as I was wondering today through my alpha diversity measures from QIIME2 and phyloseq I found differences in all my samples’ Shannon diversity measures, but curiously not in my Simpson diversity measures. I wonder why would that happen if the same table is being used in both programs. I checked samples, features abundances and they are the same, I guess the Shannon diversity formula implemented is the same either. Do you have any idea of what is going on?
I was going to check if there is a linearity between the Inverse Simpson index (1/D) calculated by phyloseq’s estimate richness, and the exponential of the Shannon index (e^H’) based on my H’ provided by QIIME2, as suggested by phyloseq’s supporting information. Right before doing it I found those differences.
I appreciate any help or insights,