title: Estimating diversity via frequency ratios.
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.
authors.affiliation: Department of Statistical Science, Cornell University, Ithaca, New York, U.S.A.
authors.forename: Amy
authors.initials: A
authors.lastname: Willis
authors.affiliation: Department of Statistical Science, Cornell University, Ithaca, New York, U.S.A.
authors.forename: John
authors.initials: J
authors.lastname: Bunge
mesh_terms: D044822:Biodiversity; D001699:Biometry / Q000379:methods; D003198:Computer Simulation; D030541:Databases, Genetic; D059014:High-Throughput Nucleotide Sequencing; D059013:Microbial Consortia; D017711:Nonlinear Dynamics; D011338:Probability Theory
keywords: Alpha diversity; Biodiversity; Capture-recapture; Characterization of distributions; Microbial ecology; Species richness