bio-ecological-genomics-biodiversity-metrics

Version Compatibility

Reference examples tested with: iNEXT 3.0+, iNEXT.3D 1.0+, vegan 2.6+, betapart 1.6+, picante 1.8+, ggplot2 3.5+

Before using code patterns, verify installed versions match. If versions differ:

• R: packageVersion('<pkg>') then ?function_name to verify parameters

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Biodiversity Metrics

"Calculate species diversity for my ecological samples" -> Compute Hill-number diversity (numbers-equivalent of richness, Shannon, Simpson) with coverage-based rarefaction/extrapolation, choose the richness estimator appropriate to the singleton/doubleton signature of the data, and partition beta diversity into turnover and nestedness components with a documented partition framework.

• R: iNEXT::iNEXT() for coverage-based rarefaction/extrapolation
• R: betapart::beta.multi() for Baselga turnover/nestedness partition
• R: picante::ses.mpd() for phylogenetic-community SES with explicit null model

The Single Most Important Modern Insight -- Standardize by COVERAGE not by sample size

Chao & Jost 2012 Ecology 93(12):2533-2547 established that comparing diversity across assemblages by rarefying to a common sample size systematically biases comparisons whenever assemblages differ in underlying diversity: a 100-read rarefaction of a 50-species community is essentially saturated (coverage approximately 99%) while the same 100 reads from a 500-species community covers only approximately 40% of the underlying diversity. The two rarefied diversities are not measuring the same thing. Coverage-based rarefaction with iNEXT is the postdoc-grade default; sample-size rarefaction is now considered a methodological anti-pattern for cross-site comparison.

A second insight pairs with this: raw Shannon and Simpson indices are entropies, NOT diversities. Jost 2006 Oikos 113(2):363-375 showed that only their numbers-equivalents (exp(H), 1/D) are comparable as effective species counts and have the intuitive "doubling property" (merging two equally diverse equally abundant assemblages doubles the diversity). Reporting raw Shannon = 3.2 vs 3.0 hides whether the difference is large or trivial; reporting 1D = 24.5 vs 20.1 species-equivalents makes the 22% gap visible.