Additional Information

Alpha diversity analysis algorithm 종류

알파 다양성을 분석할 수 있는 알고리즘의 종류는 매우 다양합니다. 마이크로바이옴 분석 뿐만 아니라 생태학적 분류 및 다른 분석에서도 사용되는 알파 다양성은 그 분석 업계마다 주로 사용되는 알고리즘이 다릅니다. 마이크로바이옴 분석은 Shannon, Simpson, Chao1 등을 주로 인용하며 그중, Shannon의 비중이 가장 높습니다.

No	ɑ-diversity	description
1	ace	Calculate the ACE metric(Abundance-based Coverage Estimator).
2	berger_parker_d	Calculate Berger-Parker dominance.
3	brillouin_d	Calculate Brillouin index of alpha diversity.
4	chao1	Calculate chao1 richness estimator.
5	chao1_ci	Calculate chao1 confidence interval.
6	dominance	Calculate dominance.
7	doubles	Calculate number of double occurrences(doubletons).
8	enspie	Calculate ENS_pie alpha diversity measure.
9	equitability	Calculate equitability(Shannon index corrected for number of OTUs).
10	esty_ci	Calculate Esty’s CI.
11	fisher_alpha	Calculate Fisher’s alpha, a metric of diversity.
12	gini_index	Calculate the Gini index.
13	goods_coverage	Calculate Good’s coverage of counts.
14	kempton_taylor_q	Calculate Kempton-Taylor Q index of alpha diversity.
15	heip_e	Calculate Heip’s evenness measure.
16	lladser_ci	Calculate single CI of the conditional uncovered probability.
17	lladser_pe	Calculate single point estimate of conditional uncovered probability.
18	margalef	Calculate Margalef’s richness index.
19	mcintosh_d	Calculate McIntosh dominance index D.
20	mcintosh_e	Calculate McIntosh’s evenness measure E.
21	menhinick	Calculate Menhinick’s richness index.
22	michaelis_menten_fit	Calculate Michaelis-Menten fit to rarefaction curve of observed OTUs.
23	observed_otus	Calculate the number of distinct OTUs.
24	observed_species	Calculate observed OTUs, singles, and doubles.
25	osd	Calculate observed OTUs, singles, and doubles.
26	simpson_reciprocal	Calculate observed OTUs, singles, and doubles.
27	robbins	Calculate Robbins’ estimator for the probability of unobserved outcomes.
28	shannon	Calculate Shannon entropy of counts, default in bits.
29	simpson	Calculate Simpson’s index.
30	simpson_e	Calculate Simpson’s evenness measure E.
31	singles	Calculate number of single occurrences(singletons).
32	strong	Calculate Strong’s dominance index.
33	PD_whole_tree