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

• Published in: Methods in ecology and evolution Vol. 7; no. 12; pp. 1451 - 1456
• Main Authors: Hsieh, T. C., Ma, K. H., Chao, Anne, McInerny, Greg
• Format: Journal Article
• Language: English
• Published: London John Wiley & Sons, Inc 01-12-2016
• Subjects: Abundance; abundance data; Asymptotic properties; Biodiversity; Extrapolation; incidence data; Interpolation; Rarefaction; sample coverage; Sampling; Shannon diversity; Simpson diversity; Species diversity; Species richness; Standardization
• ISSN: 2041-210X; 2041-210X
• DOI: 10.1111/2041-210X.12613

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 Hill numbers represent a unified standardization method for quantifying and comparing species diversity across multiple assemblages.
We briefly review the conceptual background of Hill numbers along with two approaches to standardization. We present an R package iNEXT (iNterpolation/EXTrapolation) which provides simple functions to compute and plot the seamless rarefaction and extrapolation sampling curves for the three most widely used members of the Hill number family (species richness, Shannon diversity and Simpson 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.