Studies of evolution at the molecular level have experienced phenomenal growth in the last few decades, due to rapid accumulation of genetic sequence data, improved computer hardware and software, and the development of sophisticated analytical methods. The flood of genomic data has generated an acute need for powerful statistical methods and efficient computational algorithms to enable their effective analysis and interpretation. Molecular Evolution: a statistical approach presents and explains modern statistical methods and computational algorithms for the comparative analysis of genetic sequence data in the fields of molecular evolution, molecular phylogenetics, statistical phylogeography, and comparative genomics. Written by an expert in the field, the book emphasizes conceptual understanding rather than mathematical proofs. The text is enlivened with numerous examples of real data analysis and numerical calculations to illustrate the theory, in addition to the working problems at the end of each chapter. The coverage of maximum likelihood and Bayesian methods are in particular up-to-date, comprehensive, and authoritative. This advanced textbook is aimed at graduate level students and professional researchers (both empiricists and theoreticians) in the fields of bioinformatics and computational biology, statistical genomics, evolutionary biology, molecular systematics, and population genetics. It will also be of relevance and use to a wider audience of applied statisticians, mathematicians, and computer scientists working in computational biology.

"Functional and Phylogenetic Ecology in R" is designed to teach readers to use R for phylogenetic and functional trait analyses. Over the past decade, a dizzying array of tools and methods were generated to incorporate phylogenetic and functional information into traditional ecological analyses. Increasingly these tools are implemented in R, thus greatly expanding their impact. Researchers getting started in R can use this volume as a step-by-step entryway into phylogenetic and functional analyses for ecology in R. More advanced users will be able to use this volume as a quick reference to understand particular analyses. The volume begins with an introduction to the R environment and handling relevant data in R. Chapters then cover phylogenetic and functional metrics of biodiversity; null modeling and randomizations for phylogenetic and functional trait analyses; integrating phylogenetic and functional trait information; and interfacing the R environment with a popular C-based program. This book presents a unique approach through its focus on ecological analyses and not macroevolutionary analyses. The author provides his own code, so that the reader is guided through the computational steps to calculate the desired metrics. This guided approach simplifies the work of determining which package to use for any given analysis. Example datasets are shared to help readers practice, and readers can then quickly turn to their own datasets.

An Up-to-Date, All-in-One Resource for Using SAS and R to Perform Frequent TasksThe first edition of this popular guide provided a path between SAS and R using an easy-to-understand, dictionary-like approach. Retaining the same accessible format, SAS and R: Data Management, Statistical Analysis, and Graphics, Second Edition explains how to easily perform an analytical task in both SAS and R, without having to navigate through the extensive, idiosyncratic, and sometimes unwieldy software documentation. The book covers many common tasks, such as data management, descriptive summaries, inferential procedures, regression analysis, and graphics, along with more complex applications. New to the Second EditionThis edition now covers RStudio, a powerful and easy-to-use interface for R. It incorporates a number of additional topics, including using application program interfaces (APIs), accessing data through database management systems, using reproducible analysis tools, and statistical analysis with Markov chain Monte Carlo (MCMC) methods and finite mixture models. It also includes extended examples of simulations and many new examples. Enables Easy Mobility between the Two SystemsThrough the extensive indexing and cross-referencing, users can directly find and implement the material they need. SAS users can look up tasks in the SAS index and then find the associated R code while R users can benefit from the R index in a similar manner. Numerous example analyses demonstrate the code in action and facilitate further exploration. The datasets and code are available for download on the book's website.

A start-to-finish guide to one of the most useful programming languages for researchers in a variety of fields In the newly revised Third Edition of The R Book, a team of distinguished teachers and researchers delivers a user-friendly and comprehensive discussion of foundational and advanced topics in the R software language, which is used widely in science, engineering, medicine, economics, and other fields. The book is designed to be used as both a complete text--readable from cover to cover--and as a reference manual for practitioners seeking authoritative guidance on particular topics. This latest edition offers instruction on the use of the RStudio GUI, an easy-to-use environment for those new to R. It provides readers with a complete walkthrough of the R language, beginning at a point that assumes no prior knowledge of R and very little previous knowledge of statistics. Readers will also find: A thorough introduction to fundamental concepts in statistics and step-by-step roadmaps to their implementation in R; Comprehensive explorations of worked examples in R; A complementary companion website with downloadable datasets that are used in the book; In-depth examination of essential R packages. Perfect for undergraduate and postgraduate students of science, engineering, medicine economics, and geography, The R Book will also earn a place in the libraries of social sciences professionals.

Instead of presenting the standard theoretical treatments that underlie the various numerical methods used by scientists and engineers, Using R for Numerical Analysis in Science and Engineering shows how to use R and its add-on packages to obtain numerical solutions to the complex mathematical problems commonly faced by scientists and engineers. This practical guide to the capabilities of R demonstrates Monte Carlo, stochastic, deterministic, and other numerical methods through an abundance of worked examples and code, covering the solution of systems of linear algebraic equations and nonlinear equations as well as ordinary differential equations and partial differential equations. It not only shows how to use R's powerful graphic tools to construct the types of plots most useful in scientific and engineering work, but also: Explains how to statistically analyze and fit data to linear and nonlinear models Explores numerical differentiation, integration, and optimization Describes how to find eigenvalues and eigenfunctions Discusses interpolation and curve fitting Considers the analysis of time series Using R for Numerical Analysis in Science and Engineering provides a solid introduction to the most useful numerical methods for scientific and engineering data analysis using R.

An R Companion to Applied Regression is a broad introduction to the R statistical computing environment in the context of applied regression analysis. John Fox and Sanford Weisberg provide a step-by-step guide to using the free statistical software R, an emphasis on integrating statistical computing in R with the practice of data analysis, coverage of generalized linear models, and substantial web-based support materials. The Third Edition has been reorganized and includes a new chapter on mixed-effects models, new and updated data sets, and a de-emphasis on statistical programming, while retaining a general introduction to basic R programming. The authors have substantially updated both the car and effects packages for R for this edition, introducing additional capabilities and making the software more consistent and easier to use. They also advocate an everyday data-analysis workflow that encourages reproducible research. To this end, they provide coverage of RStudio, an interactive development environment for R that allows readers to organize and document their work in a simple and intuitive fashion, and then easily share their results with others. Also included is coverage of R Markdown, showing how to create documents that mix R commands with explanatory text. "An R Companion to Applied Regression continues to provide the most comprehensive and user-friendly guide to estimating, interpreting, and presenting results from regression models in R." -Christopher Hare, University of California, Davis

Statistics is of ever-increasing importance in Science and Technology and this book presents the essentials of the subject in a form suitable either as the basis of a course of lectures or to be read and/or used on its own. It assumes very little in the way of mathematical knowledge-just the ability to substitute numerically in a few simple formulae. However, some mathematical proofs are outlined or given in full to illustrate the derivation of the subject; these can be omitted without loss of understanding. The book does aim at making clear the scope and nature of those essential tests and methods that a scientist or technologist is likely to need; to this end each chapter has been divided into sections with their own subheadings and some effort has been made to make the text unambiguous (if any reader finds a misleading point anywhere I hope he will write to me about it). Also with this aim in view, the equality of probability to proportion of population is stated early, then the normal distribution and the taking of samples is discussed. This occupies the first five chapters. With the principles of these chapters understood, the student can immediately learn the significance tests of Chapter 6 and, if he needs it, the analysis of variance of Chapter 7. For some scientists this will be most of what they need. Howcver, they will be in a position to read and/or use the remaining chapters without undue difficulty.

Mathematical Models of Biological Systems provides a practical introduction to basic mathematical modelling methodology and analysis. It covers a variety of biological applications and uses these topics in turn to highlight key components in the art of modelling. Its primary aim is to give students the tools to translate simple, real-world biological problems into rigorous mathematical models. A secondary aim is to teach the reader how to critically assess the modelling components in the primary life science literature.
The book covers deterministic as well as stochastic dynamics, continuous-time as well as discrete-time dynamics, partial differential equations, dimensional analysis, and curve fitting/parameter estimation. It contains numerous case studies, graded from elementary examples to more complicated problems, as well as a general treatment of good modelling practice. Although the book assumes a basic background in mathematics, specifically beginning calculus and elementary statistics, all requisite material is included in a series of appendices.

Mathematical Models of Biological Systems provides a practical introduction to basic mathematical modelling methodology and analysis. It covers a variety of biological applications and uses these topics in turn to highlight key components in the art of modelling. Its primary aim is to give students the tools to translate simple, real-world biological problems into rigorous mathematical models. A secondary aim is to teach the reader how to critically assess the modelling components in the primary life science literature. The book covers deterministic as well as stochastic dynamics, continuous-time as well as discrete-time dynamics, partial differential equations, dimensional analysis, and curve fitting/parameter estimation. It contains numerous case studies, graded from elementary examples to more complicated problems, as well as a general treatment of good modelling practice. Although the book assumes a basic background in mathematics, specifically beginning calculus and elementary statistics, all requisite material is included in a series of appendices.

Employ essential tools and functions of the MATLAB and Simulink packages, which are explained and demonstrated via interactive examples and case studies. This revised edition covers features from the latest MATLAB 2022b release, as well as other features that have been released since the first edition published. This book contains dozens of simulation models and solved problems via m-files/scripts and Simulink models which will help you to learn programming and modelling essentials. You'll become efficient with many of the built-in tools and functions of MATLAB/Simulink while solving engineering and scientific computing problems. Beginning MATLAB and Simulink, Second Edition explains various practical issues of programming and modelling in parallel by comparing MATLAB and Simulink. After studying and using this book, you'll be proficient at using MATLAB and Simulink and applying the source code and models from the book's examples as templates for your own projects in data science or engineering. What You Will Learn Master the programming and modelling essentials of MATLAB and Simulink Carry out data visualization with MATLAB Build a GUI and develop App with MATLAB Work with integration and numerical root finding methods Apply MATLAB to differential equations-based models and simulations Use MATLAB and Simulink for data science projects Who This Book Is ForEngineers, programmers, data scientists, and students majoring in engineering and scientific computing who are new to MATLAB and Simulink.

This highly anticipated second edition features new chapters and sections, 225 new references, and comprehensive R software. In keeping with the previous edition, this book is about the art and science of data analysis and predictive modelling, which entails choosing and using multiple tools. Instead of presenting isolated techniques, this text emphasises problem solving strategies that address the many issues arising when developing multi-variable models using real data and not standard textbook examples. Regression Modelling Strategies presents full-scale case studies of non-trivial data-sets instead of over-simplified illustrations of each method. These case studies use freely available R functions that make the multiple imputation, model building, validation and interpretation tasks described in the book relatively easy to do. Most of the methods in this text apply to all regression models, but special emphasis is given to multiple regression using generalised least squares for longitudinal data, the binary logistic model, models for ordinal responses, parametric survival regression models and the Cox semi parametric survival model. A new emphasis is given to the robust analysis of continuous dependent variables using ordinal regression. As in the first edition, this text is intended for Masters' or PhD. level graduate students who have had a general introductory probability and statistics course and who are well versed in ordinary multiple regression and intermediate algebra. The book will also serve as a reference for data analysts and statistical methodologists, as it contains an up-to-date survey and bibliography of modern statistical modelling techniques.

Learn How to Program Stochastic Models Highly recommended, the best-selling first edition of Introduction to Scientific Programming and Simulation Using R was lauded as an excellent, easy-to-read introduction with extensive examples and exercises. This second edition continues to introduce scientific programming and stochastic modelling in a clear, practical, and thorough way. Readers learn programming by experimenting with the provided R code and data. The book's four parts teach: Core knowledge of R and programming concepts How to think about mathematics from a numerical point of view, including the application of these concepts to root finding, numerical integration, and optimisation Essentials of probability, random variables, and expectation required to understand simulation Stochastic modelling and simulation, including random number generation and Monte Carlo integration In a new chapter on systems of ordinary differential equations (ODEs), the authors cover the Euler, midpoint, and fourth-order Runge-Kutta (RK4) schemes for solving systems of first-order ODEs. They compare the numerical efficiency of the different schemes experimentally and show how to improve the RK4 scheme by using an adaptive step size. Another new chapter focuses on both discrete- and continuous-time Markov chains. It describes transition and rate matrices, classification of states, limiting behaviour, Kolmogorov forward and backward equations, finite absorbing chains, and expected hitting times. It also presents methods for simulating discrete- and continuous-time chains as well as techniques for defining the state space, including lumping states and supplementary variables. Building readers' statistical intuition, Introduction to Scientific Programming and Simulation Using R, Second Edition shows how to turn algorithms into code. It is designed for those who want to make tools, not just use them. The code and data are available for download from CRAN.

An authoritative, up-to-date graduate textbook on machine learning that highlights its historical context and societal impacts Patterns, Predictions, and Actions introduces graduate students to the essentials of machine learning while offering invaluable perspective on its history and social implications. Beginning with the foundations of decision making, Moritz Hardt and Benjamin Recht explain how representation, optimization, and generalization are the constituents of supervised learning. They go on to provide self-contained discussions of causality, the practice of causal inference, sequential decision making, and reinforcement learning, equipping readers with the concepts and tools they need to assess the consequences that may arise from acting on statistical decisions. Provides a modern introduction to machine learning, showing how data patterns support predictions and consequential actions Pays special attention to societal impacts and fairness in decision making Traces the development of machine learning from its origins to today Features a novel chapter on machine learning benchmarks and datasets Invites readers from all backgrounds, requiring some experience with probability, calculus, and linear algebra An essential textbook for students and a guide for researchers

This open access book contains review papers authored by thirteen plenary invited speakers to the 9th International Congress on Industrial and Applied Mathematics (Valencia, July 15-19, 2019). Written by top-level scientists recognized worldwide, the scientific contributions cover a wide range of cutting-edge topics of industrial and applied mathematics: mathematical modeling, industrial and environmental mathematics, mathematical biology and medicine, reduced-order modeling and cryptography. The book also includes an introductory chapter summarizing the main features of the congress. This is the first volume of a thematic series dedicated to research results presented at ICIAM 2019-Valencia Congress.

Now in its third edition, this outstanding textbook explains everything you need to get started using MATLAB (R). It contains concise explanations of essential MATLAB commands, as well as easily understood instructions for using MATLAB's programming features, graphical capabilities, simulation models, and rich desktop interface. MATLAB 8 and its new user interface is treated extensively in the book. New features in this edition include: a complete treatment of MATLAB's publish feature; new material on MATLAB graphics, enabling the user to master quickly the various symbolic and numerical plotting routines; and a robust presentation of MuPAD (R) and how to use it as a stand-alone platform. The authors have also updated the text throughout, reworking examples and exploring new applications. The book is essential reading for beginners, occasional users and experienced users wishing to brush up their skills. Further resources are available from the authors' website at www-math.umd.edu/schol/a-guide-to-matlab.html.

Conquer the complexities of this open source statistical language

R is fast becoming the de facto standard for statistical computing and analysis in science, business, engineering, and related fields. This book examines this complex language using simple statistical examples, showing how R operates in a user-friendly context. Both students and workers in fields that require extensive statistical analysis will find this book helpful as they learn to use R for simple summary statistics, hypothesis testing, creating graphs, regression, and much more. It covers formula notation, complex statistics, manipulating data and extracting components, and rudimentary programming.R, the open source statistical language increasingly used to handle statistics and produces publication-quality graphs, is notoriously complex This book makes R easier to understand through the use of simple statistical examples, teaching the necessary elements in the context in which R is actually usedCovers getting started with R and using it for simple summary statistics, hypothesis testing, and graphsShows how to use R for formula notation, complex statistics, manipulating data, extracting components, and regressionProvides beginning programming instruction for those who want to write their own scripts

"Beginning R" offers anyone who needs to perform statistical analysis the information necessary to use R with confidence.

This revised and updated edition focuses on constrained ordination (RDA, CCA), variation partitioning and the use of permutation tests of statistical hypotheses about multivariate data. Both classification and modern regression methods (GLM, GAM, loess) are reviewed and species functional traits and spatial structures analysed. Nine case studies of varying difficulty help to illustrate the suggested analytical methods, using the latest version of Canoco 5. All studies utilise descriptive and manipulative approaches, and are supported by data sets and project files available from the book website: http: //regent.prf.jcu.cz/maed2/. Written primarily for community ecologists needing to analyse data resulting from field observations and experiments, this book is a valuable resource to students and researchers dealing with both simple and complex ecological problems, such as the variation of biotic communities with environmental conditions or their response to experimental manipulation

An SPSS Companion for the Third Edition of The Fundamentals of Political Science Research offers students a chance to delve into the world of SPSS using real political science data sets and statistical analysis techniques directly from Paul M. Kellstedt and Guy D. Whitten's best-selling textbook. Built in parallel with the main text, this workbook teaches students to apply the techniques they learn in each chapter by reproducing the analyses and results from each lesson using SPSS. Students will also learn to create all of the tables and figures found in the textbook, leading to an even greater mastery of the core material. This accessible, informative, and engaging companion walks through the use of SPSS step-by-step, using command lines and screenshots to demonstrate proper use of the software. With the help of these guides, students will become comfortable creating, editing, and using data sets in SPSS to produce original statistical analyses for evaluating causal claims. End-of-chapter exercises encourage this innovation by asking students to formulate and evaluate their own hypotheses.

Learn how to program by diving into the R language, and then use your newfound skills to solve practical data science problems. With this book, you'll learn how to load data, assemble and disassemble data objects, navigate R's environment system, write your own functions, and use all of R's programming tools. RStudio Master Instructor Garrett Grolemund not only teaches you how to program, but also shows you how to get more from R than just visualizing and modeling data. You'll gain valuable programming skills and support your work as a data scientist at the same time. Work hands-on with three practical data analysis projects based on casino games Store, retrieve, and change data values in your computer's memory Write programs and simulations that outperform those written by typical R users Use R programming tools such as if else statements, for loops, and S3 classes Learn how to write lightning-fast vectorized R code Take advantage of R's package system and debugging tools Practice and apply R programming concepts as you learn them

For over two decades, this comprehensive manual has been the standard introduction and complete reference for writing articles and books containing mathematical formulas. If the reader requires a streamlined approach to learning LaTeX for composing everyday documents, Gratzer's (c) 2014 Practical LaTeX may also be a good choice. In this carefully revised fifth edition, the Short Course has been brought up to date and reflects a modern and practical approach to LaTeX usage. New chapters have been added on illustrations and how to use LaTeX on an iPad. Key features: An example-based, visual approach and a gentle introduction with the Short Course A detailed exposition of multiline math formulas with a Visual Guide A unified approach to TeX, LaTeX, and the AMS enhancements A quick introduction to creating presentations with formulas From earlier reviews: Gratzer's book is a solution. -European Mathematical Society Newsletter There are several LaTeX guides, but this one wins hands down for the elegance of its approach and breadth of coverage. -Amazon.com, Best of 2000, Editor's choice A novice reader will be able to learn the most essential features of LaTeX sufficient to begin typesetting papers within a few hours of time... An experienced TeX user, on the other hand, will find a systematic and detailed discussion of LaTeX fea tures. -Report on Mathematical Physics A very helpful and useful tool for all scientists and engineers. -Review of Astronomical Tools

Text Mining with MATLAB (R) provides a comprehensive introduction to text mining using MATLAB. It is designed to help text mining practitioners, as well as those with little-to-no experience with text mining in general, familiarize themselves with MATLAB and its complex applications. The book is structured in three main parts: The first part, Fundamentals, introduces basic procedures and methods for manipulating and operating with text within the MATLAB programming environment. The second part of the book, Mathematical Models, is devoted to motivating, introducing, and explaining the two main paradigms of mathematical models most commonly used for representing text data: the statistical and the geometrical approach. Eventually, the third part of the book, Techniques and Applications, addresses general problems in text mining and natural language processing applications such as document categorization, document search, content analysis, summarization, question answering, and conversational systems. This second edition includes updates in line with the recently released "Text Analytics Toolbox" within the MATLAB product and introduces three new chapters and six new sections in existing ones. All descriptions presented are supported with practical examples that are fully reproducible. Further reading, as well as additional exercises and projects, are proposed at the end of each chapter for those readers interested in conducting further experimentation.

The ability to summarise data, compare models and apply computer-based analysis tools are vital skills necessary for studying and working in the physical sciences. This textbook supports undergraduate students as they develop and enhance these skills. Introducing data analysis techniques, this textbook pays particular attention to the internationally recognised guidelines for calculating and expressing measurement uncertainty. This new edition has been revised to incorporate Excel (R) 2010. It also provides a practical approach to fitting models to data using non-linear least squares, a powerful technique which can be applied to many types of model. Worked examples using actual experimental data help students understand how the calculations apply to real situations. Over 200 in-text exercises and end-of-chapter problems give students the opportunity to use the techniques themselves and gain confidence in applying them. Answers to the exercises and problems are given at the end of the book.

This proceedings volume features top contributions in modern statistical methods from Statistics 2021 Canada, the 6th Annual Canadian Conference in Applied Statistics, held virtually on July 15-18, 2021. Papers are contributed from established and emerging scholars, covering cutting-edge and contemporary innovative techniques in statistics and data science. Major areas of contribution include Bayesian statistics; computational statistics; data science; semi-parametric regression; and stochastic methods in biology, crop science, ecology and engineering. It will be a valuable edited collection for graduate students, researchers, and practitioners in a wide array of applied statistical and data science methods.

As explored in this open access book, higher education in STEM fields is influenced by many factors, including education research, government and school policies, financial considerations, technology limitations, and acceptance of innovations by faculty and students. In 2018, Drs. Ryoo and Winkelmann explored the opportunities, challenges, and future research initiatives of innovative learning environments (ILEs) in higher education STEM disciplines in their pioneering project: eXploring the Future of Innovative Learning Environments (X-FILEs). Workshop participants evaluated four main ILE categories: personalized and adaptive learning, multimodal learning formats, cross/extended reality (XR), and artificial intelligence (AI) and machine learning (ML). This open access book gathers the perspectives expressed during the X-FILEs workshop and its follow-up activities. It is designed to help inform education policy makers, researchers, developers, and practitioners about the adoption and implementation of ILEs in higher education.

This textbook provides a step-by-step introduction to the tools and principles of high-dimensional statistics. Each chapter is complemented by numerous exercises, many of them with detailed solutions, and computer labs in R that convey valuable practical insights. The book covers the theory and practice of high-dimensional linear regression, graphical models, and inference, ensuring readers have a smooth start in the field. It also offers suggestions for further reading. Given its scope, the textbook is intended for beginning graduate and advanced undergraduate students in statistics, biostatistics, and bioinformatics, though it will be equally useful to a broader audience.