SHE analysis

I am currently working with biofilms obtained from a brevery enviroment. When analyzing my data with the collect.single or rarefaction.single command i observed an constant Shannon-Index even at a small sample size with low evenness values. So far nothing to be worry about. Next i was curious about the proportion of richness and evenness on the Shannon-Index at the different sample sizes. Itried to use the SHE analysis method based on Buzas and Hayek which uses the formula:

H(Shannon)= lnE + lnS

I compared the sum of the lnE- and lnS-values with the Shannon-Index obtained by mothur and found that they differ. For example i obtained 48 OTU´s and E=0,3361. The Shannon-Index calculated by mothur is 1,3301 but my calculation with the formula above is 2,78. Do you have any experience with this?

Thanks in advance


Using the shannon index, evenness is calculated as shannon/ln(S). I’m not familiar with “SHE analysis” and my rules of logarithms are a bit rusty, but I don’t know how you get from E=H/ln(S) to H=ln(E) + ln(S)

My fault…

This formula just works if you are analyzing a given community, e.g watching the changes for a given set of species. If new species steadily approach the formula make now sense (as you assumed).

By the way, thank you for providing the mothur-software and for the support.

Have a nice weekend.