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61
Markov chains for exploring posterior distributions
 Annals of Statistics
, 1994
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Cited by 751 (6 self)
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Your use of the JSTOR archive indicates your acceptance of JSTOR's Terms and Conditions of Use, available at
Using simulation methods for Bayesian econometric models: Inference, development and communication
 Econometric Review
, 1999
"... This paper surveys the fundamental principles of subjective Bayesian inference in econometrics and the implementation of those principles using posterior simulation methods. The emphasis is on the combination of models and the development of predictive distributions. Moving beyond conditioning on a ..."
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Cited by 199 (15 self)
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This paper surveys the fundamental principles of subjective Bayesian inference in econometrics and the implementation of those principles using posterior simulation methods. The emphasis is on the combination of models and the development of predictive distributions. Moving beyond conditioning on a fixed number of completely specified models, the paper introduces subjective Bayesian tools for formal comparison of these models with as yet incompletely specified models. The paper then shows how posterior simulators can facilitate communication between investigators (for example, econometricians) on the one hand and remote clients (for example, decision makers) on the other, enabling clients to vary the prior distributions and functions of interest employed by investigators. A theme of the paper is the practicality of subjective Bayesian methods. To this end, the paper describes publicly available software for Bayesian inference, model development, and communication and provides illustrations using two simple econometric models. *This paper was originally prepared for the Australasian meetings of the Econometric Society in Melbourne, Australia,
Inference in Generalized Additive Mixed Models Using Smoothing Splines
, 1999
"... this paper, we propose generalized additive mixed models (GAMMs), which are an additive extension of generalized linear mixed models in the spirit of Hastie and Tibshirani (1990). This new class of models uses additive nonparametric functions to model covariate effects while accounting for overdispe ..."
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Cited by 45 (4 self)
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this paper, we propose generalized additive mixed models (GAMMs), which are an additive extension of generalized linear mixed models in the spirit of Hastie and Tibshirani (1990). This new class of models uses additive nonparametric functions to model covariate effects while accounting for overdispersion and correlation by adding random effects to the additive predictor. GAMMs encompass nested and crossed designs and are applicable to clustered, hierarchical and spatial data. We estimate the nonparametric functions using smoothing splines, and jointly estimate the smoothing parameters and the variance components using marginal quasilikelihood. This marginal quasilikelihood approach is an extension of the restricted maximum likelihood approach used by Wahba (1985) and Kohn, et al. (1991) in the classical nonparametric regression model (Kohn, et al. 1991, eq 2.1), and by Zhang, et al. (1998) in Gaussian nonparametric mixed models, where they treated the smoothing parameter as an extra variance component. In view of numerical integration often required by maximizing the objective functions, double penalized quasilikelihood (DPQL) is proposed to make approximate inference. Frequentist and Bayesian inferences are compared. A key feature of the proposed method is that it allows us to make systematic inference on all model components of GAMMs within a unified parametric mixed model framework. Specifically, our estimation of the nonparametric functions, the smoothing parameters and the variance components in GAMMs can proceed by fitting a working GLMM using existing statistical software, which iteratively fits a linear mixed model to a modified dependent variable. When the data are sparse (e.g., binary), the DPQL estimators of the variance components are found to be subject t...
Geoadditive Models
, 2000
"... this paper is a recent article on modelbased geostatistics by Diggle, Tawn and Moyeed (1998) where pure kriging (i.e. no covariates) is the focus. Our paper inherits some of its aspects: modelbased and with mixed model connections. In particular the comment by Bowman (1998) in the ensuing discussi ..."
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Cited by 33 (1 self)
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this paper is a recent article on modelbased geostatistics by Diggle, Tawn and Moyeed (1998) where pure kriging (i.e. no covariates) is the focus. Our paper inherits some of its aspects: modelbased and with mixed model connections. In particular the comment by Bowman (1998) in the ensuing discussion suggested that additive modelling would be a worthwhile extension. This paper essentially follows this suggestion. However, this paper is not the first to combine the notions of geostatistics and additive modelling. References known to us are Kelsall and Diggle (1998), Durban Reguera (1998) and Durban, Hackett, Currie and Newton (2000). Nevertheless, we believe that our approach has a number of attractive features (see (1)(4) above), not all shared by these references. Section 2 describes the motivating application and data in detail. Section 3 shows how one can express additive models as a mixed model, while Section 4 does the same for kriging and merges the two into the geoadditive model. Issues concerning the amount of smoothing are discussed in Section 5 and inferential aspects are treated in Section 6. Our analysis of the Upper Cape Cod reproductive data is presented in Section 7. Section 8 discusses extension to the generalised context.We close the paper with some disussion in Section 9. 2 Description of the application and data
Modeling Multilevel Data Structures
 AMERICAN JOURNAL OF POLITICAL SCIENCE
, 1997
"... Although integrating multiple levels of data into an analysis can often yield better inferences about the phenomenon under study, traditional methodologies used to combine multiple levels of data are problematic. In this paper, we discuss several methodologies under the rubric of multilevel analys ..."
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Cited by 17 (0 self)
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Although integrating multiple levels of data into an analysis can often yield better inferences about the phenomenon under study, traditional methodologies used to combine multiple levels of data are problematic. In this paper, we discuss several methodologies under the rubric of multilevel analysis. Multilevel methods, we argue, provide researchers, particularly researchers using comparative data, substantial leverage in overcoming the typical problems associated with either ignoring multiple levels of data, or problems associated with combining lowerlevel and higherlevel data (including overcoming implicit assumptions of fixed and constant effects). The paper discusses several variants of the multilevel model and provides an application of individuallevel support for European integration using comparative political data from Western Europe.
p_2: A Random Effects Model with Covariates for Directed Graphs
, 2004
"... A random effects model is proposed for the analysis of binary dyadic data that represent a social network or directed graph, using nodal and/or dyadic attributes as covariates. The network structure is reflected by modeling the dependence between the relations to and from the same actor or node. Par ..."
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Cited by 15 (2 self)
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A random effects model is proposed for the analysis of binary dyadic data that represent a social network or directed graph, using nodal and/or dyadic attributes as covariates. The network structure is reflected by modeling the dependence between the relations to and from the same actor or node. Parameter estimates are proposed that are based on an iterated generalized least squares procedure. An application is presented to a data set on friendship relations between American lawyers.
A Bayesian population model with hierarchical mixture priors applied to blood count data
 JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION
, 1997
"... Population pharmacokinetic and pharmacodynamic studies require one to analyze nonlinear growth curves fit to multiple measurements from study subjects. We propose a class of nonlinear population models with nonparametric secondstage priors for analyzing such data. The proposed models apply a flexib ..."
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Cited by 14 (4 self)
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Population pharmacokinetic and pharmacodynamic studies require one to analyze nonlinear growth curves fit to multiple measurements from study subjects. We propose a class of nonlinear population models with nonparametric secondstage priors for analyzing such data. The proposed models apply a flexible class of mixtures to implement the nonparametric second stage. The discussion is based on a pharmacodynamic study involving longitudinal data consisting of hematologic profiles (i.e., blood counts measured over time) of cancer patients undergoing chemotherapy. We describe a full posterior analysis in a Bayesian framework. This includes prediction of future observations (profiles and end points for new patients), estimation of the mean response function for observed individuals, and inference on population characteristics. The mixture model is specified and given a hyperprior distribution by means of a Dirichlet processes prior on the mixing measure. Estimation is implemented by a combinat...
Gibbs Sampling
 Journal of the American Statistical Association
, 1995
"... 8> R f(`)d`. To marginalize, say for ` i ; requires h(` i ) = R f(`)d` (i) = R f(`)d` where ` (i) denotes all components of ` save ` i : To obtain Eg(` i ) requires similar integration; to obtain the marginal distribution of say g(`) or its expectation requires similar integration. When p is l ..."
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Cited by 10 (0 self)
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8> R f(`)d`. To marginalize, say for ` i ; requires h(` i ) = R f(`)d` (i) = R f(`)d` where ` (i) denotes all components of ` save ` i : To obtain Eg(` i ) requires similar integration; to obtain the marginal distribution of say g(`) or its expectation requires similar integration. When p is large (as it will be in the applications we envision) such integration is analytically infeasible (the socalled curse of dimensionality*). Gibbs sampling provides a Monte Carlo approach for carrying out such integrations. In what sorts of settings would we have need to mar
A Bayesian Analysis of Ordinal Data Using Mixtures
, 1993
"... In this paper, we discuss a Bayesian method for the analysis of ordinal data. It is assumed that the ordinal data arise from an underlying latent variable which is related to a set of covariates in a generalized linear model sense. The link function which associates the class probabilities to the se ..."
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Cited by 8 (0 self)
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In this paper, we discuss a Bayesian method for the analysis of ordinal data. It is assumed that the ordinal data arise from an underlying latent variable which is related to a set of covariates in a generalized linear model sense. The link function which associates the class probabilities to the set of covariates is estimated as a finite mixture of probit links, thereby introducing flexibility in the choice of the link function. The Bayesian model provides an easytoimplement simulation environment and therefore avoids pitfalls of the expensive and numerically unstable maximum likelihood analysis. The class probabilities are estimated by considering the predictive distribution of a future observation given the set of covariates. Computations are performed using Gibbs sampling. The method is illustrated by using both simulated and real data sets.
Generalized Nonlinear Modelling with Multivariate Smoothing Splines
, 1999
"... A Bayesian method is presented for the nonparametric modelling of univariate and multivariate nonGaussian response data. Data adaptive multivariate smoothing splines are employed where the number and location of the knot points are treated as random. The posterior model space is explored using ..."
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Cited by 8 (2 self)
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A Bayesian method is presented for the nonparametric modelling of univariate and multivariate nonGaussian response data. Data adaptive multivariate smoothing splines are employed where the number and location of the knot points are treated as random. The posterior model space is explored using a reversible jump Markov chain Monte Carlo sampler. Computational difficulties are partly alleviated by introducing a residual effect in the model that leaves many of the posterior distributions of the model parameters in standard form. The use of the latent residual effect provides a convenient vehicle for modelling correlation in multivariate response data and as such our method can be seen to generalize the seemingly unrelated regression model (Zellner, 1962) to nonGaussian data. KEYWORDS: Bayesian nonlinear regression; multivariate splines; piecewise linear; local linear regression; SUR; multivariate nonlinear regression; generalised nonlinear regression. 1 1 Introduction R...