mothur

Summary.single() ave versus std

I ran summary.single() on a shared file & the output game me two methods by which the calculators (e.g. Chao, sobs, ACE, etc.) ran the analysis: ave & std.

label	group	method	sobs	chao	chao_lci	chao_hci	ace	ace_lci	ace_hci	jackknife	jackknife_lci	jackknife_hci	shannon	shannon_lci	shannon_hci	npshannon	simpson	simpson_lci	simpson_hci
0.05	HCO3	ave	6.752000	7.569167	6.840955	14.641948	9.537776	7.370929	21.407214	3.974326	1.795485	6.153167	0.999295	0.766923	1.231666	1.104084	0.488413	0.383873	0.592953

0.05	HCO3	std	0.484248	1.412939	0.554057	8.965902	3.897642	1.126922	20.396557	7.177237	2.614336	12.070562	0.046137	0.042362	0.051051	0.051313	0.018970	0.016418	0.022096

What is the difference in those values? If I am exporting to R for downstream analyses, which values should I use? I guess I’m not fully understanding how those values are computed for each method & what they actually mean in terms of “which value do I use for a specific test?”

the top is the average and the second is standard deviation. I wouldn’t use any estimator (chao, ace, etc) if you want to talk about just species, use sobs (species observed).

Ahh, that makes total sense. Thanks for the reply!

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