Bayesian Methods : A Social and Behavioral Sciences Approach

BACKGROUND AND INTRODUCTION Introduction Motivation and Justification Why Are We Uncertain about Probability? Bayes' Law Conditional Inference with Bayes' Law Historical Comments The Scientific Process in Our Social Sciences Introducing Markov Chain Monte Carlo Techniques Exercises SPECIFYING BAYESIAN MODELS Purpose Likelihood Theory and Estimation The Basic Bayesian Framework Bayesian "Learning" Comments on Prior Distributions Bayesian versus Non-Bayesian Approaches Exercises Computational Addendum: R for Basic Analysis THE NORMAL AND STUDENT'S-T MODELS Why Be Normal? The Normal Model with Variance Known The Normal Model with Mean Known The Normal Model with Both Mean and Variance Unknown Multivariate Normal Model, and S Both Unknown Simulated Effects of Differing Priors Some Normal Comments The Student's t Model Normal Mixture Models Exercises Computational Addendum: Normal Examples THE BAYESIAN LINEAR MODEL The Basic Regression Model Posterior Predictive Distribution for the Data The Bayesian Linear Regression Model with Heteroscedasticity Exercises Computational Addendum THE BAYESIAN PRIOR A Prior Discussion of Priors A Plethora of Priors Conjugate Prior Forms Uninformative Prior Distributions Informative Prior Distributions Hybrid Prior Forms Nonparametric Priors Bayesian Shrinkage Exercises ASSESSING MODEL QUALITY Motivation Basic Sensitivity Analysis Robustness Evaluation Comparing Data to the Posterior Predictive Distribution Simple Bayesian Model Averaging Concluding Comments on Model Quality Exercises Computational Addendum BAYESIAN HYPOTHESIS TESTING AND THE BAYES' FACTOR Motivation Bayesian Inference and Hypothesis Testing The Bayes' Factor as Evidence The Bayesian Information Criterion (BIC) The Deviance Information Criterion (DIC) Comparing Posteriors with the Kullback-Leibler Distance Laplace Approximation of Bayesian Posterior Densities Exercises Bayesian Decision Theory Introducing Decision Theory Basic Definitions Regression-Style Models with Decision Theory James-Stein Estimation Empirical Bayes Exercises Monte Carlo and Related Iterative Methods Background Basic Monte Carlo Integration Rejection Sampling Classical Numerical Integration Gaussian Quadrature Importance Sampling/Sampling Importance Resampling Mode Finding and the EM Algorithm Survey of Random Number Generation Concluding Remarks Exercises Computational Addendum: R Code for Importance Sampling BASICS OF MARKOV CHAIN MONTE CARLO Who Is Markov and What Is He Doing with Chains? General Properties of Markov Chains The Gibbs Sampler The Metropolis-Hastings Algorithm The Hit-and-Run Algorithm The Data Augmentation Algorithm Historical Comments Exercises Computational Addendum: Simple R Graphing Routines for MCMC Implementing Bayesian Models with Markov Chain Monte Carlo Introduction to Bayesian Software Solutions It's Only a Name: BUGS Model Specification with BUGS Differences between WinBUGS and JAGS Code Technical Background about the Algorithm Epilogue Exercises BAYESIAN HIERARCHICAL MODELS Introduction to Multilevel Models Standard Multilevel Linear Models A Poisson-Gamma Hierarchical Model The General Role of Priors and Hyperpriors Exchangeability Empirical Bayes Exercises Computational Addendum: Instructions for Running JAGS, Trade Data Model SOME MARKOV CHAIN MONTE CARLO THEORY Motivation Measure and Probability Preliminaries Specific Markov Chain Properties Defining and Reaching Convergence Rates of Convergence Implementation Concerns Exercises UTILITARIAN MARKOV CHAIN MONTE CARLO Practical Considerations and Admonitions Assessing Convergence of Markov Chains Mixing and Acceleration Producing the Marginal Likelihood Integral from Metropolis- Hastings Output Rao-Blackwellizing for Improved Variance Estimation Exercises Computational Addendum: R Code for the Death Penalty Support Model and BUGS Code for the Military Personnel Model Markov Chain Monte Carlo Extensions Simulated Annealing Reversible Jump Algorithms Perfect Sampling Exercises APPENDIX A: GENERALIZED LINEAR MODEL REVIEW Terms The Generalized Linear Model Numerical Maximum Likelihood Quasi-Likelihood Exercises R for Generalized Linear Models APPENDIX B: COMMON PROBABILITY DISTRIBUTIONS REFERENCES AUTHOR INDEX SUBJECT INDEX