A hierarchical Bayesian approach to record linkage and population size problems

We propose and illustrate a hierarchical Bayesian approach for matching statistical records observed on different occasions. We show how this model can be profitably adopted both in record linkage problems and in capture--recapture setups, where the size of a finite population is the real object of interest. There are at least two important differences between the proposed model-based approach and the current practice in record linkage. First, the statistical model is built up on the actually observed categorical variables and no reduction (to 0--1 comparisons) of the available information takes place. Second, the hierarchical structure of the model allows a two-way propagation of the uncertainty between the parameter estimation step and the matching procedure so that no plug-in estimates are used and the correct uncertainty is accounted for both in estimating the population size and in performing the record linkage. We illustrate and motivate our proposal through a real data example and simulations.Comment: Published in at http://dx.doi.org/10.1214/10-AOAS447 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Bayesian inference of natural selection from allele frequency time series

The advent of accessible ancient DNA technology now allows the direct ascertainment of allele frequencies in ancestral populations, thereby enabling the use of allele frequency time series to detect and estimate natural selection. Such direct observations of allele frequency dynamics are expected to be more powerful than inferences made using patterns of linked neutral variation obtained from modern individuals. We develop a Bayesian method to make use of allele frequency time series data and infer the parameters of general diploid selection, along with allele age, in non-equilibrium populations. We introduce a novel path augmentation approach, in which we use Markov chain Monte Carlo to integrate over the space of allele frequency trajectories consistent with the observed data. Using simulations, we show that this approach has good power to estimate selection coefficients and allele age. Moreover, when applying our approach to data on horse coat color, we find that ignoring a relevant demographic history can significantly bias the results of inference. Our approach is made available in a C++ software package.Comment: 27 page

Bayesian Estimation Under Informative Sampling

Bayesian analysis is increasingly popular for use in social science and other application areas where the data are observations from an informative sample. An informative sampling design leads to inclusion probabilities that are correlated with the response variable of interest. Model inference performed on the observed sample taken from the population will be biased for the population generative model under informative sampling since the balance of information in the sample data is different from that for the population. Typical approaches to account for an informative sampling design under Bayesian estimation are often difficult to implement because they require re-parameterization of the hypothesized generating model, or focus on design, rather than model-based, inference. We propose to construct a pseudo-posterior distribution that utilizes sampling weights based on the marginal inclusion probabilities to exponentiate the likelihood contribution of each sampled unit, which weights the information in the sample back to the population. Our approach provides a nearly automated estimation procedure applicable to any model specified by the data analyst for the population and retains the population model parameterization and posterior sampling geometry. We construct conditions on known marginal and pairwise inclusion probabilities that define a class of sampling designs where $L_{1}$ consistency of the pseudo posterior is guaranteed. We demonstrate our method on an application concerning the Bureau of Labor Statistics Job Openings and Labor Turnover Survey.Comment: 24 pages, 3 figure