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Case Studies in Bayesian Statistical Modelling and Analysis WILEY SERIES IN PROBABILITY AND STATISTICS Established by WALTER A SHEWHART and SAMUEL S WILKS Editors David J Balding, Noel A.C Cressie, Garrett M Fitzmaurice, Harvey Goldstein, Iain M Johnstone, Geert Molenberghs, David W Scott, Adrian F.M Smith, Ruey S Tsay, Sanford Weisberg Editors Emeriti Vic Barnett, Ralph A Bradley, J Stuart Hunter, J.B Kadane, David G Kendall, Jozef L Teugels A complete list of the titles in this series appears at the end of this volume Case Studies in Bayesian Statistical Modelling and Analysis Edited by Clair L Alston, Kerrie L Mengersen and Anthony N Pettitt Queensland University of Technology, Brisbane, Australia This edition first published 2013 © 2013 John Wiley & Sons, Ltd Registered office John Wiley & Sons Ltd, The Atrium, Southern Gate, Chichester, West Sussex, PO19 8SQ, United Kingdom For details of our global editorial offices, for customer services and for information about how to apply for permission to reuse the copyright material in this book please see our website at www.wiley.com The right of the author to be identified as the author of this work has been asserted in accordance with the Copyright, Designs and Patents Act 1988 All rights reserved No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording or otherwise, except as permitted by the UK Copyright, Designs and Patents Act 1988, without the prior permission of the publisher Wiley also publishes its books in a variety of electronic formats Some content that appears in print may not be available in electronic books Designations used by companies to distinguish their products are often claimed as trademarks All brand names and product names used in this book are trade names, service marks, trademarks or registered trademarks of their respective owners The publisher is not associated with any product or vendor mentioned in this book This publication is designed to provide accurate and authoritative information in regard to the subject matter covered It is sold on the understanding that the publisher is not engaged in rendering professional services If professional advice or other expert assistance is required, the services of a competent professional should be sought Library of Congress Cataloging-in-Publication Data Case studies in Bayesian statistical modelling and analysis / edited by Clair Alston, Kerrie Mengersen, and Anthony Pettitt pages cm Includes bibliographical references and index ISBN 978-1-119-94182-8 (cloth) Bayesian statistical decision theory I Alston, Clair II Mengersen, Kerrie L III Pettitt, Anthony (Anthony N.) QA279.5.C367 2013 519.5’42–dc23 2012024683 A catalogue record for this book is available from the British Library ISBN: 978-1-119-94182-8 Typeset in 10/12pt Times Roman by Thomson Digital, Noida, India Contents Preface xvii List of contributors xix Introduction Clair L Alston, Margaret Donald, Kerrie L Mengersen and Anthony N Pettitt 1.1 1.2 1.3 Introduction Overview Further reading 1.3.1 Bayesian theory and methodology 1.3.2 Bayesian methodology 1.3.3 Bayesian computation 1.3.4 Bayesian software 1.3.5 Applications References 1 8 10 10 11 13 13 Introduction to MCMC Anthony N Pettitt and Candice M Hincksman 17 2.1 2.2 Introduction Gibbs sampling 2.2.1 Example: Bivariate normal 2.2.2 Example: Change-point model 2.3 Metropolis–Hastings algorithms 2.3.1 Example: Component-wise MH or MH within Gibbs 2.3.2 Extensions to basic MCMC 2.3.3 Adaptive MCMC 2.3.4 Doubly intractable problems 2.4 Approximate Bayesian computation 2.5 Reversible jump MCMC 2.6 MCMC for some further applications References 17 18 18 19 19 20 21 22 22 24 25 26 27 Priors: Silent or active partners of Bayesian inference? Samantha Low Choy 30 3.1 30 32 Priors in the very beginning 3.1.1 Priors as a basis for learning vi CONTENTS 3.1.2 Priors and philosophy 3.1.3 Prior chronology 3.1.4 Pooling prior information 3.2 Methodology I: Priors defined by mathematical criteria 3.2.1 Conjugate priors 3.2.2 Impropriety and hierarchical priors 3.2.3 Zellner’s g-prior for regression models 3.2.4 Objective priors 3.3 Methodology II: Modelling informative priors 3.3.1 Informative modelling approaches 3.3.2 Elicitation of distributions 3.4 Case studies 3.4.1 Normal likelihood: Time to submit research dissertations 3.4.2 Binomial likelihood: Surveillance for exotic plant pests 3.4.3 Mixture model likelihood: Bioregionalization 3.4.4 Logistic regression likelihood: Mapping species distribution via habitat models 3.5 Discussion 3.5.1 Limitations 3.5.2 Finding out about the problem 3.5.3 Prior formulation 3.5.4 Communication 3.5.5 Conclusion Acknowledgements References 32 33 34 35 35 37 37 38 40 40 42 44 Bayesian analysis of the normal linear regression model Christopher M Strickland and Clair L Alston 66 4.1 4.2 66 67 67 Introduction Case studies 4.2.1 Case study 1: Boston housing data set 4.2.2 Case study 2: Production of cars and station wagons 4.3 Matrix notation and the likelihood 4.4 Posterior inference 4.4.1 Natural conjugate prior 4.4.2 Alternative prior specifications 4.4.3 Generalizations of the normal linear model 4.4.4 Variable selection 4.5 Analysis 4.5.1 Case study 1: Boston housing data set 4.5.2 Case study 2: Car production data set References 44 47 50 53 57 57 58 59 60 61 61 61 67 67 68 69 73 74 78 81 81 85 88 CONTENTS Adapting ICU mortality models for local data: A Bayesian approach Petra L Graham, Kerrie L Mengersen and David A Cook 5.1 5.2 Introduction Case study: Updating a known risk-adjustment model for local use 5.3 Models and methods 5.4 Data analysis and results 5.4.1 Updating using the training data 5.4.2 Updating the model yearly 5.5 Discussion References A Bayesian regression model with variable selection for genome-wide association studies Carla Chen, Kerrie L Mengersen, Katja Ickstadt and Jonathan M Keith vii 90 90 91 92 96 96 98 100 101 103 6.1 6.2 6.3 6.4 Introduction Case study: Case–control of Type diabetes Case study: GENICA Models and methods 6.4.1 Main effect models 6.4.2 Main effects and interactions 6.5 Data analysis and results 6.5.1 WTCCC TID 6.5.2 GENICA 6.6 Discussion Acknowledgements References 6.A Appendix: SNP IDs 103 104 105 105 105 108 109 109 110 112 115 115 117 Bayesian meta-analysis Jegar O Pitchforth and Kerrie L Mengersen 118 7.1 7.2 118 7.3 Introduction Case study 1: Association between red meat consumption and breast cancer 7.2.1 Background 7.2.2 Meta-analysis models 7.2.3 Computation 7.2.4 Results 7.2.5 Discussion Case study 2: Trends in fish growth rate and size 7.3.1 Background 119 119 121 125 125 129 130 130 viii CONTENTS 7.3.2 Meta-analysis models 7.3.3 Computation 7.3.4 Results 7.3.5 Discussion Acknowledgements References 131 134 134 135 137 138 Bayesian mixed effects models Clair L Alston, Christopher M Strickland, Kerrie L Mengersen and Graham E Gardner 141 8.1 8.2 141 142 Introduction Case studies 8.2.1 Case study 1: Hot carcase weight of sheep carcases 8.2.2 Case study 2: Growth of primary school girls 8.3 Models and methods 8.3.1 Model for Case study 8.3.2 Model for Case study 8.3.3 MCMC estimation 8.4 Data analysis and results 8.5 Discussion References Ordering of hierarchies in hierarchical models: Bone mineral density estimation Cathal D Walsh and Kerrie L Mengersen 9.1 9.2 Introduction Case study 9.2.1 Measurement of bone mineral density 9.3 Models 9.3.1 Hierarchical model 9.3.2 Model H1 9.3.3 Model H2 9.4 Data analysis and results 9.4.1 Model H1 9.4.2 Model H2 9.4.3 Implication of ordering 9.4.4 Simulation study 9.4.5 Study design 9.4.6 Simulation study results 9.5 Discussion References 9.A Appendix: Likelihoods 142 142 146 147 148 149 150 158 158 159 159 160 160 161 162 163 163 164 164 165 166 166 166 167 168 168 170 CONTENTS ix 10 Bayesian Weibull survival model for gene expression data Sri Astuti Thamrin, James M McGree and Kerrie L Mengersen 171 10.1 Introduction 10.2 Survival analysis 10.3 Bayesian inference for the Weibull survival model 10.3.1 Weibull model without covariates 10.3.2 Weibull model with covariates 10.3.3 Model evaluation and comparison 10.4 Case study 10.4.1 Weibull model without covariates 10.4.2 Weibull survival model with covariates 10.4.3 Model evaluation and comparison 10.5 Discussion References 171 172 174 174 175 176 178 178 180 182 182 183 11 Bayesian change point detection in monitoring clinical outcomes Hassan Assareh, Ian Smith and Kerrie L Mengersen 11.1 11.2 11.3 11.4 11.5 11.6 11.7 Introduction Case study: Monitoring intensive care unit outcomes Risk-adjusted control charts Change point model Evaluation Performance analysis Comparison of Bayesian estimator with other methods 11.8 Conclusion References 12 Bayesian splines Samuel Clifford and Samantha Low Choy 12.1 Introduction 12.2 Models and methods 12.2.1 Splines and linear models 12.2.2 Link functions 12.2.3 Bayesian splines 12.2.4 Markov chain Monte Carlo 12.2.5 Model choice 12.2.6 Posterior diagnostics 12.3 Case studies 12.3.1 Data 12.3.2 Analysis 186 186 187 187 188 189 190 194 194 195 197 197 197 197 198 198 204 206 207 207 207 208 Index action potentials, 310–329 adaptive design, 361–373 adaptive MCMC, 22, 206, 209–211, 418 adaptive random walk, 205 adaptive SMC, 383–384 adjusted BIC, 297, 300 Akaike Information Criterion (AIC), 114, 206, 300 approximate Bayesian computation (ABC), 24–25, 374–375, 382–384 autoregressive regression, 446–449 basis function, 198–218, 244–245 Bayes factor, 61, 183, 206, 297, 300, 327 Bayesian hierarchical model, 17, 32, 34, 36, 107, 118, 123, 133, 137, 141, 159–169, 172–175, 221–237 Bayesian Information Criterion (BIC), 176–177, 182, 206, 260–262, 277, 425, 435 Bayesian lasso, 66, 78, 80–86 Bayesian network (BN), 348–360 Bayesian optimal design, 361–373 Bernoulli, 94, 107, 183, 187–190, 211, 216, 291, 298, 300, 355, 363 Bernoulli prior, 78 Besag, York and Mollie (BYM) model, 240 beta distribution, 36, 42, 45, 56, 318 birth death move, 26, 217, 337, 338, 341 Brook’s lemma, 244 B-spline, 177, 200–204, 208–210, 213–215, 217–218 capital asset pricing model (CAPM), 253 change point model, 19, 186–197, 208, 215, 293 Cholesky decomposition, 77, 258, 447 class membership, 293–295, 306 classification, 270, 292, 299, 330–347 classification and regression trees (CART), 330–347 clustering, 172, 223, 268, 273, 287, 290–291, 297, 396 CODA, 164, 190, 247, 423, 426 compartment model, 376 compiled languages, 422, 452 complexity, 27, 177, 241, 262, 292, 296, 367, 379, 389, 396, 422 conditional autoregressive (CAR), 225, 232, 240, 346 conditional probability table, 56, 349 confusion matrix, 339 control chart, 186–196 convergence, 20–22, 26, 81, 94, 125, 134, 164, 178, 205–207, 233–236, 265, 296, 404, 422 Case Studies in Bayesian Statistical Modelling and Analysis, First Edition Edited by Clair L Alston, Kerrie L Mengersen and Anthony N Pettitt © 2013 John Wiley & Sons, Ltd Published 2013 by John Wiley & Sons, Ltd 462 INDEX core process, 349, 350 cost effectiveness, 417 covariates, 37, 66, 105, 118, 125, 132–137, 175–176 Cox proportional hazards model, 177, 183 cubic regression spline, 200, 217 degeneracy, 383, 404, 409, 411 delayed rejection algorithm, 404–418 density estimation, 159–170, 267–286 deviance information criteria (DIC), 134, 151, 158, 165, 177, 182, 206, 230, 232, 244–245 diagnostics, 20, 95, 125, 207, 232, 337, 339–340 diffuse prior, 40, 175, 203 directed acyclic graph (DAG), 17, 348 direct elicitation, 41, 50, 60 Dirichlet process mixtures, 223 disease mapping, 221–239 dynamic linear model, 223 EM algorithm, 17, 267 ESS, 20–21, 362, 365–370, 412–416 prior elicitation, 33–34, 41–45, 50, 54–56, 60, 261 experts, 33–34, 41–61, 100, 331, 337, 340, 349, 352, 364 excess mortality, 229, 234, 236 exchangeable, 123, 168 exponentially weighted moving average (EWMA), 186–195 factor models, 223, 253 factorial hidden Markov model (HMM), 313, 315–317 false negative rate, 48, 331, 340 Fama–French model, 252–266 filtering, 257–259, 317 finite mixture models, 31, 267–280, 288–292, 311, 388–400 first order serial correlation, 75–76, 85, 87 Fortran, 422, 452, 455–456, 459 forward–backward algorithm, 317–318 Gaussian Markov random field (GMRF), 240 Gelman–Rubin statistic, 125, 179, 230, 295, 302 generalized linear mixed model (GLMM), 198, 204, 222–223 generalized linear model (GLM), 56, 101, 197, 208, 222, 362, 388 generalized additive model (GAM), 197–198 GeoBUGS, 246 GeoDa, 228 Geweke diagnostics, 232 Gibbs sampling, 17–19, 79, 273–275, 298, 318–319, 437 Gillespie’s algorithm, 380 goodness-of-fit, 95, 176–177, 206, 232, 296–297, 334, 357 graphical model, 348 growth mixture models, 292–295 hazard function, 172–174 hidden Markov model (HMM), 310–329 hierarchical model, 17, 34, 134–137, 162–163, 166, 168, 175–176, 223–225, 232–234, 268 hierarchical prior, 36–38, 50, 52–53, 80, 316 hierarchical random effects, 163 hybrid algorithm, 403–420 hyperparameter, 33, 38, 41, 177–178, 233, 276–277, 389, 394 importance distribution, 364–365 importance sampling, 23–24, 75, 363–368, 404, 407 importance weights, 364–365, 367, 404, 407, 411 impurity function, 334 incremental weights, 365 indirect elicitation, 41 informative priors, 40–41 intrinsic CAR prior, 226, 240 inverse gamma distribution, 69–70 iterative process, 349–351, 382–383 Jeffreys’ prior, 38–39, 48–49, 66, 73, 433 Kullback–Leibler divergence, 298, 392 label switching, 297–298, 323 Langevin algorithm, 404–405 INDEX latent class analysis, 268, 288 latent class model, 287, 309 latent growth process, 392–393 latent variable, 17, 50, 104, 279, 287, 289, 291, 294, 297, 311, 392–393 likelihood-free inference, 374–387 linear mixed effects model (LMM), 141–158, 198 linear regression, 36–38, 66–89, 132, 198–199, 208–209, 433, 437 logistic regression, 53–54, 91–101, 106, 211, 294–295, 363–364 Markov chain Monte Carlo (MCMC), 17–29 Markov process, 378–380 Markov random field (MRF), 274–275, 388 MATLAB, 208, 298, 339, 395, 412 matrix exponential, 378–380 meta-analysis, 118–140 Metroplis–Hastings algorthim (MH), 20–21, 75–77, 205, 404–407, 423, 427–429 Metropolis adjusted Langevin algorithm (MALA), 404, 407–408 misclassification rate, 340 mixed effects, 141–158, 198 mixed model, 137, 141–158 mixed treatment comparisons, 159 mixture model, 50–53, 267–286, 290–296, 388–400 mixture prior, 223 model choice, 206–207, 390 multimodal problem, 40, 383, 404, 413, 417 multinomial logistic regression, 295 multivariate random walk, 255–256 mutation step, 362, 382 mutual information, 351, 355 463 orientational bias Monte Carlo (OBMC), 429–430 piecewise polynomial spline, 293 pinball sampler, 404, 411 Poisson regression, 216–217 population Monte Carlo (PMC), 410–412 posterior predictive check, 95, 177, 331 posterior probabilities, 25, 71, 107, 256, 322, 335, 423 Potts model, 22, 274–275 prior distributions, 30–65, 69, 106, 273 prior elicitation, 30–65, 261 proportional hazards, 171, 236 pseudolikelihood, 24, 275 PyMCMC, 421–460 Python, 421–460 R2WinBUGS, 164, 189, 299 random walk proposal, 20, 22, 205, 383 rate of convergence, 417 relative excess risk (RER), 229–230, 234 repulsive proposal, 405–407, 410 reversible jump MCMC (RJMCMC), 25–26 risk-adjusted, 186–188 ROC, 95 roughness penalty, 202 neighbourhood matrices, 227–229, 236, 243, 246 nested structure, 162 noninformative prior, 38 sequential design, 361–367 sequential Monte Carlo (SMC), 361–373 slice sampler, 106, 108, 431–433 spatial correlation, 227, 243–247 spatial mixture model, 274–275, 278–279 spatial prior, 223 spatial smoothing, 223, 244 spatially structured random effects, 223, 227, 230 spike detection, 311 state space model, 252–266 stochastic search, 78–80, 107, 337–338, 437 subjective prior, 33 objective prior, 32–33, 38–39, 48–49 odds ratio, 121–123, 187–189 optimal design, 361–373 tempering, 21, 408–409 time series, 74–75, 132–134, 252–266 time varying regressors, 252–266 464 INDEX Toeplitz block circulation matrix, 204 transition matrix, 255, 313, 317, 327, 378 variable selection, 78–80, 103–117, 437 variational Bayes, 388–400 uniform prior, 30–31, 39 unsupervised detection, 311 unsupervised spatial clustering, 223, 291 utility function, 362, 367–368 Weibull model, 171–185 Wishart priors, 58, 147, 257, 260, 401 Zellner’s g-prior, 37–38, 69, 73, 434 WILEY SERIES IN PROBABILITY AND STATISTICS ESTABLISHED BY WALTER A SHEWHART AND SAMUEL S WILKS Editors: David J Balding, Noel A.C Cressie, Garrett M Fitzmaurice, Harvey Goldstein, Iain M Johnstone, Geert Molenberghs, David W Scott, Adrian F M Smith, Ruey S Tsay, Sanford Weisberg Editors Emeriti: Vic Barnett, Ralph A Bradley, J Stuart Hunter, J.B Kadane, David G Kendall, Jozef L Teugels The Wiley Series in Probability and Statistics is well established and 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Cataloging -in- Publication Data Case studies in Bayesian statistical modelling and analysis / edited by Clair Alston, Kerrie Mengersen, and Anthony Pettitt pages cm Includes bibliographical references and index ISBN.. .Case Studies in Bayesian Statistical Modelling and Analysis WILEY SERIES IN PROBABILITY AND STATISTICS Established by WALTER A SHEWHART and SAMUEL S WILKS Editors David J Balding, Noel

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