What is the difference?
Single calculates alpha diversity and species richness (e.g. Chao1, shannon)
Shared calculate beta diversity and build matrix (e.g. Bray-curtis)
Am I right?
collect.shared really only makes sense with calc=sobs. so to make the comparison…
collect.single - constructs a collector’s curve where the x-axis is the number of sequences sampled
collect.shared - constructs a collector’s curve where the x-axis is the number of samples sampled
So if you wanted to know how many OTUs were added by adding a sample you’d get that from collect.shared. Not sure what you mean by “inters”, perhaps freq? Generally nowadays people have ~5000 sequences per sample so it makes sense to only output data every 100 sequences or so. However they rarely have 100s of samples so we haven’t seen the need to incorporate a freq option for collect.shared.
Pat
Thank you, Pat.
“inters” is a typo. I mean “iters”
If I use Rarefaction.single, there is an option “iters”. ("To improve the accuracy of the calculations you can change the number of randomizations that are performed using the iters option; the default value is 1,000.)
I was wondering if collect.single or collect.shared also has this option to allow me do many times of randomizations.
Ben
Ok - well we seem to have a typo as well in the help documentation - there’s no iters option in collect.single or collect.shared. You will get an error message if you try it.