beta diversity among two sample

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)

what is the script I have to use?

Thanks for your answear

Hi @rparadiso,

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.