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

ace(counts[, rare_threshold])	Calculate the ACE metric (Abundance-based Coverage Estimator).
berger_parker_d(counts)	Calculate Berger-Parker dominance index.
brillouin_d(counts)	Calculate Brillouin's diversity index.
chao1(counts[, bias_corrected])	Calculate chao1 richness estimator.
chao1_ci(counts[, bias_corrected, zscore])	Calculate chao1 confidence interval.
dominance(counts)	Calculate Simpson's dominance index.
doubles(counts)	Calculate number of double-occurrence taxa (doubletons).
enspie(counts)	Calculate ENS_pie alpha diversity measure.
esty_ci(counts)	Calculate Esty's confidence interval of Good's coverage estimator.
faith_pd(counts[, taxa, tree, validate, otu_ids])	Calculate Faith's phylogenetic diversity (Faith's PD) metric.
fisher_alpha(counts)	Calculate Fisher's alpha, a metric of diversity.
gini_index(data[, method])	Calculate the Gini index.
goods_coverage(counts)	Calculate Good's coverage estimator.
heip_e(counts)	Calculate Heip's evenness measure.
kempton_taylor_q(counts[, lower_quantile, ...])	Calculate Kempton-Taylor Q index of alpha diversity.
lladser_ci(counts, r[, alpha, f, ci_type])	Calculate single CI of the conditional uncovered probability.
lladser_pe(counts[, r])	Calculate single point estimate of conditional uncovered probability.
margalef(counts)	Calculate Margalef's richness index.
mcintosh_d(counts)	Calculate McIntosh dominance index.
mcintosh_e(counts)	Calculate McIntosh's evenness measure E.
menhinick(counts)	Calculate Menhinick's richness index.
michaelis_menten_fit(counts[, num_repeats, ...])	Calculate Michaelis-Menten fit to rarefaction curve of observed taxa.
observed_features(counts)	Calculate the number of distinct features.
observed_otus(counts)	Calculate the number of distinct OTUs.
osd(counts)	Calculate observed taxa, singletons, and doubletons.
phydiv(counts[, taxa, tree, rooted, weight, ...])	Calculate generalized phylogenetic diversity (PD) metrics.
pielou_e(counts)	Calculate Pielou's evenness index.
robbins(counts)	Calculate Robbins' estimator for probability of unobserved outcomes.
shannon(counts[, base])	Calculate Shannon's diversity index, default in bits.
simpson(counts)	Calculate Simpson's diversity index.
simpson_e(counts)	Calculate Simpson's evenness index.
singles(counts)	Calculate number of single-occurrence taxa (singletons).
sobs(counts)	Calculate the observed species richness of a sample.
strong(counts)	Calculate Strong's dominance index.