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102
Bayes Factors
, 1995
"... 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 ..."
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Cited by 1826 (74 self)
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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 onehalf. 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.
Approximate Bayes Factors and Accounting for Model Uncertainty in Generalized Linear Models
, 1993
"... Ways of obtaining approximate Bayes factors for generalized linear models are described, based on the Laplace method for integrals. I propose a new approximation which uses only the output of standard computer programs such as GUM; this appears to be quite accurate. A reference set of proper priors ..."
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Cited by 151 (28 self)
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Ways of obtaining approximate Bayes factors for generalized linear models are described, based on the Laplace method for integrals. I propose a new approximation which uses only the output of standard computer programs such as GUM; this appears to be quite accurate. A reference set of proper priors is suggested, both to represent the situation where there is not much prior information, and to assess the sensitivity of the results to the prior distribution. The methods can be used when the dispersion parameter is unknown, when there is overdispersion, to compare link functions, and to compare error distributions and variance functions. The methods can be used to implement the Bayesian approach to accounting for model uncertainty. I describe an application to inference about relative risks in the presence of control factors where model uncertainty is large and important. Software to implement the
Bayes factors and model uncertainty
 DEPARTMENT OF STATISTICS, UNIVERSITY OFWASHINGTON
, 1993
"... 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 ..."
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Cited by 124 (6 self)
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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 onehalf. Although there has been much discussion of Bayesian hypothesis testing in the context of criticism of Pvalues, 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 "nonstandard " statistical models that do not satisfy common regularity conditions, it can be technically simpler to calculate Bayes factors than to derive nonBayesian significance
The insignificance of statistical significance testing.
 Journal of Wildlife Management,
, 1999
"... Abstract: Despite their wide use in scientific journals such as The Journal of Wildlife Management, statistical hypothesis tests add very little value to the products of research. Indeed, they frequently confuse the interpretation of data. This paper describes how statistical hypothesis tests are o ..."
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Cited by 92 (0 self)
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Abstract: Despite their wide use in scientific journals such as The Journal of Wildlife Management, statistical hypothesis tests add very little value to the products of research. Indeed, they frequently confuse the interpretation of data. This paper describes how statistical hypothesis tests are often viewed, and then contrasts that interpretation with the correct one. I discuss the arbitrariness of Pvalues, conclusions that the null hypothesis is true, power analysis, and distinctions between statistical and biological significance. Statistical hypothesis testing, in which the null hypothesis about the properties of a population is almost always known a priori to be false, is contrasted with scientific hypothesis testing, which examines a credible null hypothesis about phenomena in nature. More meaningful alternatives are briefly outlined, including estimation and confidence intervals for determining the importance of factors, decision theory for guiding actions in the face of uncertainty, and Bayesian approaches to hypothesis testing and other statistical practices.
The Horseshoe Estimator for Sparse Signals
, 2008
"... This paper proposes a new approach to sparsity called the horseshoe estimator. The horseshoe is a close cousin of other widely used Bayes rules arising from, for example, doubleexponential and Cauchy priors, in that it is a member of the same family of multivariate scale mixtures of normals. But th ..."
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Cited by 77 (13 self)
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This paper proposes a new approach to sparsity called the horseshoe estimator. The horseshoe is a close cousin of other widely used Bayes rules arising from, for example, doubleexponential and Cauchy priors, in that it is a member of the same family of multivariate scale mixtures of normals. But the horseshoe enjoys a number of advantages over existing approaches, including its robustness, its adaptivity to different sparsity patterns, and its analytical tractability. We prove two theorems that formally characterize both the horseshoe’s adeptness at large outlying signals, and its superefficient rate of convergence to the correct estimate of the sampling density in sparse situations. Finally, using a combination of real and simulated data, we show that the horseshoe estimator corresponds quite closely to the answers one would get by pursuing a full Bayesian modelaveraging approach using a discrete mixture prior to model signals and noise.
Bayesian model averaging
 STAT.SCI
, 1999
"... Standard statistical practice ignores model uncertainty. Data analysts typically select a model from some class of models and then proceed as if the selected model had generated the data. This approach ignores the uncertainty in model selection, leading to overcon dent inferences and decisions tha ..."
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Cited by 66 (1 self)
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Standard statistical practice ignores model uncertainty. Data analysts typically select a model from some class of models and then proceed as if the selected model had generated the data. This approach ignores the uncertainty in model selection, leading to overcon dent inferences and decisions that are more risky than one thinks they are. Bayesian model averaging (BMA) provides a coherent mechanism for accounting for this model uncertainty. Several methods for implementing BMA haverecently emerged. We discuss these methods and present anumber of examples. In these examples, BMA provides improved outofsample predictive performance. We also provide a catalogue of
Why Psychologists Must Change the Way They Analyze Their Data: The Case of Psi
"... Does psi exist? In a recent article, Dr. Bem conducted nine studies with over a thousand participants in an attempt to demonstrate that future events retroactively affect people’s responses. Here we discuss several limitations of Bem’s experiments on psi; in particular, we show that the data analysi ..."
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Cited by 52 (9 self)
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Does psi exist? In a recent article, Dr. Bem conducted nine studies with over a thousand participants in an attempt to demonstrate that future events retroactively affect people’s responses. Here we discuss several limitations of Bem’s experiments on psi; in particular, we show that the data analysis was partly exploratory, and that onesided pvalues may overstate the statistical evidence against the null hypothesis. We reanalyze Bem’s data using a default Bayesian ttest and show that the evidence for psi is weak to nonexistent. We argue that in order to convince a skeptical audience of a controversial claim, one needs to conduct strictly confirmatory studies and analyze the results with statistical tests that are conservative rather than liberal. We conclude that Bem’s pvalues do not indicate evidence in favor of precognition; instead, they indicate that experimental psychologists need to change the way they conduct their experiments and analyze their data.
Bayesian Model Averaging in proportional hazard models: Assessing the risk of a stroke
 Applied Statistics
, 1997
"... Evaluating the risk of stroke is important in reducing the incidence of this devastating disease. Here, we apply Bayesian model averaging to variable selection in Cox proportional hazard models in the context of the Cardiovascular Health Study, a comprehensive investigation into the risk factors for ..."
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Cited by 45 (5 self)
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Evaluating the risk of stroke is important in reducing the incidence of this devastating disease. Here, we apply Bayesian model averaging to variable selection in Cox proportional hazard models in the context of the Cardiovascular Health Study, a comprehensive investigation into the risk factors for stroke. We introduce a technique based on the leaps and bounds algorithm which e ciently locates and ts the best models in the very large model space and thereby extends all subsets regression to Cox models. For each independent variable considered, the method provides the posterior probability that it belongs in the model. This is more directly interpretable than the corresponding Pvalues, and also more valid in that it takes account of model uncertainty. Pvalues from models preferred by stepwise methods tend to overstate the evidence for the predictive value of a variable. In our data Bayesian model averaging predictively outperforms standard model selection methods for assessing
Bayesian hypothesis testing for psychologists: A tutorial on the SavageDickey method.
 Cognitive Psychology,
, 2010
"... a b s t r a c t In the field of cognitive psychology, the pvalue hypothesis test has established a stranglehold on statistical reporting. This is unfortunate, as the pvalue provides at best a rough estimate of the evidence that the data provide for the presence of an experimental effect. An alter ..."
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Cited by 34 (13 self)
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a b s t r a c t In the field of cognitive psychology, the pvalue hypothesis test has established a stranglehold on statistical reporting. This is unfortunate, as the pvalue provides at best a rough estimate of the evidence that the data provide for the presence of an experimental effect. An alternative and arguably more appropriate measure of evidence is conveyed by a Bayesian hypothesis test, which prefers the model with the highest average likelihood. One of the main problems with this Bayesian hypothesis test, however, is that it often requires relatively sophisticated numerical methods for its computation. Here we draw attention to the SavageDickey density ratio method, a method that can be used to compute the result of a Bayesian hypothesis test for nested models and under certain plausible restrictions on the parameter priors. Practical examples demonstrate the method's validity, generality, and flexibility.
Bayesian hypothesis testing: A reference approach
 Internat. Statist. Rev
, 2002
"... For any probability model M ≡{p(x  θ, ω), θ ∈ Θ, ω ∈ Ω} assumed to describe the probabilistic behaviour of data x ∈ X, it is argued that testing whether or not the available data are compatible with the hypothesis H0 ≡{θ = θ0} is best considered as a formal decision problem on whether to use (a0), ..."
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Cited by 31 (6 self)
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For any probability model M ≡{p(x  θ, ω), θ ∈ Θ, ω ∈ Ω} assumed to describe the probabilistic behaviour of data x ∈ X, it is argued that testing whether or not the available data are compatible with the hypothesis H0 ≡{θ = θ0} is best considered as a formal decision problem on whether to use (a0), or not to use (a1), the simpler probability model (or null model) M0 ≡{p(x  θ0, ω), ω ∈ Ω}, where the loss difference L(a0, θ, ω) − L(a1, θ, ω) is proportional to the amount of information δ(θ0, θ, ω) which would be lost if the simplified model M0 were used as a proxy for the assumed model M. For any prior distribution π(θ, ω), the appropriate normative solution is obtained by rejecting the null model M0 whenever the corresponding posterior expectation ∫ ∫ δ(θ0, θ, ω) π(θ, ω  x) dθ dω is sufficiently large. Specification of a subjective prior is always difficult, and often polemical, in scientific communication. Information theory may be used to specify a prior, the reference prior, which only depends on the assumed model M, and mathematically describes a situation where no prior information is available about the quantity of interest. The reference posterior expectation, d(θ0, x) = ∫ δπ(δ  x) dδ, of the amount of information δ(θ0, θ, ω) which could be lost if the null model were used, provides an attractive nonnegative test function, the intrinsic statistic, which is