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biodiversity-metrics

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Quantifies biodiversity from species abundance/incidence tables using Hill numbers (iNEXT) with coverage-based rarefaction-extrapolation (Chao & Jost 2012), asymptotic richness via Chao1/ACE/jackknife as a lower bound, Baselga turnover/nestedness partition with the Podani alternative as sensitivity check, mandatory Hellinger transformation before ordination (Legendre & Gallagher 2001), Faith PD and SES_MPD/SES_MNTD with explicit null-model choice, and Maire 2015 functional-diversity dimensionality optimization. Use when comparing diversity across sites with unequal sampling effort, picking the right richness estimator for singleton-heavy amplicon data, partitioning beta diversity into turnover vs nestedness, reporting Hill-number effective species counts rather than raw entropies, computing SES_MPD with explicit null-model justification, or deciding whether to apply standard metrics to compositional amplicon data. Not for clinical 16S microbiome diversity (see microbiome/diversity-ana…

When to use

• comparing diversity across sites with unequal sampling effort
• picking the right richness estimator for singleton-heavy amplicon data
• partitioning beta diversity into turnover vs nestedness
• reporting Hill-number effective species counts
• computing SES_MPD with explicit null-model justification
• deciding whether to apply standard metrics to compositional amplicon data

When not to use

• clinical 16S microbiome diversity

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