set subsample level for phylo.diversity

What am I missing? I’m wanting faith’s d for my samples so am running phylo.diversity with rarefaction. However, it seems like it’d make more sense to do it with repeated subsampling to a specific level like I’ve done for all the other diversity measures. Is there some mathmatical/philosophical reason that this isn’t an option?

Sorry, I’m not sure what you’re asking exactly. If you look at the MiSeq SOP, you’ll see this command:

phylo.diversity(tree=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.phylip.tre, count=stability.trim.contigs.good.unique.good.filter.unique.precluster.uchime.pick.pick.pick.count_table, rarefy=T)

The rarefy=T will rarefy the data. You can then extract the depth of coverage you want from the output. The default is to rarefy the samples 1000 times.


I don’t want it to rarefy, I just want it to subset to 1500 seqs, iters=1000. The dataset is large and since I’m not going to look at any of the levels above 1500, I’d rather not waste time calculating them