Journal ArticleDOI
iNEXT: an R package for rarefaction and extrapolation of species diversity (Hill numbers)
T. C. Hsieh,K. H. Ma,Anne Chao +2 more
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TLDR
In this article, the authors 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.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 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.read more
Citations
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High frequency of shared clonotypes in human B cell receptor repertoires
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References
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Journal ArticleDOI
Quantifying biodiversity: procedures and pitfalls in the measurement and comparison of species richness
TL;DR: A series of common pitfalls in quantifying and comparing taxon richness are surveyed, including category‐subcategory ratios (species-to-genus and species-toindividual ratios) and rarefaction methods, which allow for meaningful standardization and comparison of datasets.
Journal ArticleDOI
Diversity and Evenness: A Unifying Notation and Its Consequences
TL;DR: Three commonly used measures of diversity, Simpson's index, Shannon's entropy, and the total number of species, are related to Renyi's definition of a generalized entropy, according to which there is a continuum of possible diversity measures.
Journal ArticleDOI
Rarefaction and extrapolation with Hill numbers: a framework for sampling and estimation in species diversity studies
Anne Chao,Nicholas J. Gotelli,T. C. Hsieh,Elizabeth L. Sander,K. H. Ma,Robert K. Colwell,Robert K. Colwell,Aaron M. Ellison +7 more
TL;DR: In this article, the authors extended previous rarefaction and extrapolation models for species richness (Hill number q D, where q ¼ 0) to measures of taxon diversity incorporating relative abundance (i.e., for any Hill number qD, q. 0) and presented a unified approach for both individual-based (abundance) data and sample-based data.
Journal ArticleDOI
Models and estimators linking individual-based and sample-based rarefaction, extrapolation and comparison of assemblages
Robert K. Colwell,Anne Chao,Nicholas J. Gotelli,Shang Yi Lin,Chang Xuan Mao,Robin L. Chazdon,John T. Longino +6 more
TL;DR: In this paper, the authors provide new unconditional variance estimators for classical, individual-based rarefaction and for Coleman Rarefaction under two sampling models: sampling-theoretic predictors for the number of species in a larger sample (multinomial model), a larger area (Poisson model) or a larger number of sampling units (Bernoulli product model), based on an estimate of asymptotic species richness.
Journal ArticleDOI
Coverage‐based rarefaction and extrapolation: standardizing samples by completeness rather than size
Anne Chao,Lou Jost +1 more
TL;DR: An integrated sampling, rarefaction, and extrapolation methodology to compare species richness of a set of communities based on samples of equal completeness (as measured by sample coverage) instead of equal size is proposed.