The first seven chapters use R for probability simulation and computation, including random number generation, numerical and Monte Carlo integration, and finding limiting distributions of Markov Chains with both discrete and continuous states. Applications include coverage probabilities of binomial confidence intervals, estimation of disease prevalence from screening tests, parallel redundancy for improved reliability of systems, and various kinds of genetic modeling. These initial chapters can be used for a non-Bayesian course in the simulation of applied probability models and Markov Chains. Chapters 8 through 10 give a brief introduction to Bayesian estimation and illustrate the use of Gibbs samplers to find posterior distributions and interval estimates, including some examples in which traditional methods do not give satisfactory results. WinBUGS software is introduced with a detailed explanation of its interface and examples of its use for Gibbs sampling for Bayesian estimation. No previous experience using R is required. An appendix introduces R, and complete R code is included for almost all computational examples and problems (along with comments and explanations). Noteworthy features of the book are its intuitive approach, presenting ideas with examples from biostatistics, reliability, and other fields; its large number of figures; and its extraordinarily large number of problems (about a third of the pages), ranging from simple drill to presentation of additional topics. Hints and answers are provided for many of the problems. These features make the book ideal for students of statistics at the senior undergraduate and at the beginning graduate levels.
Cohesively Incorporates Statistical Theory with R Implementation Since the publication of the popular first edition of this comprehensive textbook, the contributed R packages on CRAN have increased from around 1,000 to over 6,000. Designed for an intermediate undergraduate course, Probability and Statistics with R, Second Edition explores how some of these new packages make analysis easier and more intuitive as well as create more visually pleasing graphs. New to the Second Edition Improvements to existing examples, problems, concepts, data, and functions New examples and exercises that use the most modern functions Coverage probability of a confidence interval and model validation Highlighted R code for calculations and graph creation Gets Students Up to Date on Practical Statistical Topics Keeping pace with today’s statistical landscape, this textbook expands your students’ knowledge of the practice of statistics. It effectively links statistical concepts with R procedures, empowering students to solve a vast array of real statistical problems with R. Web Resources A supplementary website offers solutions to odd exercises and templates for homework assignments while the data sets and R functions are available on CRAN.
There has been dramatic growth in the development and application of Bayesian inference in statistics. Berger (2000) documents the increase in Bayesian activity by the number of published research articles, the number of books,andtheextensivenumberofapplicationsofBayesianarticlesinapplied disciplines such as science and engineering. One reason for the dramatic growth in Bayesian modeling is the availab- ity of computational algorithms to compute the range of integrals that are necessary in a Bayesian posterior analysis. Due to the speed of modern c- puters, it is now possible to use the Bayesian paradigm to ?t very complex models that cannot be ?t by alternative frequentist methods. To ?t Bayesian models, one needs a statistical computing environment. This environment should be such that one can: write short scripts to de?ne a Bayesian model use or write functions to summarize a posterior distribution use functions to simulate from the posterior distribution construct graphs to illustrate the posterior inference An environment that meets these requirements is the R system. R provides a wide range of functions for data manipulation, calculation, and graphical d- plays. Moreover, it includes a well-developed, simple programming language that users can extend by adding new functions. Many such extensions of the language in the form of packages are easily downloadable from the Comp- hensive R Archive Network (CRAN).
Through this book, researchers and students will learn to use R for analysis of large-scale genomic data and how to create routines to automate analytical steps. The philosophy behind the book is to start with real world raw datasets and perform all the analytical steps needed to reach final results. Though theory plays an important role, this is a practical book for graduate and undergraduate courses in bioinformatics and genomic analysis or for use in lab sessions. How to handle and manage high-throughput genomic data, create automated workflows and speed up analyses in R is also taught. A wide range of R packages useful for working with genomic data are illustrated with practical examples. The key topics covered are association studies, genomic prediction, estimation of population genetic parameters and diversity, gene expression analysis, functional annotation of results using publically available databases and how to work efficiently in R with large genomic datasets. Important principles are demonstrated and illustrated through engaging examples which invite the reader to work with the provided datasets. Some methods that are discussed in this volume include: signatures of selection, population parameters (LD, FST, FIS, etc); use of a genomic relationship matrix for population diversity studies; use of SNP data for parentage testing; snpBLUP and gBLUP for genomic prediction. Step-by-step, all the R code required for a genome-wide association study is shown: starting from raw SNP data, how to build databases to handle and manage the data, quality control and filtering measures, association testing and evaluation of results, through to identification and functional annotation of candidate genes. Similarly, gene expression analyses are shown using microarray and RNAseq data. At a time when genomic data is decidedly big, the skills from this book are critical. In recent years R has become the de facto tool for analysis of gene expression data, in addition to its prominent role in analysis of genomic data. Benefits to using R include the integrated development environment for analysis, flexibility and control of the analytic workflow. Included topics are core components of advanced undergraduate and graduate classes in bioinformatics, genomics and statistical genetics. This book is also designed to be used by students in computer science and statistics who want to learn the practical aspects of genomic analysis without delving into algorithmic details. The datasets used throughout the book may be downloaded from the publisher’s website./p
Master predictive analytics, from start to finish Start with strategy and management Master methods and build models Transform your models into highly-effective code—in both Python and R This one-of-a-kind book will help you use predictive analytics, Python, and R to solve real business problems and drive real competitive advantage. You’ll master predictive analytics through realistic case studies, intuitive data visualizations, and up-to-date code for both Python and R—not complex math. Step by step, you’ll walk through defining problems, identifying data, crafting and optimizing models, writing effective Python and R code, interpreting results, and more. Each chapter focuses on one of today’s key applications for predictive analytics, delivering skills and knowledge to put models to work—and maximize their value. Thomas W. Miller, leader of Northwestern University’s pioneering program in predictive analytics, addresses everything you need to succeed: strategy and management, methods and models, and technology and code. If you’re new to predictive analytics, you’ll gain a strong foundation for achieving accurate, actionable results. If you’re already working in the field, you’ll master powerful new skills. If you’re familiar with either Python or R, you’ll discover how these languages complement each other, enabling you to do even more. All data sets, extensive Python and R code, and additional examples available for download at http://www.ftpress.com/miller/ Python and R offer immense power in predictive analytics, data science, and big data. This book will help you leverage that power to solve real business problems, and drive real competitive advantage. Thomas W. Miller’s unique balanced approach combines business context and quantitative tools, illuminating each technique with carefully explained code for the latest versions of Python and R. If you’re new to predictive analytics, Miller gives you a strong foundation for achieving accurate, actionable results. If you’re already a modeler, programmer, or manager, you’ll learn crucial skills you don’t already have. Using Python and R, Miller addresses multiple business challenges, including segmentation, brand positioning, product choice modeling, pricing research, finance, sports, text analytics, sentiment analysis, and social network analysis. He illuminates the use of cross-sectional data, time series, spatial, and spatio-temporal data. You’ll learn why each problem matters, what data are relevant, and how to explore the data you’ve identified. Miller guides you through conceptually modeling each data set with words and figures; and then modeling it again with realistic code that delivers actionable insights. You’ll walk through model construction, explanatory variable subset selection, and validation, mastering best practices for improving out-of-sample predictive performance. Miller employs data visualization and statistical graphics to help you explore data, present models, and evaluate performance. Appendices include five complete case studies, and a detailed primer on modern data science methods. Use Python and R to gain powerful, actionable, profitable insights about: Advertising and promotion Consumer preference and choice Market baskets and related purchases Economic forecasting Operations management Unstructured text and language Customer sentiment Brand and price Sports team performance And much more
This book covers the main tools used in statistical simulation from a programmer’s point of view, explaining the R implementation of each simulation technique and providing the output for better understanding and comparison.
Stochastic Simulation for Bayesian Inference, Second Edition
Author: Dani Gamerman
Publisher: CRC Press
While there have been few theoretical contributions on the Markov Chain Monte Carlo (MCMC) methods in the past decade, current understanding and application of MCMC to the solution of inference problems has increased by leaps and bounds. Incorporating changes in theory and highlighting new applications, Markov Chain Monte Carlo: Stochastic Simulation for Bayesian Inference, Second Edition presents a concise, accessible, and comprehensive introduction to the methods of this valuable simulation technique. The second edition includes access to an internet site that provides the code, written in R and WinBUGS, used in many of the previously existing and new examples and exercises. More importantly, the self-explanatory nature of the codes will enable modification of the inputs to the codes and variation on many directions will be available for further exploration. Major changes from the previous edition: · More examples with discussion of computational details in chapters on Gibbs sampling and Metropolis-Hastings algorithms · Recent developments in MCMC, including reversible jump, slice sampling, bridge sampling, path sampling, multiple-try, and delayed rejection · Discussion of computation using both R and WinBUGS · Additional exercises and selected solutions within the text, with all data sets and software available for download from the Web · Sections on spatial models and model adequacy The self-contained text units make MCMC accessible to scientists in other disciplines as well as statisticians. The book will appeal to everyone working with MCMC techniques, especially research and graduate statisticians and biostatisticians, and scientists handling data and formulating models. The book has been substantially reinforced as a first reading of material on MCMC and, consequently, as a textbook for modern Bayesian computation and Bayesian inference courses.
This collection of methodological developments and applications of simulation-based methods were presented at a workshop at Louisiana State University in November, 2009. Topics include: extensions of the GHK simulator; maximum-simulated likelihood; composite marginal likelihood; and modelling and forecasting volatility in a bayesian approach.
Computational statistics and statistical computing are two areas that employ computational, graphical, and numerical approaches to solve statistical problems, making the versatile R language an ideal computing environment for these fields. One of the first books on these topics to feature R, Statistical Computing with R covers the traditional core material of computational statistics, with an emphasis on using the R language via an examples-based approach. Suitable for an introductory course in computational statistics or for self-study, it includes R code for all examples and R notes to help explain the R programming concepts. After an overview of computational statistics and an introduction to the R computing environment, the book reviews some basic concepts in probability and classical statistical inference. Each subsequent chapter explores a specific topic in computational statistics. These chapters cover the simulation of random variables from probability distributions, the visualization of multivariate data, Monte Carlo integration and variance reduction methods, Monte Carlo methods in inference, bootstrap and jackknife, permutation tests, Markov chain Monte Carlo (MCMC) methods, and density estimation. The final chapter presents a selection of examples that illustrate the application of numerical methods using R functions. Focusing on implementation rather than theory, this text serves as a balanced, accessible introduction to computational statistics and statistical computing.
Mathematical Statistics with Applications in R, Second Edition, offers a modern calculus-based theoretical introduction to mathematical statistics and applications. The book covers many modern statistical computational and simulation concepts that are not covered in other texts, such as the Jackknife, bootstrap methods, the EM algorithms, and Markov chain Monte Carlo (MCMC) methods such as the Metropolis algorithm, Metropolis-Hastings algorithm and the Gibbs sampler. By combining the discussion on the theory of statistics with a wealth of real-world applications, the book helps students to approach statistical problem solving in a logical manner. This book provides a step-by-step procedure to solve real problems, making the topic more accessible. It includes goodness of fit methods to identify the probability distribution that characterizes the probabilistic behavior or a given set of data. Exercises as well as practical, real-world chapter projects are included, and each chapter has an optional section on using Minitab, SPSS and SAS commands. The text also boasts a wide array of coverage of ANOVA, nonparametric, MCMC, Bayesian and empirical methods; solutions to selected problems; data sets; and an image bank for students. Advanced undergraduate and graduate students taking a one or two semester mathematical statistics course will find this book extremely useful in their studies. Step-by-step procedure to solve real problems, making the topic more accessible Exercises blend theory and modern applications Practical, real-world chapter projects Provides an optional section in each chapter on using Minitab, SPSS and SAS commands Wide array of coverage of ANOVA, Nonparametric, MCMC, Bayesian and empirical methods