In a 1935 paper, and in his book Theory of Probability, Jeffreys developed a methodology for quantifying the evidence in favor of a scientific theory. The centerpiece was a number, now called the Bayes factor, which is the posterior odds of the null hypothesis when the prior probability on the null is one-half. Although there has been much discussion of Bayesian hypothesis testing in the context of criticism of P -values, less attention has been given to the Bayes factor as a practical tool of applied statistics. In this paper we review and discuss the uses of Bayes factors in the context of five scientific applications in genetics, sports, ecology, sociology and psychology.

Computing (ratios of) normalizing constants of probability models is a fundamental computational problem for many statistical and scientific studies. Monte Carlo simulation is an effective technique, especially with complex and high-dimensional models. This paper aims to bring to the attention of general statistical audiences of some effective methods originating from theoretical physics and at the same time to explore these methods from a more statistical perspective, through establishing theoretical connections and illustrating their uses with statistical problems. We show that the acceptance ratio method and thermodynamic integration are natural generalizations of importance sampling, which is most familiar to statistical audiences. The former generalizes importance sampling through the use of a single "bridge" density and is thus a case of bridge sampling in the sense of Meng and Wong (1996). Thermodynamic integration, which is also known in the numerical analysis literature as Oga...

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The key quantity needed for Bayesian hypothesis testing and model selection is the marginal likelihood for a model, also known as the integrated likelihood, or the marginal probability of the data. In this paper we describe a way to use posterior simulation output to estimate marginal likelihoods. We describe the basic LaplaceMetropolis estimator for models without random effects. For models with random effects the compound Laplace-Metropolis estimator is introduced. This estimator is applied to data from the World Fertility Survey and shown to give accurate results. Batching of simulation output is used to assess the uncertainty involved in using the compound Laplace-Metropolis estimator. The method allows us to test for the effects of independent variables in a random effects model, and also to test for the presence of the random effects. KEY WORDS: Laplace-Metropolis estimator; Random effects models; Marginal likelihoods; Posterior simulation; World Fertility Survey. 1 Introduction...

This paper integrates and extends some recent computational advances in Bayesian inference with the objective of more fully realizing the Bayesian promise of coherent inference and model comparison in economics. It combines Markov chain Monte Carlo and independence Monte Carlo with importance sampling to provide an efficient and generic method for updating posterior distributions. It exploits the multiplicative decomposition of marginalized likelihood into predictive factors, to compute posterior odds ratios efficiently and with minimal further investment in software. It argues for the use of predictive odds ratios in model comparison in economics. Finally, it suggests procedures for public reporting that will enable remote clients to conveniently modify priors, form posterior expectations of their own functions of interest, and update the posterior distribution with new observations. A series of examples explores the practicality and efficiency of these methods.

Introduction To motivate the methods described in this chapter, consider the following inference problem in astronomy (Soubiran, 1993). Until fairly recently, it has been believed that the Galaxy consists of two stellar populations, the disk and the halo. More recently, it has been hypothesized that there are in fact three stellar populations, the old (or thin) disk, the thick disk, and the halo, distinguished by their spatial distributions, their velocities, and their metallicities. These hypotheses have different implications for theories of the formation of the Galaxy. Some of the evidence for deciding whether there are two or three populations is shown in Figure 1, which shows radial and rotational velocities for n = 2; 370 stars. A natural model for this situation is a mixture model with J components, namely y i = J X j=1 ae j

We propose a method for optimal portfolio selection using a Bayesian framework that addresses two major shortcomings of the Markowitz approach: the ability to handle higher moments and estimation error. We employ the skew normal distribution which has many attractive features for modeling multivariate returns. Our results suggest that it is important to incorporate higher order moments in portfolio selection. Further, our comparison to other methods where parameter uncertainty is either ignored or accommodated in an ad hoc way, shows that our approach leads to higher expected utility than the resampling methods that are common in the practice of finance.

The effecTS of MoneTary Policy on uneMPloyMenT dynaMicS under Model uncerTainTy

This note is concerned with specification for modelling financial leverage effect in the context of stochastic volatility (SV) models. Two alternative specifications coexist in the literature. One is the Euler approximation to the well known continuous time SV model with leverage effect and the other is the discrete time SV model of Jacquier, Polson and Rossi (2004, Journal of Econometrics, forthcoming). Using a Gaussian nonlinear state space form with uncorrelated measurement and transition errors, I show that it is easy to interpret the leverage e#ect in the conventional model whereas it is not clear how to obtain the leverage effect in the model of Jacquier et al. Empirical comparisons of these two models via Bayesian Markov chain Monte Carlo (MCMC) methods reveal that the specification of Jacquier et al is inferior. Simulation experiments are conducted to study the sampling properties of the Bayes MCMC for the conventional model.

The integrated likelihood (also called the marginal likelihood or the normalizing constant) is a central quantity in Bayesian model selection and model averaging. It is defined as the integral over the parameter space of the likelihood times the prior density. The Bayes factor for model comparison and Bayesian testing is a ratio of integrated likelihoods, and the model weights in Bayesian model averaging are proportional to the integrated likelihoods. We consider the estimation of the integrated likelihood from posterior simulation output, aiming at a generic method that uses only the likelihoods from the posterior simulation iterations. The key is the harmonic mean identity, which says that the reciprocal of the integrated likelihood is equal to the posterior harmonic mean of the likelihood. The simplest estimator based on the identity is thus the harmonic mean of the likelihoods. While this is an unbiased and simulation-consistent estimator, its reciprocal can have infinite variance and so it is unstable in general. We describe two methods for stabilizing the harmonic mean estimator. In the first one, the parameter space is reduced in such a way that the modified estimator involves a harmonic mean of heavier-tailed densities, thus resulting in a finite variance estimator. The resulting