Hello,
I’m a novice with ecology stats and Mothur’s implementation thereof, so I’m hoping someone can answer two questions for me:
- How is the ‘sharedchao’ calculation applied to unshared OTUs in Mothur’s Venn() command?
- Why would my unshared OTU estimates decrease when comparing sharedchao to sharedobs?
I've run Mothur's venn() command on three groups with the following command: ```text mothur v.1.35.0 Last updated: 03/23/2014 ... mothur > venn(shared=file.shared, calc=sharedsobs-sharedchao, nseqs=T) ``` As expected, the sharedchao outputs (mostly) show higher shared OTU estimates between the three groups.
However, I didn’t expect the number of unshared OTUs to decrease in the sharedchao output, and I don’t even understand what calculations Mothur may be using to adjust the unshared OTU estimate. I’ve reviewed the sharedchao wiki page (http://www.mothur.org/wiki/Sharedchao), and the “Chao1 shared” equations in the SPADE User guide, but I’m still confused because the terms for shared chao (shared singletons and doubletons) don’t seem to apply to a batch of unshared OTUs. What am I missing?
For reference, my sharedobs OTUs were as follows: A=42 B=28 C=23 AB shared=28 AC shared=26 BC shared=14 ABC shared=70
My sharedchao OTUs were as follows:
A=26.6
B=27.5
C=38.4
AB shared=41.9
AC shared=25.1
BC shared=10.8
ABC shared=114.4
Thanks