Hello,
It seems that it is generally suggested to remove the low abundance otu-s from your analysis.
How will it effect community richness calculators - as chao1 uses specifically singleton OTU-s in its calculator then this seems to completely lose its meaning.
Similarily ACE uses in its calculation the deifintion fo rare and abundant species by default rare being below 10 sequences per otu. (Which is the default to remove by split.abund). What kind of richness esitmators on what settings would be left to use for what effect after split.abund command? (Lets say on default settings)
Yeah, I think it’s a horrible idea - I’ve never suggested removing rare OTUs. We put this in because people kept asking. We like to give people lots of rope to hang themselves by 