[R-sig-eco] How to calculate relative abundance along taxonomical hierarchy

[Rich Shepard]

On Thu, 25 Jun 2015, Gian Maria Niccolò Benucci wrote:

> I am working on a fungal dataset with 151 OTUs distributed in 20 samples.
> I have imported it as phyloseq object and as normal species matrix as well
> to work with the vegan package. I am trying to find a way to get relative
> abundances at different hierarchical level goruping the abundances of the
> OTUs present in my dataset. For example, if I want to know what is the
> relative abundance of each Phylum (or of each Family, or each Genus) how
> can I do? There is a way to do that inside R? Thank you very much in
> advance,

   I suggest that you treat your data as compositional. There are several R
packages for compositional data analysis (CoDA), including compositions,
robCompositions, and zCompositions. Search the Web for CoDA and you'll find
backgroud materials by Aitchison and others. There are published papers on
the application of CoDA to biotic data.

Rich