Additional Information

Kind of Alpha diversity analysis algorithm

There are a wide variety of algorithms that can analyze alpha diversity. Alpha diversity, which is used not only in microbiome analysis, but also in ecological classification and other analysis, has different algorithms that are mainly used in each analysis industry. The microbiome analysis mainly cites Shannon, Simpson, and Chao1, among which Shannon has the highest proportion.

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