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Bayesian nonparametric inference for species variety with a two parameter Poisson-Dirichlet process prior


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  • Stefano Favaro
  • Antonio Lijoi
  • Ramsés H. Mena
  • Igor Prünster
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    A Bayesian nonparametric methodology has been recently proposed in order to deal with the issue of prediction within species sampling problems. Such problems concern the evaluation, conditional on a sample of size n, of the species variety featured by an additional sample of size m. Genomic applications pose the additional challenge of having to deal with large values of both n and m. In such a case the computation of the Bayesian nonparametric estimators is cumbersome and prevents their implementation. In this paper we focus on the two parameter Poisson-Dirichlet model and provide completely explicit expressions for the corresponding estimators, which can be easily evaluated for any sizes of n and m. We also study the asymptotic behaviour of the number of new species conditionally on the observed sample: such an asymptotic result allows, combined with a suitable simulation scheme, to derive asymptotic highest posterior density intervals for the estimates of interest. Finally, we illustrate the implementation of the proposed methodology by the analysis of five Expressed Sequence Tags (EST) datasets.

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    Bibliographic Info

    Paper provided by Collegio Carlo Alberto in its series Carlo Alberto Notebooks with number 123.

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    Length: 24 pages
    Date of creation: 2009
    Date of revision:
    Handle: RePEc:cca:wpaper:123

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    Keywords: Asymptotics; Bayesian nonparametrics; EST analysis; Posterior probability of discovering a new species; Sample coverage; Species sampling; Two parameter Poisson-Dirichlet process;


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    Cited by:
    1. Pierpaolo De Blasi & Stefano Favaro & Antonio Lijoi & Ramsés H. Mena & Igor Prünster & Mattteo Ruggiero, 2013. "Are Gibbs-type priors the most natural generalization of the Dirichlet process?," DEM Working Papers Series 054, University of Pavia, Department of Economics and Management.
    2. Stefano Favaro & Antonio Lijoi & Igor Prunster, 2011. "Asymptotics for a Bayesian nonparametric estimator of species richness," Quaderni di Dipartimento 144, University of Pavia, Department of Economics and Quantitative Methods.


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