Estimating diversity via frequency ratios

DOI10.1111/BIOM.12332zbMATH Open1419.62476arXiv1408.3333OpenAlexW1903024071WikidataQ35650618 ScholiaQ35650618MaRDI QIDQ88012FDOQ88012

Authors: Amy Willis, John Bunge 

Publication date: 2 June 2015

Published in: Biometrics (Search for Journal in Brave)

Abstract: We wish to estimate the total number of classes in a population based on sample counts, especially in the presence of high latent diversity. Drawing on probability theory that characterizes distributions on the integers by ratios of consecutive probabilities, we construct a nonlinear regression model for the ratios of consecutive frequency counts. This allows us to predict the unobserved count and hence estimate the total diversity. We believe that this is the first approach to depart from the classical mixed Poisson model in this problem. Our method is geometrically intuitive and yields good fits to data with reasonable standard errors. It is especially well-suited to analyzing high diversity datasets derived from next-generation sequencing in microbial ecology. We demonstrate the method's performance in this context and via simulation, and we present a dataset for which our method outperforms all competitors.

Full work available at URL: https://arxiv.org/abs/1408.3333

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• scientific article; zbMATH DE number 10134

zbMATH Keywords

alpha diversitybiodiversitycapture-recapturecharacterization of distributionsmicrobial ecologyspecies richness

Mathematics Subject Classification ID

General nonlinear regression (62J02) Applications of statistics to biology and medical sciences; meta analysis (62P10) Characterization and structure theory of statistical distributions (62E10)

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Cited In (10)

• Effective numbers in the partitioning of biological diversity
• Analyzing fractal property of species abundance distribution and diversity indexes
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• A flexible ratio regression approach for zero-truncated capture-recapture counts
• breakaway
• A note on marginal count distributions for diversity estimation
• A modification of Chao's lower bound estimator in the case of one-inflation
• Limit theorems for empirical Rényi entropy and divergence with applications to molecular diversity analysis
• Clonality: point estimation
• Tuning parameter selection for a penalized estimator of species richness

Uses Software

• R
• SPECIES
• UPARSE

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