Gian, Once you have your samples by OTU matrix row standardized, you can use a level of your hierarchy (a vector matching the columns) and the groupSums(your-matrix, 2, your-groups) function in the mefa4 package to get your relative abundances.
Cheers, Peter Gian Maria Niccolò Benucci <gian.benu...@gmail.com> ezt írta (2015. június 25., csütörtök): > Hello everyone, > 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, > > > -- > Gian > > > > *----- Do not print this email unless you really need to. Save paper and > protect the environment! -----* > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-ecology mailing list > R-sig-ecology@r-project.org <javascript:;> > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- -- Péter Sólymos 780-492-8534 | soly...@ualberta.ca | peter.solymos.org Alberta Biodiversity Monitoring Institute http://www.abmi.ca Boreal Avian Modelling Project http://www.borealbirds.ca [[alternative HTML version deleted]] _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
