

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