Offering a rich diversity of models, Bayesian phylogenetics allows evolutionary biologists, systematists, ecologists, and epidemiologists to obtain answers to very detailed phylogenetic questions. Suitable for graduate-level researchers in statistics and biology, Bayesian Phylogenetics: Methods, Algorithms, and Applications presents a snapshot of current trends in Bayesian phylogenetic research. Encouraging interdisciplinary research, this book introduces state-of-the-art phylogenetics to the Bayesian statistical community and, likewise, presents state-of-the-art Bayesian statistics to the phylogenetics community. The book emphasizes model selection, reflecting recent interest in accurately estimating marginal likelihoods. It also discusses new approaches to improve mixing in Bayesian phylogenetic analyses in which the tree topology varies. In addition, the book covers divergence time estimation, biologically realistic models, and the burgeoning interface between phylogenetics and population genetics.

Offering a rich diversity of models, Bayesian phylogenetics allows evolutionary biologists, systematists, ecologists, and epidemiologists to obtain answers to very detailed phylogenetic questions. Suitable for graduate-level researchers in statistics and biology, Bayesian Phylogenetics: Methods, Algorithms, and Applications presents a snapshot of current trends in Bayesian phylogenetic research.

Encouraging interdisciplinary research, this book introduces state-of-the-art phylogenetics to the Bayesian statistical community and, likewise, presents state-of-the-art Bayesian statistics to the phylogenetics community. The book emphasizes model selection, reflecting recent interest in accurately estimating marginal likelihoods. It also discusses new approaches to improve mixing in Bayesian phylogenetic analyses in which the tree topology varies. In addition, the book covers divergence time estimation, biologically realistic models, and the burgeoning interface between phylogenetics and population genetics.

Research in Bayesian analysis and statistical decision theory is rapidly expanding and diversifying, making it increasingly more difficult for any single researcher to stay up to date on all current research frontiers. This book provides a review of current research challenges and opportunities. While the book can not exhaustively cover all current research areas, it does include some exemplary discussion of most research frontiers. Topics include objective Bayesian inference, shrinkage estimation and other decision based estimation, model selection and testing, nonparametric Bayes, the interface of Bayesian and frequentist inference, data mining and machine learning, methods for categorical and spatio-temporal data analysis and posterior simulation methods. Several major application areas are covered: computer models, Bayesian clinical trial design, epidemiology, phylogenetics, bioinformatics, climate modeling and applications in political science, finance and marketing. As a review of current research in Bayesian analysis the book presents a balance between theory and applications. The lack of a clear demarcation between theoretical and applied research is a reflection of the highly interdisciplinary and often applied nature of research in Bayesian statistics. The book is intended as an update for researchers in Bayesian statistics, including non-statisticians who make use of Bayesian inference to address substantive research questions in other fields. It would also be useful for graduate students and research scholars in statistics or biostatistics who wish to acquaint themselves with current research frontiers.

Dealing with methods for sampling from posterior distributions and how to compute posterior quantities of interest using Markov chain Monte Carlo (MCMC) samples, this book addresses such topics as improving simulation accuracy, marginal posterior density estimation, estimation of normalizing constants, constrained parameter problems, highest posterior density interval calculations, computation of posterior modes, and posterior computations for proportional hazards models and Dirichlet process models. The authors also discuss model comparisons, including both nested and non-nested models, marginal likelihood methods, ratios of normalizing constants, Bayes factors, the Savage-Dickey density ratio, Stochastic Search Variable Selection, Bayesian Model Averaging, the reverse jump algorithm, and model adequacy using predictive and latent residual approaches. The book presents an equal mixture of theory and applications involving real data, and is intended as a graduate textbook or a reference book for a one-semester course at the advanced masters or Ph.D. level. It will also serve as a useful reference for applied or theoretical researchers as well as practitioners.

Research in Bayesian analysis and statistical decision theory is rapidly expanding and diversifying, making it increasingly more difficult for any single researcher to stay up to date on all current research frontiers. This book provides a review of current research challenges and opportunities. While the book can not exhaustively cover all current research areas, it does include some exemplary discussion of most research frontiers. Topics include objective Bayesian inference, shrinkage estimation and other decision based estimation, model selection and testing, nonparametric Bayes, the interface of Bayesian and frequentist inference, data mining and machine learning, methods for categorical and spatio-temporal data analysis and posterior simulation methods. Several major application areas are covered: computer models, Bayesian clinical trial design, epidemiology, phylogenetics, bioinformatics, climate modeling and applications in political science, finance and marketing. As a review of current research in Bayesian analysis the book presents a balance between theory and applications. The lack of a clear demarcation between theoretical and applied research is a reflection of the highly interdisciplinary and often applied nature of research in Bayesian statistics. The book is intended as an update for researchers in Bayesian statistics, including non-statisticians who make use of Bayesian inference to address substantive research questions in other fields. It would also be useful for graduate students and research scholars in statistics or biostatistics who wish to acquaint themselves with current research frontiers.

Survival analysis arises in many fields of study including medicine, biology, engineering, public health, epidemiology, and economics. This book provides a comprehensive treatment of Bayesian survival analysis. Several topics are addressed, including parametric models, semiparametric models based on prior processes, proportional and non-proportional hazards models, frailty models, cure rate models, model selection and comparison, joint models for longitudinal and survival data, models with time varying covariates, missing covariate data, design and monitoring of clinical trials, accelerated failure time models, models for multivariate survival data, and special types of hierarchical survival models. Also various censoring schemes are examined including right and interval censored data. Several additional topics are discussed, including noninformative and informative prior specificiations, computing posterior qualities of interest, Bayesian hypothesis testing, variable selection, model selection with nonnested models, model checking techniques using Bayesian diagnostic methods, and Markov chain Monte Carlo (MCMC) algorithms for sampling from the posteiror and predictive distributions. The book presents a balance between theory and applications, and for each class of models discussed, detailed examples and analyses from case studies are presented whenever possible. The applications are all essentially from the health sciences, including cancer, AIDS, and the environment. The book is intended as a graduate textbook or a reference book for a one semester course at the advanced masters or Ph.D. level. This book would be most suitable for second or third year graduate students in statistics or biostatistics. It would also serve as a useful reference book for applied or theoretical researchers as well as practitioners. Joseph G. Ibrahim is Associate Professor of Biostatistics at the Harvard School of Public Health and Dana-Farber Cancer Institute; Ming-Hui Chen is Associate Professor of Mathematical Science at Worcester Polytechnic Institute; Debajyoti Sinha is Associate Professor of Biostatistics at the Medical University of South Carolina.

This book examines advanced Bayesian computational methods. It presents methods for sampling from posterior distributions and discusses how to compute posterior quantities of interest using Markov chain Monte Carlo (MCMC) samples. This book examines each of these issues in detail and heavily focuses on computing various posterior quantities of interest from a given MCMC sample. Several topics are addressed, including techniques for MCMC sampling, Monte Carlo methods for estimation of posterior quantities, improving simulation accuracy, marginal posterior density estimation, estimation of normalizing constants, constrained parameter problems, highest posterior density interval calculations, computation of posterior modes, and posterior computations for proportional hazards models and Dirichlet process models. The authors also discuss computions involving model comparisons, including both nested and non-nested models, marginal likelihood methods, ratios of normalizing constants, Bayes factors, the Savage-Dickey density ratio, Stochastic Search Variable Selection, Bayesian Model Averaging, the reverse jump algorithm, and model adequacy using predictive and latent residual approaches. The book presents an equal mixture of theory and applications involving real data. The book is intended as a graduate textbook or a reference book for a one semester course at the advanced masters or Ph.D. level. It would also serve as a useful reference book for applied or theoretical researchers as well as practitioners. Ming-Hui Chen is Associate Professor of Mathematical Sciences at Worcester Polytechnic Institute, Qu-Man Shao is Assistant Professor of Mathematics at the University of Oregon. Joseph G. Ibrahim is Associate Professor of Biostatistics at the Harvard School of Public Health and Dana-Farber Cancer Institute.

This book aims to portray ancient civilizations and the development of early states in China and the rest of the world during the Liangzhu period. From a global perspective, it describes the ancient Egyptian, Sumerian and Harappan civilizations, as well as lesser-known civilizations such as the Cyclades and Caral, underscoring the similarities and differences between their central settlements, capitals and material cultural remains. As for the national aspect, the book mainly explores the development process of east Asian civilization as represented by Chinese civilization and probes into the evolution of the Liangzhu, Dawenkou and Qujialing civilizations four to five thousand years ago in a search for the origins of Chinese civilization.

This book aims to portray ancient civilizations and the development of early states in China and the rest of the world during the Liangzhu period. From a global perspective, it describes the ancient Egyptian, Sumerian and Harappan civilizations, as well as lesser-known civilizations such as the Cyclades and Caral, underscoring the similarities and differences between their central settlements, capitals and material cultural remains. As for the national aspect, the book mainly explores the development process of east Asian civilization as represented by Chinese civilization and probes into the evolution of the Liangzhu, Dawenkou and Qujialing civilizations four to five thousand years ago in a search for the origins of Chinese civilization.

Survival analysis arises in many fields of study including medicine, biology, engineering, public health, epidemiology, and economics. This book provides a comprehensive treatment of Bayesian survival analysis. Several topics are addressed, including parametric models, semiparametric models based on prior processes, proportional and non-proportional hazards models, frailty models, cure rate models, model selection and comparison, joint models for longitudinal and survival data, models with time varying covariates, missing covariate data, design and monitoring of clinical trials, accelerated failure time models, models for multivariate survival data, and special types of hierarchical survival models. Also various censoring schemes are examined including right and interval censored data. Several additional topics are discussed, including noninformative and informative prior specificiations, computing posterior qualities of interest, Bayesian hypothesis testing, variable selection, model selection with nonnested models, model checking techniques using Bayesian diagnostic methods, and Markov chain Monte Carlo (MCMC) algorithms for sampling from the posteiror and predictive distributions. The book presents a balance between theory and applications, and for each class of models discussed, detailed examples and analyses from case studies are presented whenever possible. The applications are all essentially from the health sciences, including cancer, AIDS, and the environment. The book is intended as a graduate textbook or a reference book for a one semester course at the advanced masters or Ph.D. level. This book would be most suitable for second or third year graduate students in statistics or biostatistics. It would also serve as a useful reference book for applied or theoretical researchers as well as practitioners. Joseph G. Ibrahim is Associate Professor of Biostatistics at the Harvard School of Public Health and Dana-Farber Cancer Institute; Ming-Hui Chen is Associate Professor of Mathematical Science at Worcester Polytechnic Institute; Debajyoti Sinha is Associate Professor of Biostatistics at the Medical University of South Carolina.