skbio.diversity.alpha
)¶This package provides implementations of alpha diversity measures, including
measures of richness, dominance, and evenness. Some functions generate
confidence intervals (CIs). These functions have the suffix _ci
.
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Calculate the ACE metric (Abundance-based Coverage Estimator). |
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Calculate Berger-Parker dominance. |
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Calculate Brillouin index of alpha diversity. |
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Calculate chao1 richness estimator. |
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Calculate chao1 confidence interval. |
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Calculate dominance. |
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Calculate number of double occurrences (doubletons). |
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Calculate ENS_pie alpha diversity measure. |
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Calculate Esty’s CI. |
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Compute Faith’s phylogenetic diversity metric (PD) |
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Calculate Fisher’s alpha, a metric of diversity. |
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Calculate the Gini index. |
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Calculate Good’s coverage of counts. |
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Calculate Heip’s evenness measure. |
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Calculate Kempton-Taylor Q index of alpha diversity. |
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Calculate single CI of the conditional uncovered probability. |
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Calculate single point estimate of conditional uncovered probability. |
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Calculate Margalef’s richness index. |
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Calculate McIntosh dominance index D. |
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Calculate McIntosh’s evenness measure E. |
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Calculate Menhinick’s richness index. |
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Calculate Michaelis-Menten fit to rarefaction curve of observed OTUs. |
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Calculate the number of distinct OTUs. |
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Calculate observed OTUs, singles, and doubles. |
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Calculate Pielou’s Evenness index J’. |
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Calculate Robbins’ estimator for the probability of unobserved outcomes. |
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Calculate Shannon entropy of counts, default in bits. |
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Calculate Simpson’s index. |
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Calculate Simpson’s evenness measure E. |
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Calculate number of single occurrences (singletons). |
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Calculate Strong’s dominance index. |