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.

We consider the problem of accounting for model uncertainty in linear regression models. Conditioning on a single selected model ignores model uncertainty, and thus leads to the underestimation of uncertainty when making inferences about quantities of interest. A Bayesian solution to this problem involves averaging over all possible models (i.e., combinations of predictors) when making inferences about quantities of

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. The points we emphasize are:- from Jeffreys's Bayesian point of view, the purpose of hypothesis testing is to evaluate the evidence in favor of a scientific theory;- Bayes factors offer a way of evaluating evidence in favor ofa null hypothesis;- Bayes factors provide a way of incorporating external information into the evaluation of evidence about a hypothesis;- Bayes factors are very general, and do not require alternative models to be nested;- several techniques are available for computing Bayes factors, including asymptotic approximations which are easy to compute using the output from standard packages that maximize likelihoods;- in "non-standard " statistical models that do not satisfy common regularity conditions, it can be technically simpler to calculate Bayes factors than to derive non-Bayesian significance

We consider the problems of variable selection and accounting for model uncertainty in linear regression models. Conditioning on a single selected model ignores model uncertainty, and thus leads to the underestimation of uncertainty when making inferences about quantities of interest. The complete Bayesian solution to this problem involves averaging over all possible models when making inferences about quantities of interest. This approach is often not practical. In this paper we offer two alternative approaches. First we describe a Bayesian model selection algorithm called "Occam's "Window" which involves averaging over a reduced set of models. Second, we describe a Markov chain Monte Carlo approach which directly approximates the exact solution. Both these model averaging procedures provide better predictive performance than any single model which might reasonably have been selected. In the extreme case where there are many candidate predictors but there is no relationship between any of them and the response, standard variable selection procedures often choose some subset of variables that yields a high R² and a highly significant overall F value. We refer to this unfortunate phenomenon as "Freedman's Paradox" (Freedman, 1983). In this situation, Occam's vVindow usually indicates the null model as the only one to be considered, or else a small number of models including the null model, thus largely resolving the paradox.

Survival analysis is concerned with finding models to predict the survival of patients or to assess the efficacy of a clinical treatment. A key part of the model-building process is the selection of the predictor variables. It is standard to use a stepwise procedure guided by a series of significance tests to select a single model, and then to make inference conditionally on the selected model. However, this ignores model uncertainty, which can be substantial. We review the standard Bayesian model averaging solution to this problem and extend it to survival analysis, introducing partial Bayes factors to do so for the Cox proportional hazards model. In two examples, taking account of model uncertainty enhances predictive performance, to an extent that could be clinically useful. 1 Introduction From 1974 to 1984 the Mayo Clinic conducted a double-blinded randomized clinical trial involving 312 patients to compare the drug DPCA with a placebo in the treatment of primary biliary cirrhosis...

Abstract—We develop an approach to identify and test for bid rigging in procurement auctions. First, we introduce a general auction model with asymmetric bidders. Second, we study the problem of identi � cation in our model. We state a set of conditions that are both necessary and suf � cient for a distribution of bids to be generated by a model with competitive bidding. Third, we discuss how to elicit a prior distribution over a � rm’s structural cost parameters from industry experts. Given this prior distribution, we use Bayes’s theorem to compare competitive and collusive models of industry equilibrium. Finally, we apply our methodology to a data set of bidding by construction � rms in the Midwest. The techniques we propose are not computationally demanding, use � exible functional forms, and can be programmed using most standard statistical packages. I.

We show that the only parameter prior for complete Gaussian DAG models that satisfies global parameter independence, complete model equivalence, and some weak regularity assumptions, is the normal-Wishart distribution. Our analysis is based on the following new characterization of the Wishart distribution: let W be an n × n, n ≥ 3, positive-definite symmetric matrix of random variables and f(W) be a pdf of W. Then, f(W) is a Wishart distribution if and only if W11 − W12W −1 is independent 22 W ′ 12 of {W12, W22} for every block partitioning

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this paper I (1) examine three levels of inferential strength supported by typical social science data-gathering methods, and call for a greater degree of explicitness, when HMs and other models are applied, in identifying which level is appropriate; (2) reconsider the use of HMs in school effectiveness studies and meta-analysis from the perspective of causal inference; and (3) recommend the increased use of Gibbs sampling and other Markov-chain Monte Carlo (MCMC) methods in the application of HMs in the social sciences, so that comparisons between MCMC and better-established fitting methods---including full or restricted maximum likelihood estimation based on the EM algorithm, Fisher scoring or iterative generalized least squares---may be more fully informed by empirical practice.

Elicitation is a key task for subjectivist Bayesians. While skeptics hold that it cannot (or perhaps should not) be done, in practice it brings statisticians closer to their clients and subjectmatter-expert colleagues. This paper reviews the state-of-the-art, reflecting the experience of statisticians informed by the fruits of a long line of psychological research into how people represent uncertain information cognitively, and how they respond to questions about that information. In a discussion of the elicitation process, the first issue to address is what it means for an elicitation to be successful, i.e. what criteria should be employed? Our answer is that a successful elicitation faithfully represents the opinion of the person being elicited. It is not necessarily “true ” in some objectivistic sense, and cannot be judged that way. We see elicitation as simply part of the process of statistical modeling. Indeed in a hierarchical model it is ambiguous at which point the likelihood ends and the prior begins. Thus the same kinds of judgment that inform statistical modeling in general also inform elicitation of prior distributions.