iNEXT: an R package for rarefaction and extrapolation of species diversity (Hill numbers)

Summary

This methods paper introduces iNEXT, an R package implementing Hill numbers and standardised rarefaction/extrapolation approaches for quantifying and comparing species diversity across multiple assemblages. The package unifies sample-size-based and coverage-based diversity estimation, enabling both non-asymptotic comparisons (for equally large or complete samples) and asymptotic analysis (estimated true diversity). Although developed as a general ecological tool, the methodology is potentially applicable to soil and agricultural biodiversity assessment.

Regional applicability

This is a software methodology paper with no geographic specificity. The iNEXT package is internationally available and could be applied to UK agricultural and soil biodiversity monitoring, but the paper itself makes no region-specific claims or recommendations.

Key measures

Hill numbers (effective number of species); rarefaction and extrapolation curves; sample coverage; Shannon diversity index; Simpson diversity index

Outcomes reported

The paper presents iNEXT, an R package that computes rarefaction and extrapolation curves for Hill numbers (species richness, Shannon diversity, Simpson diversity) to standardise and compare species diversity across assemblages. The package enables assessment of sample completeness and comparison of diversity estimates across multiple samples using either abundance or incidence data.

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