Use R! Series

Applied Spatial Data Analysis with R, second edition, is divided into two basic parts, the first presenting R packages, functions, classes and methods for handling spatial data. This part is of interest to users who need to access and visualise spatial data. Data import and export for many file formats for spatial data are covered in detail, as is the interface between R and the open source GRASS GIS and the handling of spatio-temporal data. The second part showcases more specialised kinds of spatial data analysis, including spatial point pattern analysis, interpolation and geostatistics, areal data analysis and disease mapping. The coverage of methods of spatial data analysis ranges from standard techniques to new developments, and the examples used are largely taken from the spatial statistics literature. All the examples can be run using R contributed packages available from the CRAN website, with code and additional data sets from the book's own website. Compared to the first edition, the second edition covers the more systematic approach towards handling spatial data in R, as well as a number of important and widely used CRAN packages that have appeared since the first edition.   This book will be of interest to researchers who intend to use R to handle, visualise, and analyse spatial data. It will also be of interest to spatial data analysts who do not use R, but who are interested in practical aspects of implementing software for spatial data analysis. It is a suitable companion book for introductory spatial statistics courses and for applied methods courses in a wide range of subjects using spatial data, including human and physical geography, geographical information science and geoinformatics, the environmental sciences, ecology, public health and disease control, economics, publicadministration and political science.   The book has a website where complete code examples, data sets, and other support material may be found: http://www.asdar-book.org.   The authors have taken part in writing and maintaining software for spatial data handling and analysis with R in concert since 2003.

Rcpp is the glue that binds the power and versatility of R with the speed and efficiency of C++.  With Rcpp, the transfer of data between R and C++ is nearly seamless, and high-performance statistical computing is finally accessible to most R users.  Rcpp should be part of every statistician's toolbox.  -- Michael Braun, MIT Sloan School of Management  "Seamless R and C++ integration with Rcpp" is simply a wonderful book.  For anyone who uses C/C++ and R, it is an indispensable resource.  The writing is outstanding.  A huge bonus is the section on applications. This section covers the matrix packages Armadillo and Eigen and the GNU Scientific Library as well as RInside which enables you to use R inside C++. These applications are what most of us need to know to really do scientific programming with R and C++. I love this book. -- Robert McCulloch, University of Chicago Booth School of Business  Rcpp is now considered an essential package for anybody doing serious computational research using R. Dirk's book is an excellent companion and takes the reader from a gentle introduction to more advanced applications via numerous examples and efficiency enhancing gems. The book is packed with all you might have ever wanted to know about Rcpp, its cousins (RcppArmadillo, RcppEigen .etc.), modules, package development and sugar. Overall, this book is a must-have on your shelf. -- Sanjog Misra, UCLA Anderson School of Management The Rcpp package represents a major leap forward for scientific computations with R. With very few lines of C++ code, one has R's data structures readily at hand for further computations in C++. Hence, high-level numerical programming can be made in C++ almost as easily as in R, but often with a substantial speed gain. Dirk is a crucial person in these developments, and his book takes the reader from the first fragile steps on to using the full Rcpp machinery. A very recommended book! --Søren Højsgaard, Department of Mathematical Sciences, Aalborg University, Denmark    "Seamless R and C ++ Integration with Rcpp" provides the first comprehensive introduction to Rcpp. Rcpp has become the most widely-used language extension for R, and is deployed by over one-hundred different CRAN and BioConductor packages. Rcpp permits users to pass scalars, vectors, matrices, list or entire R objects back and forth between R and C++ with ease. This brings the depth of the R analysis framework together with the power, speed, and efficiency of C++. Dirk Eddelbuettel has been a contributor to CRAN for over a decade and maintains around twenty packages.  He is the Debian/Ubuntu maintainer for R and other quantitative software, edits the CRAN Task Views for Finance and High-Performance Computing, is a co-founder of the annual R/Finance conference, and an editor of the Journal of Statistical Software.  He holds a Ph.D. in Mathematical Economics from EHESS (Paris), and works in Chicago as a Senior Quantitative Analyst.

The YUIMA package is the first comprehensive R framework based on S4 classes and methods which allows for the simulation of stochastic differential equations driven by Wiener process, Lévy processes or fractional Brownian motion, as well as CARMA, COGARCH, and Point processes. The package performs various central statistical analyses such as quasi maximum likelihood estimation, adaptive Bayes estimation, structural change point analysis, hypotheses testing, asynchronous covariance estimation, lead-lag estimation, LASSO model selection, and so on. YUIMA also supports stochastic numerical analysis by fast computation of the expected value of functionals of stochastic processes through automatic asymptotic expansion by means of the Malliavin calculus. All models can be multidimensional, multiparametric or non parametric.The book explains briefly the underlying theory for simulation and inference of several classes of stochastic processes and then presents both simulation experiments and applications to real data. Although these processes have been originally proposed in physics and more recently in finance, they are becoming popular also in biology due to the fact the time course experimental data are now available. The YUIMA package, available on CRAN, can be freely downloaded and this companion book will make the user able to start his or her analysis from the first page.

Bayesian Networks in R with Applications in Systems Biology is unique as it introduces the reader to the essential concepts in Bayesian network modeling and inference in conjunction with examples in the open-source statistical environment R. The level of sophistication is also gradually increased across the chapters with exercises and solutions for enhanced understanding for hands-on experimentation of the theory and concepts. The application focuses on systems biology with emphasis on modeling pathways and signaling mechanisms from high-throughput molecular data. Bayesian networks have proven to be especially useful abstractions in this regard. Their usefulness is especially exemplified by their ability to discover new associations in addition to validating known ones across the molecules of interest. It is also expected that the prevalence of publicly available high-throughput biological data sets may encourage the audience to explore investigating novel paradigms using theapproaches presented in the book.

Based on their extensive experience with teaching R and statistics to applied scientists, the authors provide a beginner's guide to R. To avoid the difficulty of teaching R and statistics at the same time, statistical methods are kept to a minimum. The text covers how to download and install R, import and manage data, elementary plotting, an introduction to functions, advanced plotting, and common beginner mistakes. This book contains everything you need to know to get started with R.

This book is designed to be a practical study in infectious disease dynamics. The book offers an easy to follow implementation and analysis of mathematical epidemiology. The book focuses on recent case studies in order to explore various conceptual, mathematical, and statistical issues. The dynamics of infectious diseases shows a wide diversity of pattern. Some have locally persistent chains-of-transmission, others persist spatially in ‘consumer-resource metapopulations’. Some infections are prevalent among the young, some among the old and some are age-invariant. Temporally, some diseases have little variation in prevalence, some have predictable seasonal shifts and others exhibit violent epidemics that may be regular or irregular in their timing. Models and ‘models-with-data’ have proved invaluable for understanding and predicting this diversity, and thence help improve intervention and control. Using mathematical models to understand infectious disease dynamics has a very rich history in epidemiology. The field has seen broad expansions of theories as well as a surge in real-life application of mathematics to dynamics and control of infectious disease. The chapters of Epidemics: Models and Data using R have been organized in a reasonably logical way: Chapters 1-10 is a mix and match of models, data and statistics pertaining to local disease dynamics; Chapters 11-13 pertains to spatial and spatiotemporal dynamics; Chapter 14 highlights similarities between the dynamics of infectious disease and parasitoid-host dynamics; Finally, Chapters 15 and 16 overview additional statistical methodology useful in studies of infectious disease dynamics. This book can be used as a guide for working with data, models and ‘models-and-data’ to understand epidemics and infectious disease dynamics in space and time.

Networks have permeated everyday life through everyday realities like the Internet, social networks, and viral marketing. As such, network analysis is an important growth area in the quantitative sciences, with roots in social network analysis going back to the 1930s and graph theory going back centuries. Measurement and analysis are integral components of network research. As a result, statistical methods play a critical role in network analysis. This book is the first of its kind in network research. It can be used as a stand-alone resource in which multiple R packages are used to illustrate how to conduct a wide range of network analyses, from basic manipulation and visualization, to summary and characterization, to modeling of network data. The central package is igraph, which provides extensive capabilities for studying network graphs in R. This text builds on Eric D. Kolaczyk’s book Statistical Analysis of Network Data (Springer, 2009).

The 2nd edition of R for Marketing Research and Analytics continues to be the best place to learn R for marketing research. This book is a complete introduction to the power of R for marketing research practitioners. The text describes statistical models from a conceptual point of view with a minimal amount of mathematics, presuming only an introductory knowledge of statistics. Hands-on chapters accelerate the learning curve by asking readers to interact with R from the beginning. Core topics include the R language, basic statistics, linear modeling, and data visualization, which is presented throughout as an integral part of analysis. Later chapters cover more advanced topics yet are intended to be approachable for all analysts. These sections examine logistic regression, customer segmentation, hierarchical linear modeling, market basket analysis, structural equation modeling, and conjoint analysis in R. The text uniquely presents Bayesian models with a minimally complex approach, demonstrating and explaining Bayesian methods alongside traditional analyses for analysis of variance, linear models, and metric and choice-based conjoint analysis. With its emphasis on data visualization, model assessment, and development of statistical intuition, this book provides guidance for any analyst looking to develop or improve skills in R for marketing applications. The 2nd edition increases the book’s utility for students and instructors with the inclusion of exercises and classroom slides. At the same time, it retains all of the features that make it a vital resource for practitioners: non-mathematical exposition, examples modeled on real world marketing problems, intuitive guidance on research methods, and immediately applicable code. 

This new edition of Numerical Ecology with R guides readers through an applied exploration of the major methods of multivariate data analysis, as seen through the eyes of three ecologists. It provides a bridge between a textbook of numerical ecology and the implementation of this discipline in the R language. The book begins by examining some exploratory approaches. It proceeds logically with the construction of the key building blocks of most methods, i.e. association measures and matrices, and then submits example data to three families of approaches: clustering, ordination and canonical ordination. The last two chapters make use of these methods to explore important and contemporary issues in ecology: the analysis of spatial structures and of community diversity. The aims of methods thus range from descriptive to explanatory and predictive and encompass a wide variety of approaches that should provide readers with an extensive toolbox that can address a wide palette of questions arising in contemporary multivariate ecological analysis. The second edition of this book features a complete revision to the R code and offers improved procedures and more diverse applications of the major methods. It also highlights important changes in the methods and expands upon topics such as multiple correspondence analysis, principal response curves and co-correspondence analysis. New features include the study of relationships between species traits and the environment, and community diversity analysis. This book is aimed at professional researchers, practitioners, graduate students and teachers in ecology, environmental science and engineering, and in related fields such as oceanography, molecular ecology, agriculture and soil science, who already have a background in general and multivariate statistics and wish to apply this knowledge to their data using the R language, as well as people willing to accompany their disciplinary learning with practical applications. People from other fields (e.g. geology, geography, paleoecology, phylogenetics, anthropology, the social and education sciences, etc.) may also benefit from the materials presented in this book. Users are invited to use this book as a teaching companion at the computer. All the necessary data files, the scripts used in the chapters, as well as extra R functions and packages written by the authors of the book, are available online (URL: http://adn.biol.umontreal.ca/~numericalecology/numecolR/).

Today, information technology plays a pivotal role in financial control and audit: most financial data is now digitally recorded and dispersed among servers, clouds and networks over which the audited firm has no control. Additionally, a firm’s data—particularly in the case of finance, software, insurance and biotech firms— comprises most of the audited value of the firm. Financial audits are critical mechanisms for ensuring the integrity of information systems and the reporting of organizational finances. They help avoid the abuses that led to passage of legislation such as the Foreign Corrupt Practices Act (1977), and the Sarbanes-Oxley Act (2002). Audit effectiveness has declined over the past two decades as auditor skillsets have failed to keep up with advances in information technology. Information and communication technology lie at the core of commerce today and are integrated in business processes around the world. This book is designed to meet the increasing need ofaudit professionals to understand information technology and the controls required to manage it. The material included focuses on the requirements for annual Securities and Exchange Commission audits (10-K) for listed corporations. These represent the benchmark auditing procedures for specialized audits, such as internal, governmental, and attestation audits. Using R and RStudio, the book demonstrates how to render an audit opinion that is legally and statistically defensible; analyze, extract, and manipulate accounting data; build a risk assessment matrix to inform the conduct of a cost-effective audit program; and more.

This book is a complete introduction to the power of R for marketing research practitioners. The text describes statistical models from a conceptual point of view with a minimal amount of mathematics, presuming only an introductory knowledge of statistics. Hands-on chapters accelerate the learning curve by asking readers to interact with R from the beginning. Core topics include the R language, basic statistics, linear modeling, and data visualization, which is presented throughout as an integral part of analysis. Later chapters cover more advanced topics yet are intended to be approachable for all analysts. These sections examine logistic regression, customer segmentation, hierarchical linear modeling, market basket analysis, structural equation modeling, and conjoint analysis in R. The text uniquely presents Bayesian models with a minimally complex approach, demonstrating and explaining Bayesian methods alongside traditional analyses for analysis of variance, linear models, and metric and choice-based conjoint analysis. With its emphasis on data visualization, model assessment, and development of statistical intuition, this book provides guidance for any analyst looking to develop or improve skills in R for marketing applications.

Sound is almost always around us, anywhere, at any time, reaching our ears and stimulating our brains for better or worse. Sound can be the disturbing noise of a drill, a merry little tune sung by a friend, the song of a bird in the morning or a clap of thunder at night. The science of sound, or acoustics, studies all types of sounds and therefore covers a wide range of scientific disciplines, from pure to applied acoustics. Research dealing with acoustics requires a sound to be recorded, analyzed, manipulated and, possibly, changed. This is particularly, but not exclusively, the case in bioacoustics and ecoacoustics, two life sciences disciplines that attempt to understand and to eavesdrop on the sound produced by animals. Sound analysis and synthesis can be challenging for students, researchers and practitioners who have few skills in mathematics or physics. However, deciphering the structure of a sound can be useful in behavioral and ecological research – and also very amusing. This book is dedicated to anyone who wants to practice acoustics but does not know much about sound. Acoustic analysis and synthesis are possible, with little effort, using the free and open-source software R with a few specific packages. Combining a bit of theory, a lot of step-by-step examples and a few cases studies, this book shows beginners and experts alike how to record, read, play, decompose, visualize, parametrize, change, and synthesize sound with R, opening a new way of working in bioacoustics and ecoacoustics but also in other acoustic disciplines.

This book provides computational tools that readers can use to flourish in the retirement income industry. Each chapter describes recipe-like algorithms and explains how to implement them via simple scripts in the freely available R coding language. Students can use those skills to generate quantitative answers to the most common questions in retirement income planning, as well as to develop a deeper understanding of the finance and economics underlying the field itself. The book will be an excellent asset for experienced students who are interested in advanced wealth management, and specifically within courses that focus on holistic modeling of the retirement income process. The material will also be useful to current and future wealth management professionals within the financial services industry. Readers should have a solid understanding of financial principles, as well as a rudimentary background in economics and accounting. 

This book introduces the main theoretical findings related to copulas and shows how statistical modeling of multivariate continuous distributions using copulas can be carried out in the R statistical environment with the package copula (among others).  Copulas are multivariate distribution functions with standard uniform univariate margins. They are increasingly applied to modeling dependence among random variables in fields such as risk management, actuarial science, insurance, finance, engineering, hydrology, climatology, and meteorology, to name a few. In the spirit of the Use R! series, each chapter combines key theoretical definitions or results with illustrations in R. Aimed at statisticians, actuaries, risk managers, engineers and environmental scientists wanting to learn about the theory and practice of copula modeling using R without an overwhelming amount of mathematics, the book can also be used for teaching a course on copula modeling.

The practice of business is changing. More and more companies are amassing larger and larger amounts of data, and storing them in bigger and bigger data bases. Consequently, successful applications of data-driven decision making are plentiful and increasing on a daily basis. This book will motivate the need for data and data-driven solutions, using real data from real business scenarios. It will allow managers to better interact with personnel specializing in analytics by exposing managers and decision makers to the key ideas and concepts of data-driven decision making. Business Analytics for Managers conveys ideas and concepts from both statistics and data mining with the goal of extracting knowledge from real business data and actionable insight for managers. Throughout, emphasis placed on conveying data-driven thinking.  While the ideas discussed in this book can be implemented using many different software solutions from many different vendors, it also provides a quick-start to one of the most powerful software solutions available. The main goals of this book are as follows: to excite managers and decision makers about the potential that resides in data and the value that data analytics can add to business processes and provide managers with a basic understanding of the main concepts of data analytics and a common language to convey data-driven decision problems so they can better communicate with personnel specializing in data mining or statistics.

This comprehensive and richly illustrated volume provides up-to-date material on Singular Spectrum Analysis (SSA). SSA is a well-known methodology for the analysis and forecasting of time series. Since quite recently, SSA is also being used to analyze digital images and other objects that are not necessarily of planar or rectangular form and may contain gaps. SSA is multi-purpose and naturally combines both model-free and parametric techniques, which makes it a very special and attractive methodology for solving a wide range of problems arising in diverse areas, most notably those associated with time series and digital images. An effective, comfortable and accessible implementation of SSA is provided by the R-package Rssa, which is available from CRAN and reviewed in this book. Written by prominent statisticians who have extensive experience with SSA, the book (a) presents the up-to-date SSA methodology, including multidimensional extensions, in language accessible to a large circle of users, (b) combines different versions of SSA into a single tool, (c) shows the diverse tasks that SSA can be used for, (d) formally describes the main SSA methods and algorithms, and (e) provides tutorials on the Rssa package and the use of SSA. The book offers a valuable resource for a very wide readership, including professional statisticians, specialists in signal and image processing, as well as specialists in numerous applied disciplines interested in using statistical methods for time series analysis, forecasting, signal and image processing. The book is written on a level accessible to a broad audience and includes a wealth of examples; hence it can also be used as a textbook for undergraduate and postgraduate courses on time series analysis and signal processing.

This book offers an application-oriented guide to random forests: a statistical learning method extensively used in many fields of application, thanks to its excellent predictive performance, but also to its flexibility, which places few restrictions on the nature of the data used. Indeed, random forests can be adapted to both supervised classification problems and regression problems. In addition, they allow us to consider qualitative and quantitative explanatory variables together, without pre-processing. Moreover, they can be used to process standard data for which the number of observations is higher than the number of variables, while also performing very well in the high dimensional case, where the number of variables is quite large in comparison to the number of observations. Consequently, they are now among the preferred methods in the toolbox of statisticians and data scientists. The book is primarily intended for students in academic fields such as statistical education, but also for practitioners in statistics and machine learning. A scientific undergraduate degree is quite sufficient to take full advantage of the concepts, methods, and tools discussed. In terms of computer science skills, little background knowledge is required, though an introduction to the R language is recommended. Random forests are part of the family of tree-based methods; accordingly, after an introductory chapter, Chapter 2 presents CART trees. The next three chapters are devoted to random forests. They focus on their presentation (Chapter 3), on the variable importance tool (Chapter 4), and on the variable selection problem (Chapter 5), respectively. After discussing the concepts and methods, we illustrate their implementation on a running example. Then, various complements are provided before examining additional examples. Throughout the book, each result is given together with the code (in R) that can be used to reproduce it. Thus, the book offers readersessential information and concepts, together with examples and the software tools needed to analyse data using random forests. 

The new edition of this book provides an easily accessible introduction to the statistical analysis of network data using R. It has been fully revised and can be used as a stand-alone resource in which multiple R packages are used to illustrate how to conduct a wide range of network analyses, from basic manipulation and visualization, to summary and characterization, to modeling of network data. The central package is igraph, which provides extensive capabilities for studying network graphs in R. The new edition of this book includes an overhaul to recent changes in igraph. The material in this book is organized to flow from descriptive statistical methods to topics centered on modeling and inference with networks, with the latter separated into two sub-areas, corresponding first to the modeling and inference of networks themselves, and then, to processes on networks.  The book begins by covering tools for the manipulation of network data. Next, it addresses visualizationand characterization of networks. The book then examines mathematical and statistical network modeling. This is followed by a special case of network modeling wherein the network topology must be inferred. Network processes, both static and dynamic are addressed in the subsequent chapters. The book concludes by featuring chapters on network flows, dynamic networks, and networked experiments. Statistical Analysis of Network Data with R, 2nd Ed. has been written at a level aimed at graduate students and researchers in quantitative disciplines engaged in the statistical analysis of network data, although advanced undergraduates already comfortable with R should find the book fairly accessible as well.