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1,012
WinBUGS  a Bayesian modelling framework: concepts, structure, and extensibility
 Statistics and Computing
, 2000
"... WinBUGS is a fully extensible modular framework for constructing and analysing Bayesian full probability models. Models may be specified either textually via the BUGS language or pictorially using a graphical interface called DoodleBUGS. WinBUGS processes the model specification and constructs an ob ..."
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Cited by 262 (4 self)
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WinBUGS is a fully extensible modular framework for constructing and analysing Bayesian full probability models. Models may be specified either textually via the BUGS language or pictorially using a graphical interface called DoodleBUGS. WinBUGS processes the model specification and constructs an objectoriented representation of the model. The software offers a userinterface, based on dialogue boxes and menu commands, through which the model may then be analysed using Markov chain Monte Carlo techniques. In this paper we discuss how and why various modern computing concepts, such as objectorientation and runtime linking, feature in the software’s design. We also discuss how the framework may be extended. It is possible to write specific applications that form an apparently seamless interface with WinBUGS for users with specialized requirements. It is also possible to interface with WinBUGS at a lower level by incorporating new object types that may be used by WinBUGS without knowledge of the modules in which they are implemented. Neither of these types of extension require access to, or even recompilation of, the WinBUGS sourcecode.
Prior distributions for variance parameters in hierarchical models
 Bayesian Analysis
, 2006
"... Various noninformative prior distributions have been suggested for scale parameters in hierarchical models. We construct a new foldednoncentralt family of conditionally conjugate priors for hierarchical standard deviation parameters, and then consider noninformative and weakly informative priors i ..."
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Cited by 250 (14 self)
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Various noninformative prior distributions have been suggested for scale parameters in hierarchical models. We construct a new foldednoncentralt family of conditionally conjugate priors for hierarchical standard deviation parameters, and then consider noninformative and weakly informative priors in this family. We use an example to illustrate serious problems with the inversegamma family of “noninformative ” prior distributions. We suggest instead to use a uniform prior on the hierarchical standard deviation, using the halft family when the number of groups is small and in other settings where a weakly informative prior is desired.
Slice sampling
 Annals of Statistics
, 2000
"... Abstract. Markov chain sampling methods that automatically adapt to characteristics of the distribution being sampled can be constructed by exploiting the principle that one can sample from a distribution by sampling uniformly from the region under the plot of its density function. A Markov chain th ..."
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Cited by 234 (5 self)
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Abstract. Markov chain sampling methods that automatically adapt to characteristics of the distribution being sampled can be constructed by exploiting the principle that one can sample from a distribution by sampling uniformly from the region under the plot of its density function. A Markov chain that converges to this uniform distribution can be constructed by alternating uniform sampling in the vertical direction with uniform sampling from the horizontal ‘slice ’ defined by the current vertical position, or more generally, with some update that leaves the uniform distribution over this slice invariant. Variations on such ‘slice sampling ’ methods are easily implemented for univariate distributions, and can be used to sample from a multivariate distribution by updating each variable in turn. This approach is often easier to implement than Gibbs sampling, and more efficient than simple Metropolis updates, due to the ability of slice sampling to adaptively choose the magnitude of changes made. It is therefore attractive for routine and automated use. Slice sampling methods that update all variables simultaneously are also possible. These methods can adaptively choose the magnitudes of changes made to each variable, based on the local properties of the density function. More ambitiously, such methods could potentially allow the sampling to adapt to dependencies between variables by constructing local quadratic approximations. Another approach is to improve sampling efficiency by suppressing random walks. This can be done using ‘overrelaxed ’ versions of univariate slice sampling procedures, or by using ‘reflective ’ multivariate slice sampling methods, which bounce off the edges of the slice.
Nonparametric regression using Bayesian variable selection
 Journal of Econometrics
, 1996
"... This paper estimates an additive model semiparametrically, while automatically selecting the significant independent variables and the app~opriatc power transformation of the dependent variable. The nonlinear variables arc modeled as regression splincs, with significant knots selected fiom a large ..."
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Cited by 175 (16 self)
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This paper estimates an additive model semiparametrically, while automatically selecting the significant independent variables and the app~opriatc power transformation of the dependent variable. The nonlinear variables arc modeled as regression splincs, with significant knots selected fiom a large number of candidate knots. The estimation is made robust by modeling the errors as a mixture of normals. A Bayesian approach is used to select the significant knots, the power transformation, and to identify oatliers using the Gibbs sampler to curry out the computation. Empirical evidence is given that the sampler works well on both simulated and real examples and that in the univariate case it compares faw)rably with a kernelweighted local linear smoother, The variable selection algorithm in the paper is substantially fasler than previous Bayesian variable sclcclion algorithms. K('I ' word~': Additive nlodel, Pov¢¢r Iransformalio:l: Robust cslinlalion
Statistical algorithms for models in state space using SsfPack 2.2
 The Econometrics Journal
, 1999
"... ..."
Simulating Normalized Constants: From Importance Sampling to Bridge Sampling to Path Sampling
, 1998
"... 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 highdimensional models. This paper aims to bring to the attention of ..."
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Cited by 172 (4 self)
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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 highdimensional 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. Thermodynamic integration, which is also known in the numerical analysis literature as Ogata’s method for highdimensional integration, corresponds to the use of infinitely many and continuously connected bridges (and thus a “path”). Our path sampling formulation offers more flexibility and thus potential efficiency to thermodynamic integration, and the search of optimal paths turns out to have close connections with the Jeffreys prior density and the Rao and Hellinger distances between two densities. We provide an informative theoretical example as well as two empirical examples (involving 17 to 70dimensional integrations) to illustrate the potential and implementation of path sampling. We also discuss some open problems.
Marginal Likelihood From the MetropolisHastings
 Output,Journal of the American Statistical Association
, 2001
"... This article provides a framework for estimating the marginal likelihood for the purpose of Bayesian model comparisons. The approach extends and completes the method presented in Chib (1995) by overcoming the problems associated with the presence of intractable full conditional densities. The propos ..."
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Cited by 168 (16 self)
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This article provides a framework for estimating the marginal likelihood for the purpose of Bayesian model comparisons. The approach extends and completes the method presented in Chib (1995) by overcoming the problems associated with the presence of intractable full conditional densities. The proposed method is developed in the context of MCMC chains produced by the Metropolis–Hastings algorithm, whose building blocks are used both for sampling and marginal likelihood estimation, thus economizing on prerun tuning effort and programming. Experiments involving the logit model for binary data, hierarchical random effects model for clustered Gaussian data, Poisson regression model for clustered count data, and the multivariate probit model for correlated binary data, are used to illustrate the performance and implementation of the method. These examples demonstrate that the method is practical and widely applicable.
Analysis of multivariate probit models
 BIOMETRIKA
, 1998
"... This paper provides a practical simulationbased Bayesian and nonBayesian analysis of correlated binary data using the multivariate probit model. The posterior distribution is simulated by Markov chain Monte Carlo methods and maximum likelihood estimates are obtained by a Monte Carlo version of the ..."
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Cited by 155 (13 self)
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This paper provides a practical simulationbased Bayesian and nonBayesian analysis of correlated binary data using the multivariate probit model. The posterior distribution is simulated by Markov chain Monte Carlo methods and maximum likelihood estimates are obtained by a Monte Carlo version of the EM algorithm. A practical approach for the computation of Bayes factors from the simulation output is also developed. The methods are applied to a dataset with a bivariate binary response, to a fouryear longitudinal dataset from the Six Cities study of the health effects of air pollution and to a sevenvariate binary response dataset on the labour supply of married women from the Panel Survey of Income Dynamics.
An exact likelihood analysis of the multinomial probit model
, 1994
"... We develop new methods for conducting a finite sample, likelihoodbased analysis of the multinomial probit model. Using a variant of the Gibbs sampler, an algorithm is developed to draw from the exact posterior of the multinomial probit model with correlated errors. This approach avoids direct evalu ..."
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Cited by 144 (6 self)
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We develop new methods for conducting a finite sample, likelihoodbased analysis of the multinomial probit model. Using a variant of the Gibbs sampler, an algorithm is developed to draw from the exact posterior of the multinomial probit model with correlated errors. This approach avoids direct evaluation of the likelihood and, thus, avoids the problems associated with calculating choice probabilities which affect both the standard likelihood and method of simulated moments approaches. Both simulated and actual consumer panel data are used to fit sixdimensional choice models. We also develop methods for analyzing random coefficient and multiperiod probit models.