A guide to Bayesian model checking for ecologists

Conn, Paul B.; Johnson, Devin S.; Williams, Perry J.; Melin, Sharon R.; Hooten, Mevin B.

doi:10.7287/peerj.preprints.3390

Cited by 69 publications

(106 citation statements)

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“…Following model convergence, we performed a posterior predictive check (Conn et al. ), in which we simulated replacement data sets based on parameter values from posterior distributions of our converged model that were relevant to each sub‐model (i.e., CMR, age‐ratio model, band ratio model) and determined whether these simulated data sets were different from the observed data that informed each model. We reported Bayesian p ‐values based on comparisons between the estimated Freeman–Tukey statistic (Kéry and Schaub ) for both the observed and simulated data sets, in which Bayesian p ‐values near 0.5 indicate goodness of fit and values that approach 0.0 or 1.0 indicate lack of fit.…”

Section: Methodsmentioning

confidence: 99%

Application of Bayesian robust design model to assess the impacts of a hurricane on shorebird demography

et al. 2018

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Abstract. The increasing use of Bayesian inference in population demography requires rapid advancements in modeling frameworks to approach the rigor and flexibility of the current suite of maximum-likelihood models. We developed an unbiased, Jolly-Seber robust design (JSRD) model that is both accessible and generalizable in a Bayesian hierarchical multistate framework. We integrated band and age-classification data to estimate site entry, temporary emigration, and apparent survival rates, as well as estimate ageclass specific abundances. The complete model parameterization is provided in the Appendix S1, as well as tools for simulating capture histories and an assessment of model fit. We applied this model to determine whether these demographic processes in non-breeding population of American oystercatchers (Haematopus palliatus) were affected by a major hurricane event (Hurricane Matthew) in coastal Georgia. The JSRD model was demonstrably unbiased at relatively small sample sizes, and the majority of parameters were identifiable in the fully saturated model parameterization. In the model application, we found that Hurricane Matthew temporarily altered local population abundances of American oystercatchers through increased movements of individuals into and out of the observable population, but mortality rates were largely unaffected. Together, our results suggest that American oystercatchers were largely able to avoid the immediate demographic consequences (i.e., reduced survival) of Hurricane Matthew. Integrating age and band ratios from survey data allowed for more descriptive and potentially less biased estimates of age-specific abundance, relative to estimates generated solely from either mark-resight or survey data.

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Section: Methodsmentioning

confidence: 99%

Application of Bayesian robust design model to assess the impacts of a hurricane on shorebird demography

et al. 2018

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“…assemblages) and the missing hatching success data, we used a 10-fold cross-validation approach to fit and validate the model , Roberts et al 2017, Conn et al 2018.…”

Section: Alien Mammal Assemblagementioning

confidence: 99%

“…The script for fitting the Bayesian hierarchical model is available in Supplementary Appendix S1 (available online). We assessed the goodness of the fit and the predictive abilities of the hierarchical model by estimating a Bayesian p-value based on the deviance of the model , Kéry & Royle 2016, Conn et al 2018. A Bayesian p-value compares the estimate of a goodness-of-fit testthe deviance in this casewith the test expected value if the model is adequate.…”

Section: Alien Mammal Assemblagementioning

confidence: 99%

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Alien mammal assemblage effects on burrow occupancy and hatching success of the vulnerable pink-footed shearwater in Chile

et al. 2020

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Summary Alien species are a driver of biodiversity loss, with impacts of different aliens on native species varying considerably. Identifying the contributions of alien species to native species declines could help target management efforts. Globally, seabirds breeding on islands have proven to be highly susceptible to alien species. The breeding colonies of the pink-footed shearwater (Ardenna creatopus) are threatened by the negative impacts of alien mammals. We combined breeding monitoring data with a hierarchical model to separate the effects of different alien mammal assemblages on the burrow occupancy and hatching success of the pink-footed shearwater in the Juan Fernández Archipelago, Chile. We show that alien mammals affected the rates of burrow occupancy, but had little effect on hatching success. Rabbits produced the highest negative impacts on burrow occupancy, whereas the effects of other alien mammals were more uncertain. In addition, we found differences in burrow occupancy between islands regardless of their alien mammal assemblages. Managing rabbits will improve the reproductive performance of this shearwater, but research is needed to clarify the mechanisms by which alien mammals affect the shearwaters and to explain why burrow occupancy varies between islands.

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“…The red dashed line indicates zero difference. 0.08 and the overdispersion parameter (ĉ ) was 1.5, indicating the absence of major lack of fit (Conn et al 2018).…”

Section: Pheasant Chick Survivalmentioning

confidence: 99%

Estimating the survival of unmarked young from repeated counts

Lyons¹,

Stodola

Benson

2019

Wildlife Biology

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A guide to Bayesian model checking for ecologists

Abstract: Abstract. Checking that models adequately represent data is an essential component

Cited by 69 publications

References 1 publication

Application of Bayesian robust design model to assess the impacts of a hurricane on shorebird demography

Application of Bayesian robust design model to assess the impacts of a hurricane on shorebird demography

Alien mammal assemblage effects on burrow occupancy and hatching success of the vulnerable pink-footed shearwater in Chile

Estimating the survival of unmarked young from repeated counts

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