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

Abstract

Summary: Hill numbers (or the effective number of species) have been increasingly used to quantify the species/taxonomic diversity of an assemblage. The sample‐size‐ and coverage‐based integrations of rarefaction (interpolation) and extrapolation (prediction) of H ill numbers represent a unified standardization method for quantifying and comparing species diversity across multiple assemblages. We briefly review the conceptual background of H ill numbers along with two approaches to standardization. We present an R package iNEXT (i N terpolation/EXT rapolation) which provides simple functions to compute and plot the seamless rarefaction and extrapolation sampling curves for the three most widely used members of the H ill number family (species richness, S hannon diversity and S impson diversity). Two types of biodiversity data are allowed: individual‐based abundance data and sampling‐unit‐based incidence data. Several applications of the iNEXT packages are reviewed: (i) Non‐asymptotic analysis: comparison of diversity estimates for equally large or equally complete samples. (ii) Asymptotic analysis: comparison of estimated asymptotic or true diversities. (iii) Assessment of sample completeness (sample coverage) across multiple samples. (iv) Comparison of estimated point diversities for a specified sample size or a specified level of sample coverage. Two examples are demonstrated, using the data (one for abundance data and the other for incidence data) included in the package, to illustrate all R functions and graphical displays.