MSMS 5010, BCOR 5570, MPSE 5010 - Biostatistics

Python for Scientists by John M. Stewart; Michael Mommert The third edition of this practical introduction to Python has been thoroughly updated, with all code migrated to Jupyter notebooks. The notebooks are available online with executable versions of all of the book's content (and more). The text starts with a detailed introduction to the basics of the Python language, without assuming any prior knowledge. Building upon each other, the most important Python packages for numerical math (NumPy), symbolic math (SymPy), and plotting (Matplotlib) are introduced, with brand new chapters covering numerical methods (SciPy) and data handling (Pandas). Further new material includes guidelines for writing efficient Python code and publishing code for other users. Simple and concise code examples, revised for compatibility with Python 3, guide the reader and support the learning process throughout the book. Readers from all of the quantitative sciences, whatever their background, will be able to quickly acquire the skills needed for using Python effectively.

Conservation and the Genomics of Populations by Fred W. Allendorf; W. Chris Funk; Sally N. Aitken; Margaret Byrne; Gordon Luikart; Agostinho Antunes (Illustrator) The relentless loss of biodiversity is among the greatest problems facing the world today. The third edition of this established textbook provides an updated and comprehensive overview of the essential background, concepts, and tools required to understand how genetics can be used to conserve species, reduce threat of extinction, and manage species of ecological or commercial importance. This edition is thoroughly revised to reflect the major contribution of genomics to conservation of populations and species. It includes two new chapters: "Genetic Monitoring" and a final "Conservation Genetics in Practice" chapter that addresses the role of science and policy in conservation genetics. New genomic techniques and statistical analyses are crucial tools for the conservation geneticist. This accessible and authoritative textbook provides an essential toolkit grounded in population genetics theory, coupled with basic and applied research examples from plants, animals, and microbes. The book examines genetic and phenotypic variation in natural populations, the principles and mechanisms of evolutionary change, evolutionary response to anthropogenic change, and applications in conservation and management.Conservation and the Genomics of Populations helps demystify genetics and genomics for conservation practitioners and early career scientists, so that population genetic theory and new genomic data can help raise the bar in conserving biodiversity in the most critical 20 year period in the history of life on Earth. It is aimed at a global market of applied population geneticists, conservation practitioners, and natural resource managers working for wildlife and habitat management agencies. It will be of particular relevance and use to upper undergraduate and graduate students taking courses in conservation biology, conservation genetics, and wildlife management.

Foundations of Biostatistics by M. Ataharul Islam; Abdullah Al-Shiha This book offers a comprehensive guide to essential techniques and methods in biostatistics, addressing the underlying concepts to aid in comprehension. The use of biostatistics techniques has increased manifold in the recent past, due to their suitability for applications in a wide range of problems in various fields. This book helps learners grasp the materials in detail, equipping them to use biostatistics techniques independently and confidently. The book starts with a summary of background materials, followed by methods and techniques. As such, with only minimum guidance from teachers, this book can provide materials for self-learning of biostatistics techniques with a deeper level of understanding.  The first two chapters focus on fundamental concepts, sources of data, data types, organization of data, and descriptive statistics, followed by the basic probability concepts, distributions and sampling distributions needed in order to combine descriptive statistics with inferential techniques. Estimation and tests of hypotheses are illustrated in two separate chapters. Important measures of association, linear regression, analysis of variance and logistic regression, and proportional hazards models are then presented systematically, ensuring that the book covers the topics most essential to students and users of biostatistics in connection with a wide range of applications in various fields. The book has been carefully structured, and the content is presented in a sequence covering the essential background in a highly systematic manner, supporting the learning process by presenting theory and applications that complement one another.

Statistical Analysis of Microbiome Data with R by Yinglin Xia; Jun Sun; Ding-Geng Chen This unique book addresses the statistical modelling and analysis of microbiome data using cutting-edge R software. It includes real-world data from the authors' research and from the public domain, and discusses the implementation of R for data analysis step by step. The data and R computer programs are publicly available, allowing readers to replicate the model development and data analysis presented in each chapter, so that these new methods can be readily applied in their own research. The book also discusses recent developments in statistical modelling and data analysis in microbiome research, as well as the latest advances in next-generation sequencing and big data in methodological development and applications. This timely book will greatly benefit all readers involved in microbiome, ecology and microarray data analyses, as well as other fields of research.

Statistics for Ecologists Using R and Excel by Mark Gardener 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, EcoBlogging A must for anyone getting to grips with data analysis using R and excel. - Amazon 5-star review It has been very easy to follow and will be perfect for anyone. - Amazon 5-star review A 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

Environmental and Ecological Statistics with R, Second Edition by Song S. Qian Emphasizing the inductive nature of statistical thinking, Environmental and Ecological Statistics with R, Second Edition, connects applied statistics to the environmental and ecological fields. Using examples from published works in the ecological and environmental literature, the book explains the approach to solving a statistical problem, covering model specification, parameter estimation, and model evaluation. It includes many examples to illustrate the statistical methods and presents R code for their implementation. The emphasis is on model interpretation and assessment, and using several core examples throughout the book, the author illustrates the iterative nature of statistical inference. The book starts with a description of commonly used statistical assumptions and exploratory data analysis tools for the verification of these assumptions. It then focuses on the process of building suitable statistical models, including linear and nonlinear models, classification and regression trees, generalized linear models, and multilevel models. It also discusses the use of simulation for model checking, and provides tools for a critical assessment of the developed models. The second edition also includes a complete critique of a threshold model. Environmental and Ecological Statistics with R, Second Editionfocuses on statistical modeling and data analysis for environmental and ecological problems. By guiding readers through the process of scientific problem solving and statistical model development, it eases the transition from scientific hypothesis to statistical model.

Introduction to Nonparametric Statistics for the Biological Sciences Using R by Thomas W. Macfarland; Jan M. Yates This book contains a rich set of tools for nonparametric analyses, and the purpose of this text is to provide guidance to students and professional researchers on how R is used for nonparametric data analysis in the biological sciences: To introduce when nonparametric approaches to data analysis are appropriate To introduce the leading nonparametric tests commonly used in biostatistics and how R is used to generate appropriate statistics for each test To introduce common figures typically associated with nonparametric data analysis and how R is used to generate appropriate figures in support of each data set The book focuses on how R is used to distinguish between data that could be classified as nonparametric as opposed to data that could be classified as parametric, with both approaches to data classification covered extensively. Following an introductory lesson on nonparametric statistics for the biological sciences, the book is organized into eight self-contained lessons on various analyses and tests using R to broadly compare differences between data sets and statistical approach.

Introductory Fisheries Analyses with R by Derek H. Ogle A How-To Guide for Conducting Common Fisheries-Related Analyses in R Introductory Fisheries Analyses with R provides detailed instructions on performing basic fisheries stock assessment analyses in the R environment. Accessible to practicing fisheries scientists as well as advanced undergraduate and graduate students, the book demonstrates the flexibility and power of R, offers insight into the reproducibility of script-based analyses, and shows how the use of R leads to more efficient and productive work in fisheries science. The first three chapters present a minimal introduction to the R environment that builds a foundation for the fisheries-specific analyses in the remainder of the book. These chapters help you become familiar with R for basic fisheries analyses and graphics. Subsequent chapters focus on methods to analyze age comparisons, age-length keys, size structure, weight-length relationships, condition, abundance (from capture-recapture and depletion data), mortality rates, individual growth, and the stock-recruit relationship. The fundamental statistical methods of linear regression, analysis of variance (ANOVA), and nonlinear regression are demonstrated within the contexts of these common fisheries analyses. For each analysis, the author completely explains the R functions and provides sufficient background information so that you can confidently implement each method. Web Resource The author's website at http://derekogle.com/IFAR/ includes the data files and R code for each chapter, enabling you to reproduce the results in the book as well as create your own scripts. The site also offers supplemental code for more advanced analyses and practice exercises for every chapter.

A primer of ecological statistics by Nicholas J. Gotelli, University of Vermont, Aaron M. Ellison, Harvard University

Discovering Statistics Using R by Andy Field; Jeremy Miles; Zoe Field Lecturers - request an e-inspection copy of this text or contact your local SAGE representative to discuss your course needs. Watch Andy Field's introductory video to Discovering Statistics Using R Keeping the uniquely humorous and self-deprecating style that has made students across the world fall in love with Andy Field's books, Discovering Statistics Using R takes students on a journey of statistical discovery using R, a free, flexible and dynamically changing software tool for data analysis that is becoming increasingly popular across the social and behavioural sciences throughout the world. The journey begins by explaining basic statistical and research concepts before a guided tour of the R software environment. Next you discover the importance of exploring and graphing data, before moving onto statistical tests that are the foundations of the rest of the book (for example correlation and regression). You will then stride confidently into intermediate level analyses such as ANOVA, before ending your journey with advanced techniques such as MANOVA and multilevel models. Although there is enough theory to help you gain the necessary conceptual understanding of what you're doing, the emphasis is on applying what you learn to playful and real-world examples that should make the experience more fun than you might expect. Like its sister textbooks, Discovering Statistics Using R is written in an irreverent style and follows the same ground-breaking structure and pedagogical approach. The core material is augmented by a cast of characters to help the reader on their way, together with hundreds of examples, self-assessment tests to consolidate knowledge, and additional website material for those wanting to learn more. Given this book's accessibility, fun spirit, and use of bizarre real-world research it should be essential for anyone wanting to learn about statistics using the freely-available R software. Available with Perusall--an eBook that makes it easier to prepare for class Perusall is an award-winning eBook platform featuring social annotation tools that allow students and instructors to collaboratively mark up and discuss their SAGE textbook. Backed by research and supported by technological innovations developed at Harvard University, this process of learning through collaborative annotation keeps your students engaged and makes teaching easier and more effective. Learn more.  

Practical Applications of Environmental Statistics and Data Analysis by Yue Rong

Robust Methods in Biostatistics by Stephane Heritier; Eva Cantoni; Samuel Copt; Maria-Pia Victoria-Feser Robust statistics is an extension of classical statistics that specifically takes into account the concept that the underlying models used to describe data are only approximate. Its basic philosophy is to produce statistical procedures which are stable when the data do not exactly match the postulated models as it is the case for example with outliers. Robust Methods in Biostatistics proposes robust alternatives to common methods used in statistics in general and in biostatistics in particular and illustrates their use on many biomedical datasets. The methods introduced include robust estimation, testing, model selection, model check and diagnostics. They are developed for the following general classes of models: Linear regression Generalized linear models Linear mixed models Marginal longitudinal data models Cox survival analysis model The methods are introduced both at a theoretical and applied level within the framework of each general class of models, with a particular emphasis put on practical data analysis. This book is of particular use for research students,applied statisticians and practitioners in the health field interested in more stable statistical techniques. An accompanying website provides R code for computing all of the methods described, as well as for analyzing all the datasets used in the book.