Statistical Aspects of BSE and vCJD


Book Description

Bovine Spongiform Encephalopathy (BSE) or "mad cow disease," first diagnosed in late 1986, is transmitted through feed, indirect horizontal transmission, apparently maternally and possibly horizontally, through cattle-to-cattle contact or a contaminated environment. With no ante-mortem test yet developed, the only information available about BSE is from case surveillance and a limited number of experiments. Only through careful and rigorous modeling and analysis can reliable estimates of past infection and predictions of future cases be made. The modeling developed for BSE utilizes a range of techniques from statistics, ecology, and demography that is of interest both as a case study and for providing tools for other modeling projects. Statistical Aspects of BSE and vCJD: Models for Epidemics presents the general methodology required for thorough analysis and modeling of novel long incubation diseases with largely unknown etiology. BSE in British cattle is the primary example system presented, but application to other diseases, particularly the transmissible spongiform encephalopathies (e.g., Scrapie in sheep and nvCJD in humans) are also highlighted. The book concentrates on presenting an exposition of the "state-of-the-art" rather than introductory material on the mathematical/statistical modeling of infectious diseases.




Inferential Models


Book Description

A New Approach to Sound Statistical ReasoningInferential Models: Reasoning with Uncertainty introduces the authors' recently developed approach to inference: the inferential model (IM) framework. This logical framework for exact probabilistic inference does not require the user to input prior information. The authors show how an IM produces meaning




Theory of Factorial Design


Book Description

Bringing together both new and old results, Theory of Factorial Design: Single- and Multi-Stratum Experiments provides a rigorous, systematic, and up-to-date treatment of the theoretical aspects of factorial design. To prepare readers for a general theory, the author first presents a unified treatment of several simple designs, including completely randomized designs, block designs, and row-column designs. As such, the book is accessible to readers with minimal exposure to experimental design. With exercises and numerous examples, it is suitable as a reference for researchers and as a textbook for advanced graduate students. In addition to traditional topics and a thorough discussion of the popular minimum aberration criterion, the book covers many topics and new results not found in existing books. These include results on the structures of two-level resolution IV designs, methods for constructing such designs beyond the familiar foldover method, the extension of minimum aberration to nonregular designs, the equivalence of generalized minimum aberration and minimum moment aberration, a Bayesian approach, and some results on nonregular designs. The book also presents a theory that provides a unifying framework for the design and analysis of factorial experiments with multiple strata (error terms) arising from complicated structures of the experimental units. This theory can be systematically applied to various structures of experimental units instead of treating each on a case-by-case basis.




Hidden Markov Models for Time Series


Book Description

Hidden Markov Models for Time Series: An Introduction Using R, Second Edition illustrates the great flexibility of hidden Markov models (HMMs) as general-purpose models for time series data. The book provides a broad understanding of the models and their uses. After presenting the basic model formulation, the book covers estimation, forecasting, decoding, prediction, model selection, and Bayesian inference for HMMs. Through examples and applications, the authors describe how to extend and generalize the basic model so that it can be applied in a rich variety of situations. The book demonstrates how HMMs can be applied to a wide range of types of time series: continuous-valued, circular, multivariate, binary, bounded and unbounded counts, and categorical observations. It also discusses how to employ the freely available computing environment R to carry out the computations. Features Presents an accessible overview of HMMs Explores a variety of applications in ecology, finance, epidemiology, climatology, and sociology Includes numerous theoretical and programming exercises Provides most of the analysed data sets online New to the second edition A total of five chapters on extensions, including HMMs for longitudinal data, hidden semi-Markov models and models with continuous-valued state process New case studies on animal movement, rainfall occurrence and capture-recapture data




Randomised Response-Adaptive Designs in Clinical Trials


Book Description

Randomised Response-Adaptive Designs in Clinical Trials presents methods for the randomised allocation of treatments to patients in sequential clinical trials. Emphasizing the practical application of clinical trial designs, the book is designed for medical and applied statisticians, clinicians, and statisticians in training. After introducing clinical trials in drug development, the authors assess a simple adaptive design for binary responses without covariates. They discuss randomisation and covariate balance in normally distributed responses and cover many important response-adaptive designs for binary responses. The book then develops response-adaptive designs for continuous and longitudinal responses, optimum designs with covariates, and response-adaptive designs with covariates. It also covers response-adaptive designs that are derived by optimising an objective function subject to constraints on the variance of estimated parametric functions. The concluding chapter explores future directions in the development of adaptive designs.




Quasi-Least Squares Regression


Book Description

Drawing on the authors’ substantial expertise in modeling longitudinal and clustered data, Quasi-Least Squares Regression provides a thorough treatment of quasi-least squares (QLS) regression—a computational approach for the estimation of correlation parameters within the framework of generalized estimating equations (GEEs). The authors present a detailed evaluation of QLS methodology, demonstrating the advantages of QLS in comparison with alternative methods. They describe how QLS can be used to extend the application of the traditional GEE approach to the analysis of unequally spaced longitudinal data, familial data, and data with multiple sources of correlation. In some settings, QLS also allows for improved analysis with an unstructured correlation matrix. Special focus is given to goodness-of-fit analysis as well as new strategies for selecting the appropriate working correlation structure for QLS and GEE. A chapter on longitudinal binary data tackles recent issues raised in the statistical literature regarding the appropriateness of semi-parametric methods, such as GEE and QLS, for the analysis of binary data; this chapter includes a comparison with the first-order Markov maximum-likelihood (MARK1ML) approach for binary data. Examples throughout the book demonstrate each topic of discussion. In particular, a fully worked out example leads readers from model building and interpretation to the planning stages for a future study (including sample size calculations). The code provided enables readers to replicate many of the examples in Stata, often with corresponding R, SAS, or MATLAB® code offered in the text or on the book’s website.




Bayesian Inference for Partially Identified Models


Book Description

Bayesian Inference for Partially Identified Models: Exploring the Limits of Limited Data shows how the Bayesian approach to inference is applicable to partially identified models (PIMs) and examines the performance of Bayesian procedures in partially identified contexts. Drawing on his many years of research in this area, the author presents a thorough overview of the statistical theory, properties, and applications of PIMs. The book first describes how reparameterization can assist in computing posterior quantities and providing insight into the properties of Bayesian estimators. It next compares partial identification and model misspecification, discussing which is the lesser of the two evils. The author then works through PIM examples in depth, examining the ramifications of partial identification in terms of how inferences change and the extent to which they sharpen as more data accumulate. He also explains how to characterize the value of information obtained from data in a partially identified context and explores some recent applications of PIMs. In the final chapter, the author shares his thoughts on the past and present state of research on partial identification. This book helps readers understand how to use Bayesian methods for analyzing PIMs. Readers will recognize under what circumstances a posterior distribution on a target parameter will be usefully narrow versus uselessly wide.




Semialgebraic Statistics and Latent Tree Models


Book Description

The first part of the book gives a general introduction to key concepts in algebraic statistics, focusing on methods that are helpful in the study of models with hidden variables. The author uses tensor geometry as a natural language to deal with multivariate probability distributions, develops new combinatorial tools to study models with hidden data, and describes the semialgebraic structure of statistical models. The second part illustrates important examples of tree models with hidden variables. The book discusses the underlying models and related combinatorial concepts of phylogenetic trees as well as the local and global geometry of latent tree models. It also extends previous results to Gaussian latent tree models. This book shows you how both combinatorics and algebraic geometry enable a better understanding of latent tree models. It contains many results on the geometry of the models, including a detailed analysis of identifiability and the defining polynomial constraints




Maximum Likelihood Estimation for Sample Surveys


Book Description

Sample surveys provide data used by researchers in a large range of disciplines to analyze important relationships using well-established and widely used likelihood methods. The methods used to select samples often result in the sample differing in important ways from the target population and standard application of likelihood methods can lead to biased and inefficient estimates. Maximum Likelihood Estimation for Sample Surveys presents an overview of likelihood methods for the analysis of sample survey data that account for the selection methods used, and includes all necessary background material on likelihood inference. It covers a range of data types, including multilevel data, and is illustrated by many worked examples using tractable and widely used models. It also discusses more advanced topics, such as combining data, non-response, and informative sampling. The book presents and develops a likelihood approach for fitting models to sample survey data. It explores and explains how the approach works in tractable though widely used models for which we can make considerable analytic progress. For less tractable models numerical methods are ultimately needed to compute the score and information functions and to compute the maximum likelihood estimates of the model parameters. For these models, the book shows what has to be done conceptually to develop analyses to the point that numerical methods can be applied. Designed for statisticians who are interested in the general theory of statistics, Maximum Likelihood Estimation for Sample Surveys is also aimed at statisticians focused on fitting models to sample survey data, as well as researchers who study relationships among variables and whose sources of data include surveys.




Mean Field Simulation for Monte Carlo Integration


Book Description

This book presents the first comprehensive and modern mathematical treatment of these mean field particle models, including refined convergence analysis on nonlinear Markov chain models. It also covers applications related to parameter estimation in hidden Markov chain models, stochastic optimization, nonlinear filtering and multiple target tracking, stochastic optimization, calibration and uncertainty propagations in numerical codes, rare event simulation, financial mathematics, and free energy and quasi-invariant measures arising in computational physics and population biology.