Foundational and Applied Statistics for Biologists Using R

Author: Ken A. Aho
Publisher: CRC Press
ISBN: 9781439873397
Release Date: 2016-03-09
Genre: Mathematics

Full of biological applications, exercises, and interactive graphical examples, Foundational and Applied Statistics for Biologists Using R presents comprehensive coverage of both modern analytical methods and statistical foundations. The author harnesses the inherent properties of the R environment to enable students to examine the code of complicated procedures step by step and thus better understand the process of obtaining analysis results. The graphical capabilities of R are used to provide interactive demonstrations of simple to complex statistical concepts. Assuming only familiarity with algebra and general calculus, the text offers a flexible structure for both introductory and graduate-level biostatistics courses. The first seven chapters address fundamental topics in statistics, such as the philosophy of science, probability, estimation, hypothesis testing, sampling, and experimental design. The remaining four chapters focus on applications involving correlation, regression, ANOVA, and tabular analyses. Unlike classic biometric texts, this book provides students with an understanding of the underlying statistics involved in the analysis of biological applications. In particular, it shows how a solid statistical foundation leads to the correct application of procedures, a clear understanding of analyses, and valid inferences concerning biological phenomena. Web Resource An R package (asbio) developed by the author is available from CRAN. Accessible to those without prior command-line interface experience, this companion library contains hundreds of functions for statistical pedagogy and biological research. The author’s website also includes an overview of R for novices.

Foundational and Applied Statistics for Biologists Using R

Author: Ken A. Aho
Publisher: CRC Press
ISBN: 9781439873380
Release Date: 2013-12-17
Genre: Mathematics

Full of biological applications, exercises, and interactive graphical examples, Foundational and Applied Statistics for Biologists Using R presents comprehensive coverage of both modern analytical methods and statistical foundations. The author harnesses the inherent properties of the R environment to enable students to examine the code of complicated procedures step by step and thus better understand the process of obtaining analysis results. The graphical capabilities of R are used to provide interactive demonstrations of simple to complex statistical concepts. Assuming only familiarity with algebra and general calculus, the text offers a flexible structure for both introductory and graduate-level biostatistics courses. The first seven chapters address fundamental topics in statistics, such as the philosophy of science, probability, estimation, hypothesis testing, sampling, and experimental design. The remaining four chapters focus on applications involving correlation, regression, ANOVA, and tabular analyses. Unlike classic biometric texts, this book provides students with an understanding of the underlying statistics involved in the analysis of biological applications. In particular, it shows how a solid statistical foundation leads to the correct application of procedures, a clear understanding of analyses, and valid inferences concerning biological phenomena. Web Resource An R package (asbio) developed by the author is available from CRAN. Accessible to those without prior command-line interface experience, this companion library contains hundreds of functions for statistical pedagogy and biological research. The author’s website also includes an overview of R for novices.

Biostatistical Design and Analysis Using R

Author: Dr Murray Logan
Publisher: John Wiley & Sons
ISBN: 9781444362473
Release Date: 2011-09-20
Genre: Science

R — the statistical and graphical environment is rapidly emerging as an important set of teaching and research tools for biologists. This book draws upon the popularity and free availability of R to couple the theory and practice of biostatistics into a single treatment, so as to provide a textbook for biologists learning statistics, R, or both. An abridged description of biostatistical principles and analysis sequence keys are combined together with worked examples of the practical use of R into a complete practical guide to designing and analyzing real biological research. Topics covered include: simple hypothesis testing, graphing exploratory data analysis and graphical summaries regression (linear, multi and non-linear) simple and complex ANOVA and ANCOVA designs (including nested, factorial, blocking, spit-plot and repeated measures) frequency analysis and generalized linear models. Linear mixed effects modeling is also incorporated extensively throughout as an alternative to traditional modeling techniques. The book is accompanied by a companion website www.wiley.com/go/logan/r with an extensive set of resources comprising all R scripts and data sets used in the book, additional worked examples, the biology package, and other instructional materials and links.

Foundations and Applications of Statistics An Introduction Using R Second Edition

Author: Randall Pruim
Publisher: American Mathematical Soc.
ISBN: 9781470428488
Release Date: 2018-04-04
Genre: Mathematical statistics

Foundations and Applications of Statistics simultaneously emphasizes both the foundational and the computational aspects of modern statistics. Engaging and accessible, this book is useful to undergraduate students with a wide range of backgrounds and career goals. The exposition immediately begins with statistics, presenting concepts and results from probability along the way. Hypothesis testing is introduced very early, and the motivation for several probability distributions comes from p-value computations. Pruim develops the students' practical statistical reasoning through explicit examples and through numerical and graphical summaries of data that allow intuitive inferences before introducing the formal machinery. The topics have been selected to reflect the current practice in statistics, where computation is an indispensible tool. In this vein, the statistical computing environment R is used throughout the text and is integral to the exposition. Attention is paid to developing students' mathematical and computational skills as well as their statistical reasoning. Linear models, such as regression and ANOVA, are treated with explicit reference to the underlying linear algebra, which is motivated geometrically. Foundations and Applications of Statistics discusses both the mathematical theory underlying statistics and practical applications that make it a powerful tool across disciplines. The book contains ample material for a two-semester course in undergraduate probability and statistics. A one-semester course based on the book will cover hypothesis testing and confidence intervals for the most common situations. In the second edition, the R code has been updated throughout to take advantage of new R packages and to illustrate better coding style. New sections have been added covering bootstrap methods, multinomial and multivariate normal distributions, the delta method, numerical methods for Bayesian inference, and nonlinear least squares. Also, the use of matrix algebra has been expanded, but remains optional, providing instructors with more options regarding the amount of linear algebra required.

Computational Genome Analysis

Author: Richard C. Deonier
Publisher: Springer Science & Business Media
ISBN: 0387987851
Release Date: 2007-08-13
Genre: Computers

This book presents the foundations of key problems in computational molecular biology and bioinformatics. It focuses on computational and statistical principles applied to genomes, and introduces the mathematics and statistics that are crucial for understanding these applications. The book features a free download of the R software statistics package and the text provides great crossover material that is interesting and accessible to students in biology, mathematics, statistics and computer science. More than 100 illustrations and diagrams reinforce concepts and present key results from the primary literature. Exercises are given at the end of chapters.

Introductory Statistics with R

Author: Peter Dalgaard
Publisher: Springer Science & Business Media
ISBN: 9780387790541
Release Date: 2008-06-27
Genre: Mathematics

This book provides an elementary-level introduction to R, targeting both non-statistician scientists in various fields and students of statistics. The main mode of presentation is via code examples with liberal commenting of the code and the output, from the computational as well as the statistical viewpoint. Brief sections introduce the statistical methods before they are used. A supplementary R package can be downloaded and contains the data sets. All examples are directly runnable and all graphics in the text are generated from the examples. The statistical methodology covered includes statistical standard distributions, one- and two-sample tests with continuous data, regression analysis, one-and two-way analysis of variance, regression analysis, analysis of tabular data, and sample size calculations. In addition, the last four chapters contain introductions to multiple linear regression analysis, linear models in general, logistic regression, and survival analysis.

Introduction to Statistical Data Analysis for the Life Sciences Second Edition

Author: Claus Thorn Ekstrom
Publisher: CRC Press
ISBN: 9781482238945
Release Date: 2014-11-06
Genre: Mathematics

A Hands-On Approach to Teaching Introductory Statistics Expanded with over 100 more pages, Introduction to Statistical Data Analysis for the Life Sciences, Second Edition presents the right balance of data examples, statistical theory, and computing to teach introductory statistics to students in the life sciences. This popular textbook covers the mathematics underlying classical statistical analysis, the modeling aspects of statistical analysis and the biological interpretation of results, and the application of statistical software in analyzing real-world problems and datasets. New to the Second Edition A new chapter on non-linear regression models A new chapter that contains examples of complete data analyses, illustrating how a full-fledged statistical analysis is undertaken Additional exercises in most chapters A summary of statistical formulas related to the specific designs used to teach the statistical concepts This text provides a computational toolbox that enables students to analyze real datasets and gain the confidence and skills to undertake more sophisticated analyses. Although accessible with any statistical software, the text encourages a reliance on R. For those new to R, an introduction to the software is available in an appendix. The book also includes end-of-chapter exercises as well as an entire chapter of case exercises that help students apply their knowledge to larger datasets and learn more about approaches specific to the life sciences.

From Numbers to Words

Author: Susan Morgan
Publisher: Routledge
ISBN: 9781317269755
Release Date: 2016-07-22
Genre: Social Science

This invaluable resource guides readers through the process of creating scholarly, publishable prose from the results of quantitative experiments and investigations. It delves into the issues commonly encountered when reporting the results of statistical experiments and investigations, and provides instruction re the representation of these results in text and visual formats. This unique research companion serves as a must-have reference for advanced students doing quantitative research and working with statistics, with the goal of writing up and publishing their findings; it also serves as a useful refresher for experienced researchers.

The New Statistics with R

Author: Andy Hector
Publisher: Oxford University Press
ISBN: 9780198729051
Release Date: 2015
Genre: Science

Statistical methods are a key tool for all scientists working with data, but learning the basic mathematical skills can be one of the most challenging components of a biologist's training. This accessible book provides a contemporary introduction to the classical techniques and modern extensions of linear model analysis: one of the most useful approaches in the analysis of scientific data in the life and environmental sciences. It emphasizes an estimation-based approach that accounts for recent criticisms of the over-use of probability values, and introduces alternative approaches using information criteria. Statistics are introduced through worked analyses performed in R, the free open source programming language for statistics and graphics, which is rapidly becoming the standard software in many areas of science and technology. These analyses use real data sets from ecology, evolutionary biology and environmental science, and the data sets and R scripts are available as support material. The book's structure and user friendly style stem from the author's 20 years of experience teaching statistics to life and environmental scientists at both the undergraduate and graduate levels. The New Statistics with R is suitable for senior undergraduate and graduate students, professional researchers, and practitioners in the fields of ecology, evolution, environmental studies, and computational biology.

Algorithms in Structural Molecular Biology

Author: Bruce R. Donald
Publisher: MIT Press
ISBN: 9780262297844
Release Date: 2011-06-01
Genre: Science

Using the tools of information technology to understand the molecular machinery of the cell offers both challenges and opportunities to computational scientists. Over the past decade, novel algorithms have been developed both for analyzing biological data and for synthetic biology problems such as protein engineering. This book explains the algorithmic foundations and computational approaches underlying areas of structural biology including NMR (nuclear magnetic resonance); X-ray crystallography; and the design and analysis of proteins, peptides, and small molecules.Each chapter offers a concise overview of important concepts, focusing on a key topic in the field. Four chapters offer a short course in algorithmic and computational issues related to NMR structural biology, giving the reader a useful toolkit with which to approach the fascinating yet thorny computational problems in this area. A recurrent theme is understanding the interplay between biophysical experiments and computational algorithms. The text emphasizes the mathematical foundations of structural biology while maintaining a balance between algorithms and a nuanced understanding of experimental data. Three emerging areas, particularly fertile ground for research students, are highlighted: NMR methodology, design of proteins and other molecules, and the modeling of protein flexibility.The next generation of computational structural biologists will need training in geometric algorithms, provably good approximation algorithms, scientific computation, and an array of techniques for handling noise and uncertainty in combinatorial geometry and computational biophysics. This book is an essential guide for young scientists on their way to research success in this exciting field.

Statistics

Author: Michael J. Crawley
Publisher: John Wiley & Sons
ISBN: 9781118941102
Release Date: 2014-09-23
Genre: Mathematics

"...I know of no better book of its kind..." (Journal of the Royal Statistical Society, Vol 169 (1), January 2006) A revised and updated edition of this bestselling introductory textbook to statistical analysis using the leading free software package R This new edition of a bestselling title offers a concise introduction to a broad array of statistical methods, at a level that is elementary enough to appeal to a wide range of disciplines. Step-by-step instructions help the non-statistician to fully understand the methodology. The book covers the full range of statistical techniques likely to be needed to analyse the data from research projects, including elementary material like t--tests and chi--squared tests, intermediate methods like regression and analysis of variance, and more advanced techniques like generalized linear modelling. Includes numerous worked examples and exercises within each chapter.

Bayesian Ideas and Data Analysis

Author: Ronald Christensen
Publisher: CRC Press
ISBN: 9781439803554
Release Date: 2011-07-07
Genre: Mathematics

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.

Applied Multivariate Statistics for the Social Sciences

Author: James Paul Stevens
Publisher: Taylor & Francis
ISBN: 9780805859010
Release Date: 2009
Genre: Social Science

This best-selling text is written for those who use, rather than develop statistical methods. Dr. Stevens focuses on a conceptual understanding of the material rather than on proving results. Helpful narrative and numerous examples enhance understanding and a chapter on matrix algebra serves as a review. Annotated printouts from SPSS and SAS indicate what the numbers mean and encourage interpretation of the results. In addition to demonstrating how to use these packages, the author stresses the importance of checking the data, assessing the assumptions, and ensuring adequate sample size by providing guidelines so that the results can be generalized. The book is noted for its extensive applied coverage of MANOVA, its emphasis on statistical power, and numerous exercises including answers to half. The new edition features: New chapters on Hierarchical Linear Modeling (Ch. 15) and Structural Equation Modeling (Ch. 16) New exercises that feature recent journal articles to demonstrate the actual use of multiple regression (Ch. 3), MANOVA (Ch. 5), and repeated measures (Ch. 13) A new appendix on the analysis of correlated observations (Ch. 6) Expanded discussions on obtaining non-orthogonal contrasts in repeated measures designs with SPSS and how to make the identification of cell ID easier in log linear analysis in 4 or 5 way designs Updated versions of SPSS (15.0) and SAS (8.0) are used throughout the text and introduced in chapter 1 A book website with data sets and more. Ideal for courses on multivariate statistics found in psychology, education, sociology, and business departments, the book also appeals to practicing researchers with little or no training in multivariate methods. Prerequisites include a course on factorial ANOVA and covariance. Working knowledge of matrix algebra is not assumed.

A Course in Complex Analysis

Author: Wolfgang Fischer
Publisher: Springer Science & Business Media
ISBN: 9783834886613
Release Date: 2011-10-21
Genre: Mathematics

This carefully written textbook is an introduction to the beautiful concepts and results of complex analysis. It is intended for international bachelor and master programmes in Germany and throughout Europe; in the Anglo-American system of university education the content corresponds to a beginning graduate course. The book presents the fundamental results and methods of complex analysis and applies them to a study of elementary and non-elementary functions (elliptic functions, Gamma- and Zeta function including a proof of the prime number theorem …) and – a new feature in this context! – to exhibiting basic facts in the theory of several complex variables. Part of the book is a translation of the authors’ German text “Einführung in die komplexe Analysis”; some material was added from the by now almost “classical” text “Funktionentheorie” written by the authors, and a few paragraphs were newly written for special use in a master’s programme.

Epistemology of the Cell

Author: Edward R. Dougherty
Publisher: John Wiley & Sons
ISBN: 1118104870
Release Date: 2011-08-17
Genre: Science

"Honorable mention – Biomedicine and Neuroscience, 2011 Prose Awards" An examination of how the cell should be described in order to effectively process biological data "The fruitful pursuit of biological knowledge requires one to take Einstein's admonition [on science without epistemology] as a practical demand for scientific research, to recognize Waddington's characterization of the subject matter of biology, and to embrace Wiener's conception of the form of biological knowledge in response to its subject matter. It is from this vantage point that we consider the epistemology of the cell." —from the Preface In the era of high biological data throughput, biomedical engineers need a more systematic knowledge of the cell in order to perform more effective data handling. Epistemology of the Cell is the first authored book to break down this knowledge. This text examines the place of biological knowledge within the framework of science as a whole and addresses issues focused on the specific nature of biology, how biology is studied, and how biological knowledge is translated into applications, in particular with regard to medicine. The book opens with a general discussion of the historical development of human understanding of scientific knowledge, the scientific method, and the manner in which scientific knowledge is represented in mathematics. The narrative then gets specific for biology, focusing on knowledge of the cell, the basic unit of life. The salient point is the analogy between a systems-based analysis of factory regulation and the regulation of the cell. Each chapter represents a key topic of current interest, including: Causality and randomness Translational science Stochastic validation: classification Stochastic validation: networks Model-based experimentation in biology Epistemology of the Cell is written for biomedical researchers whose interests include bioinformatics, biological modeling, biostatistics, and biological signal processing.