Alpha diversity measures (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
.
Functions¶
|
Calculate the ACE metric (Abundance-based Coverage Estimator). |
|
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). |
|
Calculate ENS_pie alpha diversity measure. |
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Calculate Esty's CI. |
|
Compute Faith's phylogenetic diversity metric (PD) |
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Calculate Fisher's alpha, a metric of diversity. |
|
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. |