Bayesian inference

Abstract: Tables and Figures. Glossary. 1. Introduction. 1.1 Overview. 1.2 Examples of Surveys with Nonresponse. 1.3 Properly Handling Nonresponse. 1.4 Single Imputation. 1.5 Multiple Imputation. 1.6 Numerical Example Using Multiple Imputation. 1.7 Guidance for the Reader. 2. Statistical Background. 2.1 Introduction. 2.2 Variables in the Finite Population. 2.3 Probability Distributions and Related Calculations. 2.4 Probability Specifications for Indicator Variables. 2.5 Probability Specifications for (X,Y). 2.6 Bayesian Inference for a Population Quality. 2.7 Interval Estimation. 2.8 Bayesian Procedures for Constructing Interval Estimates, Including Significance Levels and Point Estimates. 2.9 Evaluating the Performance of Procedures. 2.10 Similarity of Bayesian and Randomization--Based Inferences in Many Practical Cases. 3. Underlying Bayesian Theory. 3.1 Introduction and Summary of Repeated--Imputation Inferences. 3.2 Key Results for Analysis When the Multiple Imputations are Repeated Draws from the Posterior Distribution of the Missing Values. 3.3 Inference for Scalar Estimands from a Modest Number of Repeated Completed--Data Means and Variances. 3.4 Significance Levels for Multicomponent Estimands from a Modest Number of Repeated Completed--Data Means and Variance--Covariance Matrices. 3.5 Significance Levels from Repeated Completed--Data Significance Levels. 3.6 Relating the Completed--Data and Completed--Data Posterior Distributions When the Sampling Mechanism is Ignorable. 4. Randomization--Based Evaluations. 4.1 Introduction. 4.2 General Conditions for the Randomization--Validity of Infinite--m Repeated--Imputation Inferences. 4.3Examples of Proper and Improper Imputation Methods in a Simple Case with Ignorable Nonresponse. 4.4 Further Discussion of Proper Imputation Methods. 4.5 The Asymptotic Distibution of (Qm,Um,Bm) for Proper Imputation Methods. 4.6 Evaluations of Finite--m Inferences with Scalar Estimands. 4.7 Evaluation of Significance Levels from the Moment--Based Statistics Dm and Dm with Multicomponent Estimands. 4.8 Evaluation of Significance Levels Based on Repeated Significance Levels. 5. Procedures with Ignorable Nonresponse. 5.1 Introduction. 5.2 Creating Imputed Values under an Explicit Model. 5.3 Some Explicit Imputation Models with Univariate YI and Covariates. 5.4 Monotone Patterns of Missingness in Multivariate YI. 5.5 Missing Social Security Benefits in the Current Population Survey. 5.6 Beyond Monotone Missingness. 6. Procedures with Nonignorable Nonresponse. 6.1 Introduction. 6.2 Nonignorable Nonresponse with Univariate YI and No XI. 6.3 Formal Tasks with Nonignorable Nonresponse. 6.4 Illustrating Mixture Modeling Using Educational Testing Service Data. 6.5 Illustrating Selection Modeling Using CPS Data. 6.6 Extensions to Surveys with Follow--Ups. 6.7 Follow--Up Response in a Survey of Drinking Behavior Among Men of Retirement Age. References. Author Index. Subject Index. Appendix I. Report Written for the Social Security Administration in 1977. Appendix II. Report Written for the Census Bureau in 1983.

Abstract: The Gibbs sampler, the algorithm of Metropolis and similar iterative simulation methods are potentially very helpful for summarizing multivariate distributions. Used naively, however, iterative simulation can give misleading answers. Our methods are simple and generally applicable to the output of any iterative simulation; they are designed for researchers primarily interested in the science underlying the data and models they are analyzing, rather than for researchers interested in the probability theory underlying the iterative simulations themselves. Our recommended strategy is to use several independent sequences, with starting points sampled from an overdispersed distribution. At each step of the iterative simulation, we obtain, for each univariate estimand of interest, a distributional estimate and an estimate of how much sharper the distributional estimate might become if the simulations were continued indefinitely. Because our focus is on applied inference for Bayesian posterior distributions in real problems, which often tend toward normality after transformations and marginalization, we derive our results as normal-theory approximations to exact Bayesian inference, conditional on the observed simulations. The methods are illustrated on a random-effects mixture model applied to experimental measurements of reaction times of normal and schizophrenic patients.

Abstract: Algebra of Vectors and Matrices. Probability Theory, Tools and Techniques. Continuous Probability Models. The Theory of Least Squares and Analysis of Variance. Criteria and Methods of Estimation. Large Sample Theory and Methods. Theory of Statistical Inference. Multivariate Analysis. Publications of the Author. Author Index. Subject Index.

Abstract: Bayesian inference of phylogeny using Markov chain Monte Carlo (MCMC) plays a central role in understanding evolutionary history from molecular sequence data. Visualizing and analyzing the MCMC-generated samples from the posterior distribution is a key step in any non-trivial Bayesian inference. We present the software package Tracer (version 1.7) for visualizing and analyzing the MCMC trace files generated through Bayesian phylogenetic inference. Tracer provides kernel density estimation, multivariate visualization, demographic trajectory reconstruction, conditional posterior distribution summary, and more. Tracer is open-source and available at http://beast.community/tracer.