Hello,
in my study I have some animals and I’m studying the microbiota of the ear canal.
I had calculated alpha diversity, now I have the necessity to calculate:
the beta diversity among the right ear and left ear of the same animal
the beta diversitu among the two group of animals (healthy and sick)
Have you looked the tutorials? Both the moving pictures and PD mice tutorial talk about diversity analysis across multiple groups. The longitudinal tutorial talks abotu paired sampling.