I am having some trouble figuring out how to calculate basic richness and diversity measures for each sample defined in my group file.
Inputting a group file into summary.single doesn’t seem to work, and I don’t want the pairwise comparisons provided by summary.shared
I just want to get the diversity index values for each sample individually (as defined in my group file). Can anyone offer some advice?
The read.otu command outputs .rabund files for each group. You can do read.otu(rabund=rabundForIndividualSample), then run the collect.single, rarefaction.single or summary.single commands.
Excellent! Thanks for the tip.