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

Abstract

Summary1. 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. 2. 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. 3. 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. 4. 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.

Simple does not mean poor: grasslands and forests harbor similar ant species richness and distinct composition in highlands of southern Brazil

“…We built curves for ground pitfalls (the sampling method shared for all sampling points) and for all methods combined, which represents the sum of the strata available at each sample point. Interpolation and extrapolation curves were calculated with the R package "iNEXT" (Hsieh et al 2016) and 95% confidence intervals were estimated based on 1000 permutations. Comparison of confidence intervals was used to test for species richness differences between vegetation types.…”

Ground-Dwelling and Vegetation Ant Fauna in Southern Brazilian Grasslands

“…For example, there is a huge information gap regarding ant fauna when compared to other Brazilian biomes. Ants are abundant and diverse organisms that present very special roles as ecosystem engineering and in provision of ecosystem services (Hölldobler & Wilson, 1990). Worldwide, ant communities have been largely used as a bioindicator group for land use changes and disturbance analysis (e.g.…”

Diversity patterns, ecological associations and future of research on Costa Rican myxomycetes

“…The second one was selected based on Chiu et al (2014). Rarefaction curves and diversity profiles were created with iNEXT for R (Hsieh et al 2016) based on Chao et al (2014) for both the consolidated database constructed herein and a previous one based on Rojas et al (2010). For table creation, species selection was performed considering only those species with dissimilar diversity profiles.…”