Modeling age and nest-specific survival using a hierarchical bayesian approach

Jing Cao, Chong Z. He, Kimberly M. Suedkamp Wells, Joshua J. Millspaugh, Mark R. Ryan

Research output: Contribution to journalArticlepeer-review

Abstract

Recent studies have shown that grassland birds are declining more rapidly than any other group of terrestrial birds. Current methods of estimating avian age-specific nest survival rates require knowing the ages of nests, assuming homogeneous nests in terms of nest survival rates, or treating the hazard function as a piecewise step function. In this article, we propose a Bayesian hierarchical model with nest-specific covariates to estimate age-specific daily survival probabilities without the above requirements. The model provides a smooth estimate of the nest survival curve and identifies the factors that are related to the nest survival. The model can handle irregular visiting schedules and it has the least restrictive assumptions compared to existing methods. Without assuming proportional hazards, we use a multinomial semiparametric logit model to specify a direct relation between age-specific nest failure probability and nest-specific covariates. An intrinsic autoregressive prior is employed for the nest age effect. This nonparametric prior provides a more flexible alternative to the parametric assumptions. The Bayesian computation is efficient because the full conditional posterior distributions either have closed forms or are log concave. We use the method to analyze a Missouri dickcissel dataset and find that (1) nest survival is not homogeneous during the nesting period, and it reaches its lowest at the transition from incubation to nestling; and (2) nest survival is related to grass cover and vegetation height in the study area.

Original languageEnglish (US)
Pages (from-to)1052-1062
Number of pages11
JournalBiometrics
Volume65
Issue number4
DOIs
StatePublished - Dec 2009
Externally publishedYes

Keywords

  • Age-specific survival probability
  • Bayesian hierarchical model
  • Intrinsic autoregressive prior
  • Nest survival
  • Nest-specific covariate

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)
  • Agricultural and Biological Sciences(all)
  • Applied Mathematics

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