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Inference under unequal probability sampling with the Bayesian exponentially tilted empirical likelihood.

ABSTRACT: Fully Bayesian inference in the presence of unequal probability sampling requires stronger structural assumptions on the data-generating distribution than frequentist semiparametric methods, but offers the potential for improved small-sample inference and convenient evidence synthesis. We demonstrate that the Bayesian exponentially tilted empirical likelihood can be used to combine the practical benefits of Bayesian inference with the robustness and attractive large-sample properties of frequentist approaches. Estimators defined as the solutions to unbiased estimating equations can be used to define a semiparametric model through the set of corresponding moment constraints. We prove Bernstein-von Mises theorems which show that the posterior constructed from the resulting exponentially tilted empirical likelihood becomes approximately normal, centred at the chosen estimator with matching asymptotic variance; thus, the posterior has properties analogous to those of the estimator, such as double robustness, and the frequentist coverage of any credible set will be approximately equal to its credibility. The proposed method can be used to obtain modified versions of existing estimators with improved properties, such as guarantees that the estimator lies within the parameter space. Unlike existing Bayesian proposals, our method does not prescribe a particular choice of prior or require posterior variance correction, and simulations suggest that it provides superior performance in terms of frequentist criteria.

SUBMITTER: Yiu A

PROVIDER: S-EPMC7612173 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Large-scale phylogenies provide a valuable source to study background diversification rates and investigate if the rates have changed over time. Unfortunately most large-scale, dated phylogenies are sparsely sampled (fewer than 5% of the described species) and taxon sampling is not uniform. Instead, taxa are frequently sampled to obtain at least one representative per subgroup (e.g. family) and thus to maximize diversity (diversified sampling). So far, such complications have been ignored, potentially biasing the conclusions that have been reached. In this study I derive the likelihood of a birth-death process with non-constant (time-dependent) diversification rates and diversified taxon sampling. Using simulations I test if the true parameters and the sampling method can be recovered when the trees are small or medium sized (fewer than 200 taxa). The results show that the diversification rates can be inferred and the estimates are unbiased for large trees but are biased for small trees (fewer than 50 taxa). Furthermore, model selection by means of Akaike's Information Criterion favors the true model if the true rates differ sufficiently from alternative models (e.g. the birth-death model is recovered if the extinction rate is large and compared to a pure-birth model). Finally, I applied six different diversification rate models--ranging from a constant-rate pure birth process to a decreasing speciation rate birth-death process but excluding any rate shift models--on three large-scale empirical phylogenies (ants, mammals and snakes with respectively 149, 164 and 41 sampled species). All three phylogenies were constructed by diversified taxon sampling, as stated by the authors. However only the snake phylogeny supported diversified taxon sampling. Moreover, a parametric bootstrap test revealed that none of the tested models provided a good fit to the observed data. The model assumptions, such as homogeneous rates across species or no rate shifts, appear to be violated.

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Inference under unequal probability sampling with the Bayesian exponentially tilted empirical likelihood.

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