Doing Bayesian Data Analysis: A Tutorial Introduction with R

There is an explosion of interest in Bayesian statistics, primarily because recently created computational methods have finally made Bayesian analysis tractable and accessible to a wide audience. Doing Bayesian Data Analysis, A Tutorial Introduction with R and BUGS, is for first year graduate students or advanced undergraduates and provides an accessible approach, as all mathematics is explained intuitively and with concrete examples. It assumes only algebra and ‘rusty’ calculus. Unlike other textbooks, this book begins with the basics, including essential concepts of probability and random sampling. The book gradually climbs all the way to advanced hierarchical modeling methods for realistic data. The text provides complete examples with the R programming language and BUGS software (both freeware), and begins with basic programming examples, working up gradually to complete programs for complex analyses and presentation graphics. These templates can be easily adapted for a large variety of students and their own research needs.The textbook bridges the students from their undergraduate training into modern Bayesian methods.

Table of Contents:
This Book's Organization: Read me First!; The Basics: Parameters, Probability, Bayes' Rule and R; What is this stuff called probability?; Bayes' Rule; Part II All the Fundamental Concepts and Techniques in a Simple Scenario; Inferring a Binomial Proportion via Exact mathematical Analysis; Inferring a Binomial Proportion via Grid Approximation; Inferring a Binomial Proportion via Monte Carlo Methods; Inferences Regarding Two Binomial Proportions; Bernoulli Likelihood with Hierarchical Prior; Hierarchical modeling and model comparison; Null Hypothesis Significance Testing; Bayesian Approaches to Testing a Point ("Null") Hypothesis; Goals, Power, and Sample Size; Part III The Generalized Linear Model; Overview of the Generalized Linear Model; Metric Predicted Variable on a Single Group; Metric Predicted Variable with One Metric Predictor; Metric Predicted Variable with Multiple Metric Predictors; Metric Predicted Variable with One Nominal Predictor; Metric Predicted Variable with Multiple Nominal Predictors; Dichotomous Predicted Variable; Original Predicted Variable, Contingency Table Analysis; Part IV Tools in the Trunk; Reparameterization, a.k.a. Change of Variables; References; Index

About the Author :
John K. Kruschke is Professor of Psychological and Brain Sciences, and Adjunct Professor of Statistics, at Indiana University in Bloomington, Indiana, USA. He is eight-time winner of Teaching Excellence Recognition Awards from Indiana University. He won the Troland Research Award from the National Academy of Sciences (USA), and the Remak Distinguished Scholar Award from Indiana University. He has been on the editorial boards of various scientific journals, including Psychological Review, the Journal of Experimental Psychology: General, and the Journal of Mathematical Psychology, among others.After attending the Summer Science Program as a high school student and considering a career in astronomy, Kruschke earned a bachelor's degree in mathematics (with high distinction in general scholarship) from the University of California at Berkeley. As an undergraduate, Kruschke taught self-designed tutoring sessions for many math courses at the Student Learning Center. During graduate school he attended the 1988 Connectionist Models Summer School, and earned a doctorate in psychology also from U.C. Berkeley. He joined the faculty of Indiana University in 1989. Professor Kruschke's publications can be found at his Google Scholar page. His current research interests focus on moral psychology.Professor Kruschke taught traditional statistical methods for many years until reaching a point, circa 2003, when he could no longer teach corrections for multiple comparisons with a clear conscience. The perils of p values provoked him to find a better way, and after only several thousand hours of relentless effort, the 1st and 2nd editions of Doing Bayesian Data Analysis emerged.

Review :
"I think it fills a gaping hole in what is currently available, and will serve to create its own market as researchers and their students transition towards the routine application of Bayesian statistical methods." -Prof. Michael lee, University of California, Irvine, and president of the Society for Mathematical Psychology "Kruschke's text covers a much broader range of traditional experimental designs.has the potential to change the way most cognitive scientists and experimental psychologists approach the planning and analysis of their experiments" -Prof. Geoffrey Iverson, University of California, Irvine, and past president of the Society for Mathematical Psychology "John Kruschke has written a book on Statistics. It's better than others for reasons stylistic. It also is better because itis Bayesian. To find out why, buy it -- it's truly amazin'!"-James L. (Jay) McClelland, Lucie Stern Professor & Chair, Dept. Of Psychology, Standford University "In a December article in The New Yorker, Jonah Lehrer pointed out that some phenomena in the psychology literature are not always repeatable. One reason for this failure to replicate results comes from the kinds of statistics often used in Psychology. We use a procedure called Null Hypothesis Testing that was developed over 100 years ago. More recently, statisticians and psychologists have been working to create a new form of statistical testing based on Bayesian statistics. These methods may help us to avoid publishing studies that are not likely to replicate. John Kruschke published a nice tutorial on how to use these methods." -2010's top ten advances in psychology on Psychology Today's blog "The intended audience for this book is a first-year graduate student or advanced undergraduate in the social or biological sciences, but one whose mathematical background is sufficient for them to not be put off by occasional references to calculus. Kruschke also provides a comprehensive solution manual for the exercises in each chapter. He says he has worked on his book for six years and it shows, not least because it has few typographical errors and is well-presented. In summary, this book has several features that could make it preferable to its competitors.it is impressive that Kruschke is able to quickly bring readers up to speed on techniques such as robust regression and repeated-measures regression that would be considered "advanced" in the conventional NHST curriculum. His extensions from linear regression to logistic, ordinal probit and Poisson regression are very clearly articulated and will outfit students with a very adaptable statistical toolbox. This is the best introductory textbook on Bayesian MCMC techniques I have read, and the most suitable for psychology students. It fills a gap I described in my recent review of six other introductory Bayesian method texts (Smithson, 2010). I look forward to using it in my own teaching, and I recommend it to anyone wishing to introduce graduate or advanced undergraduate students to the emerging Bayesian revolution."--Journal of Mathematical Psychology "In sum, this is a new kind of textbook to teach a kind of statistical analysis that will be new to its audience. It uses a tutorial approach and instills in its students the tools of the trade: coding, debugging, simulating, and plotting. Though some will surely look down on its folksy tone, its extended analogies and cautious commenting, these measures will probably do much more good than harm. The text has the potential to change the methodological toolbox of a new generation of social scientists, bringing them up to a level of computation, modeling, and analysis that they might not have thought to be within their grasp. Where past approaches to teaching statistics to those in psychology and economics have not lead to widespread insight, this tutorial approach might."--Journal of Economic Psychology "I would describe this book as revolutionary, at least in the context of psychology. It is, to my knowledge, the first book of its kind in this field to provide a general introduction to exclusively Bayesian statistical methods. In addition, it does so almost entirely by way of Monte Carlo simulation methods. While reasonable minds may disagree, it is arguable that both the general Bayesian framework advocated here, and the heavy use of Monte Carlo simulations, are destined to be the future of all data-analysis, whether in psychology or elsewhere.the ideas and methods presented here will eventually be seen as the foundations for new approaches to statistics that will become commonplace in the near future."--British Journal of Mathematical and Statistical Psychology "There are quite a few books on Bayesian statistics, but what makes Doing Bayesian Data Analysis: A Tutorial With R and BUGS stand out for me is the author's focus of the book-writing for real people with real data. From the very first chapter, the engaging writing style will get readers excited about this topic, a comment one can rarely make about statistical books. Clearly a master teacher, the author, John Kruschke, uses plain language to explain complex ideas and concepts. A comprehensive website is associated with the book and provides program codes, examples, data, and solutions to the exercises. If the book is used to teach a statistics course, this set of materials will be necessary and helpful for students as they go through the materials in the book step by step."--PsycCritiques