sub.sample tax.summary

I have users who really want to do stats on the phyla level (I know, I agree). They’ve asked me to give them a subsampled phyla table. I feel like this should be possible with sub.sample on the tax.summary file but I’m not figuring out how. The specifically do not want to use 15% OTUs but rather just taxon IDs.

oh figured it out but it’s kludgy (perhaps intentionally cause I don’t think it’s a very good idea)

sub.sample(taxonomy=full.taxonomy, count=full.count_table, list=full.list, size=10000, persample=true), count=full.subsample.count_table)

this is a different subsampling than the subsampling of the shared file that I do for indicator species so that might confuse people. If there were a way to do the using the full taxonomy and the sub.sampled shared file, that would be closer to what I think I’d want.

How about using phylotype with taxlevel=2 and then following the rest of the pipeline?