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 ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.