Hi all,

I have a quick question. I have a dataframe of 10 different flowers (10 reps each) with environmental DNA done on them so that I have dataframes consisting of bacteria and fungi abundances for each of the flowers.

I've done an overalls can of alpha diversity across flower as groups, but I also want to run this by individual flower across the 10 replicate samples.

My question here is, when I split the dataframe by species (so I should get 10 dataframes per flower), should I bother removing taxa that end up having 0 counts across the samples for the flower species? Not every taxa will show up in every single flower but I cannot tell if Shannon-Weiner via vegan package in R takes this into account already? Or should I be removing taxa with 0 counts prior to running my commands to check for alpha diversity. I've searched online for this but it seems no one has asked this question before - or they use full datasets and prune taxa with 0 counts prior to this which I've done when looking at ALL flowers at once.

I guess I'm confused if I should be keeping taxa with 0 counts, knowing that these taxa DO exist in the sample region but just don't show up when focusing on a single species. Logically to me, if I know the taxa exists I should keep them when focusing on individual flowers because now it just means the diversity has decreased since that taxa is not present on it.

I hope this makes sense.