Following the 454 SOP, I generate .chao and .invsimpson files using collect.single(), and one .groups.rarefaction file using rarefaction.single() with calc=sobs 
However, I can also generate .sobs files using collect.single(), and .r_chao files using rarefaction.single() with groupmode=F 
Then, I am lost… 
What’s the difference between collect.single() and rarefaction.single()?
What’s the difference between the .chao and the .r_chao files?
In advance, thank you very much for sheding light on this obscure section of the SOP…
Best regards,
Bernard
The collect commands only do one iteration whereas the rarefaction commands do 1000 iterations and then they output the average. Generally the rarefaction is the better way to go.
Thanks! Very clear! This is what I presumed by looking at the curves.