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Bayesian estimation of population size and overlap from random subsamples

Erik K. Johnson, View ORCID ProfileDaniel B. Larremore
doi: https://doi.org/10.1101/2021.07.06.451319
Erik K. Johnson
1Department of Applied Mathematics, University of Colorado Boulder
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Daniel B. Larremore
2Department of Computer Science, University of Colorado Boulder
3BioFrontiers Institute, University of Colorado Boulder
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  • ORCID record for Daniel B. Larremore
  • For correspondence: daniel.larremore@colorado.edu
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Abstract

Counting the number of species, items, or genes that are shared between two sets is a simple calculation when sampling is complete. However, when only partial samples are available, quantifying the overlap between two sets becomes an estimation problem. Furthermore, to calculate normalized measures of β-diversity, such as the Jaccard and Sorenson-Dice indices, one must also estimate the total sizes of the sets being compared. Previous efforts to address these problems have assumed knowledge of total population sizes and then used Bayesian methods to produce unbiased estimates with quantified uncertainty. Here, we address populations of unknown size and show that this produces systematically better estimates—both in terms of central estimates and quantification of uncertainty in those estimates. We further show how to use species count data to refine estimates of population size in a Bayesian joint model of populations and overlap.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • † erik.k.johnson@colorado.edu

  • ↵‡ daniel.larremore@colorado.edu

  • https://github.com/erikj540/Bayesian-Beta-Diversity

  • ↵1 https://github.com/erikj540/Bayesian-Beta-Diversity

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted July 07, 2021.
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Bayesian estimation of population size and overlap from random subsamples
Erik K. Johnson, Daniel B. Larremore
bioRxiv 2021.07.06.451319; doi: https://doi.org/10.1101/2021.07.06.451319
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Bayesian estimation of population size and overlap from random subsamples
Erik K. Johnson, Daniel B. Larremore
bioRxiv 2021.07.06.451319; doi: https://doi.org/10.1101/2021.07.06.451319

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