Markov Chain Monte Carlo

Stochastic Simulation for Bayesian Inference, Second Edition

Author: Dani Gamerman,Hedibert F. Lopes

Publisher: CRC Press

ISBN: 9781584885870

Category: Mathematics

Page: 344

View: 9509

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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.

Markov Chain Monte Carlo in Practice

Author: W.R. Gilks,S. Richardson,David Spiegelhalter

Publisher: CRC Press

ISBN: 9780412055515

Category: Mathematics

Page: 512

View: 3802

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In a family study of breast cancer, epidemiologists in Southern California increase the power for detecting a gene-environment interaction. In Gambia, a study helps a vaccination program reduce the incidence of Hepatitis B carriage. Archaeologists in Austria place a Bronze Age site in its true temporal location on the calendar scale. And in France, researchers map a rare disease with relatively little variation. Each of these studies applied Markov chain Monte Carlo methods to produce more accurate and inclusive results. General state-space Markov chain theory has seen several developments that have made it both more accessible and more powerful to the general statistician. Markov Chain Monte Carlo in Practice introduces MCMC methods and their applications, providing some theoretical background as well. The authors are researchers who have made key contributions in the recent development of MCMC methodology and its application. Considering the broad audience, the editors emphasize practice rather than theory, keeping the technical content to a minimum. The examples range from the simplest application, Gibbs sampling, to more complex applications. The first chapter contains enough information to allow the reader to start applying MCMC in a basic way. The following chapters cover main issues, important concepts and results, techniques for implementing MCMC, improving its performance, assessing model adequacy, choosing between models, and applications and their domains. Markov Chain Monte Carlo in Practice is a thorough, clear introduction to the methodology and applications of this simple idea with enormous potential. It shows the importance of MCMC in real applications, such as archaeology, astronomy, biostatistics, genetics, epidemiology, and image analysis, and provides an excellent base for MCMC to be applied to other fields as well.

Handbook of Markov Chain Monte Carlo

Author: Steve Brooks,Andrew Gelman,Galin Jones,Xiao-Li Meng

Publisher: CRC Press

ISBN: 1420079425

Category: Mathematics

Page: 619

View: 9128

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Since their popularization in the 1990s, Markov chain Monte Carlo (MCMC) methods have revolutionized statistical computing and have had an especially profound impact on the practice of Bayesian statistics. Furthermore, MCMC methods have enabled the development and use of intricate models in an astonishing array of disciplines as diverse as fisheries science and economics. The wide-ranging practical importance of MCMC has sparked an expansive and deep investigation into fundamental Markov chain theory. The Handbook of Markov Chain Monte Carlo provides a reference for the broad audience of developers and users of MCMC methodology interested in keeping up with cutting-edge theory and applications. The first half of the book covers MCMC foundations, methodology, and algorithms. The second half considers the use of MCMC in a variety of practical applications including in educational research, astrophysics, brain imaging, ecology, and sociology. The in-depth introductory section of the book allows graduate students and practicing scientists new to MCMC to become thoroughly acquainted with the basic theory, algorithms, and applications. The book supplies detailed examples and case studies of realistic scientific problems presenting the diversity of methods used by the wide-ranging MCMC community. Those familiar with MCMC methods will find this book a useful refresher of current theory and recent developments.

Bayesian Models for Astrophysical Data

Using R, JAGS, Python, and Stan

Author: Joseph M. Hilbe,Rafael S. de Souza,Emille E. O. Ishida

Publisher: Cambridge University Press

ISBN: 1108210740

Category: Mathematics

Page: N.A

View: 887

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This comprehensive guide to Bayesian methods in astronomy enables hands-on work by supplying complete R, JAGS, Python, and Stan code, to use directly or to adapt. It begins by examining the normal model from both frequentist and Bayesian perspectives and then progresses to a full range of Bayesian generalized linear and mixed or hierarchical models, as well as additional types of models such as ABC and INLA. The book provides code that is largely unavailable elsewhere and includes details on interpreting and evaluating Bayesian models. Initial discussions offer models in synthetic form so that readers can easily adapt them to their own data; later the models are applied to real astronomical data. The consistent focus is on hands-on modeling, analysis of data, and interpretations that address scientific questions. A must-have for astronomers, its concrete approach will also be attractive to researchers in the sciences more generally.

Industrial Tomography

Systems and Applications

Author: Mi Wang

Publisher: Elsevier

ISBN: 1782421238

Category: Computers

Page: 772

View: 4684

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Industrial Tomography: Systems and Applications thoroughly explores the important tomographic techniques of industrial tomography, also discussing image reconstruction, systems, and applications. The text presents complex processes, including the way three-dimensional imaging is used to create multiple cross-sections, and how computer software helps monitor flows, filtering, mixing, drying processes, and chemical reactions inside vessels and pipelines. Readers will find a comprehensive discussion on the ways tomography systems can be used to optimize the performance of a wide variety of industrial processes. Provides a comprehensive discussion on the different formats of tomography Includes an excellent overview of image reconstruction using a wide range of applications Presents a comprehensive discussion of tomography systems and their application in a wide variety of industrial processes

Introducing Monte Carlo Methods with R

Author: Christian Robert,George Casella

Publisher: Springer Science & Business Media

ISBN: 1441915753

Category: Computers

Page: 284

View: 4408

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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.

Monte Carlo Statistical Methods

Author: Christian Robert,George Casella

Publisher: Springer Science & Business Media

ISBN: 1475741456

Category: Mathematics

Page: 649

View: 6619

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We have sold 4300 copies worldwide of the first edition (1999). This new edition contains five completely new chapters covering new developments.

Applied Stochastic Modelling, Second Edition

Author: Byron J.T. Morgan

Publisher: CRC Press

ISBN: 1420011650

Category: Mathematics

Page: 368

View: 567

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Highlighting modern computational methods, Applied Stochastic Modelling, Second Edition provides students with the practical experience of scientific computing in applied statistics through a range of interesting real-world applications. It also successfully revises standard probability and statistical theory. Along with an updated bibliography and improved figures, this edition offers numerous updates throughout. New to the Second Edition An extended discussion on Bayesian methods A large number of new exercises A new appendix on computational methods The book covers both contemporary and classical aspects of statistics, including survival analysis, Kernel density estimation, Markov chain Monte Carlo, hypothesis testing, regression, bootstrap, and generalised linear models. Although the book can be used without reference to computational programs, the author provides the option of using powerful computational tools for stochastic modelling. All of the data sets and MATLAB® and R programs found in the text as well as lecture slides and other ancillary material are available for download at www.crcpress.com Continuing in the bestselling tradition of its predecessor, this textbook remains an excellent resource for teaching students how to fit stochastic models to data.

Advanced Markov Chain Monte Carlo Methods

Learning from Past Samples

Author: Faming Liang,Chuanhai Liu,Raymond Carroll

Publisher: John Wiley & Sons

ISBN: 9780470669730

Category: Mathematics

Page: 384

View: 3988

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Markov Chain Monte Carlo (MCMC) methods are now an indispensable tool in scientific computing. This book discusses recent developments of MCMC methods with an emphasis on those making use of past sample information during simulations. The application examples are drawn from diverse fields such as bioinformatics, machine learning, social science, combinatorial optimization, and computational physics. Key Features: Expanded coverage of the stochastic approximation Monte Carlo and dynamic weighting algorithms that are essentially immune to local trap problems. A detailed discussion of the Monte Carlo Metropolis-Hastings algorithm that can be used for sampling from distributions with intractable normalizing constants. Up-to-date accounts of recent developments of the Gibbs sampler. Comprehensive overviews of the population-based MCMC algorithms and the MCMC algorithms with adaptive proposals. This book can be used as a textbook or a reference book for a one-semester graduate course in statistics, computational biology, engineering, and computer sciences. Applied or theoretical researchers will also find this book beneficial.

Stochastic Modelling for Systems Biology, Second Edition

Author: Darren J. Wilkinson

Publisher: CRC Press

ISBN: 1439837724

Category: Mathematics

Page: 363

View: 9940

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Since the first edition of Stochastic Modelling for Systems Biology, there have been many interesting developments in the use of "likelihood-free" methods of Bayesian inference for complex stochastic models. Re-written to reflect this modern perspective, this second edition covers everything necessary for a good appreciation of stochastic kinetic modelling of biological networks in the systems biology context. Keeping with the spirit of the first edition, all of the new theory is presented in a very informal and intuitive manner, keeping the text as accessible as possible to the widest possible readership. New in the Second Edition All examples have been updated to Systems Biology Markup Language Level 3 All code relating to simulation, analysis, and inference for stochastic kinetic models has been re-written and re-structured in a more modular way An ancillary website provides links, resources, errata, and up-to-date information on installation and use of the associated R package More background material on the theory of Markov processes and stochastic differential equations, providing more substance for mathematically inclined readers Discussion of some of the more advanced concepts relating to stochastic kinetic models, such as random time change representations, Kolmogorov equations, Fokker-Planck equations and the linear noise approximation Simple modelling of "extrinsic" and "intrinsic" noise An effective introduction to the area of stochastic modelling in computational systems biology, this new edition adds additional mathematical detail and computational methods that will provide a stronger foundation for the development of more advanced courses in stochastic biological modelling.

Bayesian Methods

A Social and Behavioral Sciences Approach, Third Edition

Author: Jeff Gill

Publisher: CRC Press

ISBN: 1439862494

Category: Mathematics

Page: 724

View: 5755

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An Update of the Most Popular Graduate-Level Introductions to Bayesian Statistics for Social Scientists Now that Bayesian modeling has become standard, MCMC is well understood and trusted, and computing power continues to increase, Bayesian Methods: A Social and Behavioral Sciences Approach, Third Edition focuses more on implementation details of the procedures and less on justifying procedures. The expanded examples reflect this updated approach. New to the Third Edition A chapter on Bayesian decision theory, covering Bayesian and frequentist decision theory as well as the connection of empirical Bayes with James–Stein estimation A chapter on the practical implementation of MCMC methods using the BUGS software Greatly expanded chapter on hierarchical models that shows how this area is well suited to the Bayesian paradigm Many new applications from a variety of social science disciplines Double the number of exercises, with 20 now in each chapter Updated BaM package in R, including new datasets, code, and procedures for calling BUGS packages from R This bestselling, highly praised text continues to be suitable for a range of courses, including an introductory course or a computing-centered course. It shows students in the social and behavioral sciences how to use Bayesian methods in practice, preparing them for sophisticated, real-world work in the field.

Handbook of Approximate Bayesian Computation

Author: Scott A. Sisson,Yanan Fan,Mark Beaumont

Publisher: CRC Press

ISBN: 1351643460

Category: Mathematics

Page: 666

View: 2038

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As the world becomes increasingly complex, so do the statistical models required to analyse the challenging problems ahead. For the very first time in a single volume, the Handbook of Approximate Bayesian Computation (ABC) presents an extensive overview of the theory, practice and application of ABC methods. These simple, but powerful statistical techniques, take Bayesian statistics beyond the need to specify overly simplified models, to the setting where the model is defined only as a process that generates data. This process can be arbitrarily complex, to the point where standard Bayesian techniques based on working with tractable likelihood functions would not be viable. ABC methods finesse the problem of model complexity within the Bayesian framework by exploiting modern computational power, thereby permitting approximate Bayesian analyses of models that would otherwise be impossible to implement. The Handbook of ABC provides illuminating insight into the world of Bayesian modelling for intractable models for both experts and newcomers alike. It is an essential reference book for anyone interested in learning about and implementing ABC techniques to analyse complex models in the modern world.

Introduction to Probability

Author: Joseph K. Blitzstein,Jessica Hwang

Publisher: CRC Press

ISBN: 1498759769

Category: Mathematics

Page: 596

View: 7086

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Developed from celebrated Harvard statistics lectures, Introduction to Probability provides essential language and tools for understanding statistics, randomness, and uncertainty. The book explores a wide variety of applications and examples, ranging from coincidences and paradoxes to Google PageRank and Markov chain Monte Carlo (MCMC). Additional application areas explored include genetics, medicine, computer science, and information theory. The print book version includes a code that provides free access to an eBook version. The authors present the material in an accessible style and motivate concepts using real-world examples. Throughout, they use stories to uncover connections between the fundamental distributions in statistics and conditioning to reduce complicated problems to manageable pieces. The book includes many intuitive explanations, diagrams, and practice problems. Each chapter ends with a section showing how to perform relevant simulations and calculations in R, a free statistical software environment.

Time Series

Modeling, Computation, and Inference

Author: Raquel Prado,Mike West

Publisher: CRC Press

ISBN: 1420093363

Category: Mathematics

Page: 368

View: 4978

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Focusing on Bayesian approaches and computations using simulation-based methods for inference, Time Series: Modeling, Computation, and Inference integrates mainstream approaches for time series modeling with significant recent developments in methodology and applications of time series analysis. It encompasses a graduate-level account of Bayesian time series modeling and analysis, a broad range of references to state-of-the-art approaches to univariate and multivariate time series analysis, and emerging topics at research frontiers. The book presents overviews of several classes of models and related methodology for inference, statistical computation for model fitting and assessment, and forecasting. The authors also explore the connections between time- and frequency-domain approaches and develop various models and analyses using Bayesian tools, such as Markov chain Monte Carlo (MCMC) and sequential Monte Carlo (SMC) methods. They illustrate the models and methods with examples and case studies from a variety of fields, including signal processing, biomedicine, and finance. Data sets, R and MATLAB® code, and other material are available on the authors’ websites. Along with core models and methods, this text offers sophisticated tools for analyzing challenging time series problems. It also demonstrates the growth of time series analysis into new application areas.

Probability and Statistics for Computer Scientists, Second Edition

Author: Michael Baron

Publisher: CRC Press

ISBN: 1498760600

Category: Mathematics

Page: 449

View: 415

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Student-Friendly Coverage of Probability, Statistical Methods, Simulation, and Modeling Tools Incorporating feedback from instructors and researchers who used the previous edition, Probability and Statistics for Computer Scientists, Second Edition helps students understand general methods of stochastic modeling, simulation, and data analysis; make optimal decisions under uncertainty; model and evaluate computer systems and networks; and prepare for advanced probability-based courses. Written in a lively style with simple language, this classroom-tested book can now be used in both one- and two-semester courses. New to the Second Edition Axiomatic introduction of probability Expanded coverage of statistical inference, including standard errors of estimates and their estimation, inference about variances, chi-square tests for independence and goodness of fit, nonparametric statistics, and bootstrap More exercises at the end of each chapter Additional MATLAB® codes, particularly new commands of the Statistics Toolbox In-Depth yet Accessible Treatment of Computer Science-Related Topics Starting with the fundamentals of probability, the text takes students through topics heavily featured in modern computer science, computer engineering, software engineering, and associated fields, such as computer simulations, Monte Carlo methods, stochastic processes, Markov chains, queuing theory, statistical inference, and regression. It also meets the requirements of the Accreditation Board for Engineering and Technology (ABET). Encourages Practical Implementation of Skills Using simple MATLAB commands (easily translatable to other computer languages), the book provides short programs for implementing the methods of probability and statistics as well as for visualizing randomness, the behavior of random variables and stochastic processes, convergence results, and Monte Carlo simulations. Preliminary knowledge of MATLAB is not required. Along with numerous computer science applications and worked examples, the text presents interesting facts and paradoxical statements. Each chapter concludes with a short summary and many exercises.

Bayesian Ideas and Data Analysis

An Introduction for Scientists and Statisticians

Author: Ronald Christensen,Wesley Johnson,Adam Branscum,Timothy E Hanson

Publisher: CRC Press

ISBN: 1439803552

Category: Mathematics

Page: 516

View: 2159

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Emphasizing the use of WinBUGS and R to analyze real data, Bayesian Ideas and Data Analysis: An Introduction for Scientists and Statisticians presents statistical tools to address scientific questions. It highlights foundational issues in statistics, the importance of making accurate predictions, and the need for scientists and statisticians to collaborate in analyzing data. The WinBUGS code provided offers a convenient platform to model and analyze a wide range of data. The first five chapters of the book contain core material that spans basic Bayesian ideas, calculations, and inference, including modeling one and two sample data from traditional sampling models. The text then covers Monte Carlo methods, such as Markov chain Monte Carlo (MCMC) simulation. After discussing linear structures in regression, it presents binomial regression, normal regression, analysis of variance, and Poisson regression, before extending these methods to handle correlated data. The authors also examine survival analysis and binary diagnostic testing. A complementary chapter on diagnostic testing for continuous outcomes is available on the book’s website. The last chapter on nonparametric inference explores density estimation and flexible regression modeling of mean functions. The appropriate statistical analysis of data involves a collaborative effort between scientists and statisticians. Exemplifying this approach, Bayesian Ideas and Data Analysis focuses on the necessary tools and concepts for modeling and analyzing scientific data. Data sets and codes are provided on a supplemental website.

Introduction to Bayesian Statistics

Author: William M. Bolstad,James M. Curran

Publisher: John Wiley & Sons

ISBN: 1118593227

Category: Mathematics

Page: 624

View: 4822

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"...this edition is useful and effective in teaching Bayesian inference at both elementary and intermediate levels. It is a well-written book on elementary Bayesian inference, and the material is easily accessible. It is both concise and timely, and provides a good collection of overviews and reviews of important tools used in Bayesian statistical methods." There is a strong upsurge in the use of Bayesian methods in applied statistical analysis, yet most introductory statistics texts only present frequentist methods. Bayesian statistics has many important advantages that students should learn about if they are going into fields where statistics will be used. In this third Edition, four newly-added chapters address topics that reflect the rapid advances in the field of Bayesian statistics. The authors continue to provide a Bayesian treatment of introductory statistical topics, such as scientific data gathering, discrete random variables, robust Bayesian methods, and Bayesian approaches to inference for discrete random variables, binomial proportions, Poisson, and normal means, and simple linear regression. In addition, more advanced topics in the field are presented in four new chapters: Bayesian inference for a normal with unknown mean and variance; Bayesian inference for a Multivariate Normal mean vector; Bayesian inference for the Multiple Linear Regression Model; and Computational Bayesian Statistics including Markov Chain Monte Carlo. The inclusion of these topics will facilitate readers' ability to advance from a minimal understanding of Statistics to the ability to tackle topics in more applied, advanced level books. Minitab macros and R functions are available on the book's related website to assist with chapter exercises. Introduction to Bayesian Statistics, Third Edition also features: Topics including the Joint Likelihood function and inference using independent Jeffreys priors and join conjugate prior The cutting-edge topic of computational Bayesian Statistics in a new chapter, with a unique focus on Markov Chain Monte Carlo methods Exercises throughout the book that have been updated to reflect new applications and the latest software applications Detailed appendices that guide readers through the use of R and Minitab software for Bayesian analysis and Monte Carlo simulations, with all related macros available on the book's website Introduction to Bayesian Statistics, Third Edition is a textbook for upper-undergraduate or first-year graduate level courses on introductory statistics course with a Bayesian emphasis. It can also be used as a reference work for statisticians who require a working knowledge of Bayesian statistics.

Statistical Rethinking

A Bayesian Course with Examples in R and Stan

Author: Richard McElreath

Publisher: CRC Press

ISBN: 1315362619

Category: Mathematics

Page: 487

View: 9036

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Statistical Rethinking: A Bayesian Course with Examples in R and Stan builds readers’ knowledge of and confidence in statistical modeling. Reflecting the need for even minor programming in today’s model-based statistics, the book pushes readers to perform step-by-step calculations that are usually automated. This unique computational approach ensures that readers understand enough of the details to make reasonable choices and interpretations in their own modeling work. The text presents generalized linear multilevel models from a Bayesian perspective, relying on a simple logical interpretation of Bayesian probability and maximum entropy. It covers from the basics of regression to multilevel models. The author also discusses measurement error, missing data, and Gaussian process models for spatial and network autocorrelation. By using complete R code examples throughout, this book provides a practical foundation for performing statistical inference. Designed for both PhD students and seasoned professionals in the natural and social sciences, it prepares them for more advanced or specialized statistical modeling. Web Resource The book is accompanied by an R package (rethinking) that is available on the author’s website and GitHub. The two core functions (map and map2stan) of this package allow a variety of statistical models to be constructed from standard model formulas.

Statistics for Ecologists Using R and Excel

Data Collection, Exploration, Analysis and Presentation

Author: Mark Gardener

Publisher: Pelagic Publishing Ltd

ISBN: 1784271411

Category: Science

Page: 406

View: 3094

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This is a book about the scientific process and how you apply it to data in ecology. You will learn how to plan for data collection, how to assemble data, how to analyze data and finally how to present the results. The book uses Microsoft Excel and the powerful Open Source R program to carry out data handling as well as producing graphs.Statistical approaches covered include: data exploration; tests for difference – t-test and U-test; correlation – Spearman’s rank test and Pearson product-moment; association including Chi-squared tests and goodness of fit; multivariate testing using analysis of variance (ANOVA) and Kruskal–Wallis test; and multiple regression.Key skills taught in this book include: how to plan ecological projects; how to record and assemble your data; how to use R and Excel for data analysis and graphs; how to carry out a wide range of statistical analyses including analysis of variance and regression; how to create professional looking graphs; and how to present your results.New in this edition: a completely revised chapter on graphics including graph types and their uses, Excel Chart Tools, R graphics commands and producing different chart types in Excel and in R; an expanded range of support material online, including; example data, exercises and additional notes & explanations; a new chapter on basic community statistics, biodiversity and similarity; chapter summaries and end-of-chapter exercises.Praise for the first edition:This book is a superb way in for all those looking at how to design investigations and collect data to support their findings. – Sue Townsend, Biodiversity Learning Manager, Field Studies Council[M]akes it easy for the reader to synthesise R and Excel and there is extra help and sample data available on the free companion webpage if needed. I recommended this text to the university library as well as to colleagues at my student workshops on R. Although I initially bought this book when I wanted to discover R I actually also learned new techniques for data manipulation and management in Excel – Mark Edwards, EcoBloggingA must for anyone getting to grips with data analysis using R and excel. – Amazon 5-star reviewIt has been very easy to follow and will be perfect for anyone. – Amazon 5-star reviewA solid introduction to working with Excel and R. The writing is clear and informative, the book provides plenty of examples and figures so that each string of code in R or step in Excel is understood by the reader. – Goodreads, 4-star review