In this book, we provide an easy introduction to Bayesian inference using MCMC techniques, making most topics intuitively reasonable and deriving to appendixes the more complicated matters. The biologist or the agricultural researcher does not normally have a background in Bayesian statistics, having difficulties in following the technical books introducing Bayesian techniques. The difficulties arise from the way of making inferences, which is completely different in the Bayesian school, and from the difficulties in understanding complicated matters such as the MCMC numerical methods. We compare both schools, classic and Bayesian, underlying the advantages of Bayesian solutions, and proposing inferences based in relevant differences, guaranteed values, probabilities of similitude or the use of ratios. We also give a scope of complex problems that can be solved using Bayesian statistics, and we end the book explaining the difficulties associated to model choice and the use of small samples. The book has a practical orientation and uses simple models to introduce the reader in this increasingly popular school of inference.
Doing Bayesian Data Analysis: A Tutorial with R, JAGS, and Stan, Second Edition provides an accessible approach for conducting Bayesian data analysis, as material is explained clearly with concrete examples. Included are step-by-step instructions on how to carry out Bayesian data analyses in the popular and free software R and WinBugs, as well as new programs in JAGS and Stan. The new programs are designed to be much easier to use than the scripts in the first edition. In particular, there are now compact high-level scripts that make it easy to run the programs on your own data sets. The book is divided into three parts and begins with the basics: models, probability, Bayes’ rule, and the R programming language. The discussion then moves to the fundamentals applied to inferring a binomial probability, before concluding with chapters on the generalized linear model. Topics include metric-predicted variable on one or two groups; metric-predicted variable with one metric predictor; metric-predicted variable with multiple metric predictors; metric-predicted variable with one nominal predictor; and metric-predicted variable with multiple nominal predictors. The exercises found in the text have explicit purposes and guidelines for accomplishment. This book is intended for first-year graduate students or advanced undergraduates in statistics, data analysis, psychology, cognitive science, social sciences, clinical sciences, and consumer sciences in business. Accessible, including the basics of essential concepts of probability and random sampling Examples with R programming language and JAGS software Comprehensive coverage of all scenarios addressed by non-Bayesian textbooks: t-tests, analysis of variance (ANOVA) and comparisons in ANOVA, multiple regression, and chi-square (contingency table analysis) Coverage of experiment planning R and JAGS computer programming code on website Exercises have explicit purposes and guidelines for accomplishment Provides step-by-step instructions on how to conduct Bayesian data analyses in the popular and free software R and WinBugs
Author: Aviva Petrie
Publisher: John Wiley & Sons
Release Date: 2013-02-28
Banish your fears of statistical analysis using this clearly written and highly successful textbook. Statistics for Veterinary and Animal Science Third Edition is an introductory text which assumes no previous knowledge of statistics. It starts with very basic methodology and builds on it to encompass some of the more advanced techniques that are currently used. This book will enable you to handle numerical data and critically appraise the veterinary and animal science literature. Written in a non-mathematical way, the emphasis is on understanding the underlying concepts and correctly interpreting computer output, and not on working through mathematical formulae. Key features: Flow charts are provided to enable you to choose the correct statistical analyses in different situations Numerous real worked examples are included to help you master the procedures Two statistical packages, SPSS and Stata, are used to analyse data to familiarise you with typical computer output The data sets from the examples in the book are available as electronic files to download from the book’s companion website in ASCII, Excel, SPSS, Stata and R Workspace formats, allowing you to practice using your own software and fully get to grips with the techniques A clear indication is provided of the more advanced or obscure topics so that, if desired, you can skip them without loss of continuity. New to this edition: New chapter on reporting guidelines relevant to veterinary medicine as a ready reference for those wanting to follow best practice in planning and writing up research New chapter on critical appraisal of randomized controlled trials and observational studies in the published literature: a template is provided which is used to critically appraise two papers New chapter introducing specialist topics: ethical issues of animal investigations, spatial statistics, veterinary surveillance, and statistics in molecular and quantitative genetics Expanded glossaries of notation and terms Additional exercises and further explanations added throughout to make the book more comprehensive. Carrying out statistical procedures and interpreting the results is an integral part of veterinary and animal science. This is the only book on statistics that is specifically written for veterinary science and animal science students, researchers and practitioners.
Nowadays bioinformaticians and geneticists are faced with myriad high-throughput data usually presenting the characteristics of uncertainty, high dimensionality and large complexity. These data will only allow insights into this wealth of so-called 'omics' data if represented by flexible and scalable models, prior to any further analysis. At the interface between statistics and machine learning, probabilistic graphical models (PGMs) represent a powerful formalism to discover complex networks of relations. These models are also amenable to incorporating a priori biological information. Network reconstruction from gene expression data represents perhaps the most emblematic area of research where PGMs have been successfully applied. However these models have also created renewed interest in genetics in the broad sense, in particular regarding association genetics, causality discovery, prediction of outcomes, detection of copy number variations, and epigenetics. This book provides an overview of the applications of PGMs to genetics, genomics and postgenomics to meet this increased interest. A salient feature of bioinformatics, interdisciplinarity, reaches its limit when an intricate cooperation between domain specialists is requested. Currently, few people are specialists in the design of advanced methods using probabilistic graphical models for postgenomics or genetics. This book deciphers such models so that their perceived difficulty no longer hinders their use and focuses on fifteen illustrations showing the mechanisms behind the models. Probabilistic Graphical Models for Genetics, Genomics and Postgenomics covers six main themes: (1) Gene network inference (2) Causality discovery (3) Association genetics (4) Epigenetics (5) Detection of copy number variations (6) Prediction of outcomes from high-dimensional genomic data. Written by leading international experts, this is a collection of the most advanced work at the crossroads of probabilistic graphical models and genetics, genomics, and postgenomics. The self-contained chapters provide an enlightened account of the pros and cons of applying these powerful techniques.
This book fills the gap between textbooks of quantitative genetic theory, and software manuals that provide details on analytical methods but little context or perspective on which methods may be most appropriate for a particular application. Accordingly this book is composed of two sections. The first section (Chapters 1 to 8) covers topics of classical phenotypic data analysis for prediction of breeding values in animal and plant breeding programs. In the second section (Chapters 9 to 13) we provide the concept and overall review of available tools for using DNA markers for predictions of genetic merits in breeding populations. With advances in DNA sequencing technologies, genomic data, especially single nucleotide polymorphism (SNP) markers, have become available for animal and plant breeding programs in recent years. Analysis of DNA markers for prediction of genetic merit is a relatively new and active research area. The algorithms and software to implement these algorithms are changing rapidly. This section represents state-of-the-art knowledge on the tools and technologies available for genetic analysis of plants and animals. However, readers should be aware that the methods or statistical packages covered here may not be available or they might be out of date in a few years. Ultimately the book is intended for professional breeders interested in utilizing these tools and approaches in their breeding programs. Lastly, we anticipate the usage of this volume for advanced level graduate courses in agricultural and breeding courses.
Author: Hardeo Sahai
Publisher: Springer Science & Business Media
Release Date: 2013-12-01
ANOVA models involving random effects have found widespread application to experimental design in varied fields such as biology, econometrics, and engineering. Volume I of this two-part work is a comprehensive presentation of methods and techniques for point estimation, interval estimation, and hypotheses tests for linear models involving random effects. Volume I examines models with balanced data (orthogonal models); Volume II studies models with unbalanced data (non-orthogonal models). Accessible to readers with a modest mathematical and statistical background, the work will appeal to a broad audience of graduate students, researchers, and practitioners. It can be used as a graduate text or as a self-study reference.
Author: S. James Press
Publisher: John Wiley & Sons
Release Date: 2012-01-20
Comparing and contrasting the reality of subjectivity in the work of history's great scientists and the modern Bayesian approach to statistical analysis Scientists and researchers are taught to analyze their data from an objective point of view, allowing the data to speak for themselves rather than assigning them meaning based on expectations or opinions. But scientists have never behaved fully objectively. Throughout history, some of our greatest scientific minds have relied on intuition, hunches, and personal beliefs to make sense of empirical data-and these subjective influences have often aided in humanity's greatest scientific achievements. The authors argue that subjectivity has not only played a significant role in the advancement of science, but that science will advance more rapidly if the modern methods of Bayesian statistical analysis replace some of the classical twentieth-century methods that have traditionally been taught. To accomplish this goal, the authors examine the lives and work of history's great scientists and show that even the most successful have sometimes misrepresented findings or been influenced by their own preconceived notions of religion, metaphysics, and the occult, or the personal beliefs of their mentors. Contrary to popular belief, our greatest scientific thinkers approached their data with a combination of subjectivity and empiricism, and thus informally achieved what is more formally accomplished by the modern Bayesian approach to data analysis. Yet we are still taught that science is purely objective. This innovative book dispels that myth using historical accounts and biographical sketches of more than a dozen great scientists, including Aristotle, Galileo Galilei, Johannes Kepler, William Harvey, Sir Isaac Newton, Antoine Levoisier, Alexander von Humboldt, Michael Faraday, Charles Darwin, Louis Pasteur, Gregor Mendel, Sigmund Freud, Marie Curie, Robert Millikan, Albert Einstein, Sir Cyril Burt, and Margaret Mead. Also included is a detailed treatment of the modern Bayesian approach to data analysis. Up-to-date references to the Bayesian theoretical and applied literature, as well as reference lists of the primary sources of the principal works of all the scientists discussed, round out this comprehensive treatment of the subject. Readers will benefit from this cogent and enlightening view of the history of subjectivity in science and the authors' alternative vision of how the Bayesian approach should be used to further the cause of science and learning well into the twenty-first century.
Issues in Animal Science and Research / 2011 Edition is a ScholarlyEditions™ eBook that delivers timely, authoritative, and comprehensive information about Animal Science and Research. The editors have built Issues in Animal Science and Research: 2011 Edition on the vast information databases of ScholarlyNews.™ You can expect the information about Animal Science and Research in this eBook to be deeper than what you can access anywhere else, as well as consistently reliable, authoritative, informed, and relevant. The content of Issues in Animal Science and Research: 2011 Edition has been produced by the world’s leading scientists, engineers, analysts, research institutions, and companies. All of the content is from peer-reviewed sources, and all of it is written, assembled, and edited by the editors at ScholarlyEditions™ and available exclusively from us. You now have a source you can cite with authority, confidence, and credibility. More information is available at http://www.ScholarlyEditions.com/.
Author: Daniel Sorensen
Publisher: Springer Science & Business Media
Release Date: 2007-03-22
This book, suitable for numerate biologists and for applied statisticians, provides the foundations of likelihood, Bayesian and MCMC methods in the context of genetic analysis of quantitative traits. Although a number of excellent texts in these areas have become available in recent years, the basic ideas and tools are typically described in a technically demanding style and contain much more detail than necessary. Here, an effort has been made to relate biological to statistical parameters throughout, and the book includes extensive examples that illustrate the developing argument.
Author: Allen B. Downey
Publisher: O'Reilly Germany
Release Date: 2012-05-31
Wenn Sie programmieren können, beherrschen Sie bereits Techniken, um aus Daten Wissen zu extrahieren. Diese kompakte Einführung in die Statistik zeigt Ihnen, wie Sie rechnergestützt, anstatt auf mathematischem Weg Datenanalysen mit Python durchführen können. Praktischer Programmier-Workshop statt grauer Theorie: Das Buch führt Sie anhand eines durchgängigen Fallbeispiels durch eine vollständige Datenanalyse -- von der Datensammlung über die Berechnung statistischer Kennwerte und Identifikation von Mustern bis hin zum Testen statistischer Hypothesen. Gleichzeitig werden Sie mit statistischen Verteilungen, den Regeln der Wahrscheinlichkeitsrechnung, Visualisierungsmöglichkeiten und vielen anderen Arbeitstechniken und Konzepten vertraut gemacht. Statistik-Konzepte zum Ausprobieren: Entwickeln Sie über das Schreiben und Testen von Code ein Verständnis für die Grundlagen von Wahrscheinlichkeitsrechnung und Statistik: Überprüfen Sie das Verhalten statistischer Merkmale durch Zufallsexperimente, zum Beispiel indem Sie Stichproben aus unterschiedlichen Verteilungen ziehen. Nutzen Sie Simulationen, um Konzepte zu verstehen, die auf mathematischem Weg nur schwer zugänglich sind. Lernen Sie etwas über Themen, die in Einführungen üblicherweise nicht vermittelt werden, beispielsweise über die Bayessche Schätzung. Nutzen Sie Python zur Bereinigung und Aufbereitung von Rohdaten aus nahezu beliebigen Quellen. Beantworten Sie mit den Mitteln der Inferenzstatistik Fragestellungen zu realen Daten.