I'd be grateful if you could help me. How can I calculate alpha and beta diversity indices through 'vegan' by using a matrix of read counts. Please find the attached picture that shows an Excel matrix of read counts obtained from MG-RAST (the samples are divided into 4 treatments, i.e. CON, A, B, and C). Is such kind of data suitable for performing alpha and beta diversity analyses?
I whish someone could give me some tips.
Thanks in advance!