About this Book

If you picked up this book, you probably have some data that you need to collect, summarize, transform, explore, model, visualize, or present. If so, then R is for you! R has become the world-wide language for statistics, predictive analytics, and data visualization. It offers the widest range available of methodologies for understanding data, from the most basic to the most complex and bleeding edge.

As an open source project it’s freely available for a range of platforms, including Windows, Mac OS X, and Linux. It’s under constant development, with new procedures added daily. Additionally, R is supported by a large and diverse community of data scientists and programmers who gladly offer their help and advice to users.

Although R is probably best known for its ability to create beautiful and sophisticated graphs, it can handle just about any statistical problem. The base installation provides hundreds of data-management, statistical, and graphical functions out of the box. But some of its most powerful features come from the thousands of extensions (packages) provided by contributing authors.

This breadth comes at a price. It can be hard for new users to get a handle on what R is and what it can do. Even the most experienced R user is surprised to learn about features they were unaware of.

R in Action provides you with a guided introduction to R, giving you a 2,000-foot view of the platform and its capabilities. It will introduce you to the most important functions in the base installation and more than 90 of the most useful contributed packages. Throughout the book, the goal is practical application—how you can make sense of your data and communicate that understanding to others. When you finish, you should have a good grasp of how R works and what it can do, and where you can go to learn more. You’ll be able to apply a variety of techniques for visualizing data, and you’ll have the skills to tackle both basic and advanced data analytic problems.

Who should read this book

R in Action should appeal to anyone who deals with data. No background in statistical programming or the R language is assumed. Although the book is accessible to novices, there should be enough new and practical material to satisfy even experienced R mavens.

Users without a statistical background who want to use R to manipulate, summarize, and graph data should find chapters 1–6, 11, and 16 easily accessible. Chapter 7 and 10 assume a one-semester course in statistics; and readers of chapters 8, 9, and 12–15 will benefit from two semesters of statistics. But I have tried to write each chapter in such a way that both beginning and expert data analysts will find something interesting and useful.

Roadmap

This book is designed to give you a guided tour of the R platform, with a focus on those methods most immediately applicable for manipulating, visualizing, and understanding data. There are 16 chapters divided into 4 parts: “Getting started,” “Basic methods,” “Intermediate methods,” and “Advanced methods.” Additional topics are covered in eight appendices.

Chapter 1 begins with an introduction to R and the features that make it so useful as a data-analysis platform. The chapter covers how to obtain the program and how to enhance the basic installation with extensions that are available online. The remainder of the chapter is spent exploring the user interface and learning how to run programs interactively and in batches.

Chapter 2 covers the many methods available for getting data into R. The first half of the chapter introduces the data structures R uses to hold data, and how to enter data from the keyboard. The second half discusses methods for importing data into R from text files, web pages, spreadsheets, statistical packages, and databases.

Many users initially approach R because they want to create graphs, so we jump right into that topic in chapter 3. No waiting required. We review methods of creating graphs, modifying them, and saving them in a variety of formats.

Chapter 4 covers basic data management, including sorting, merging, and subsetting datasets, and transforming, recoding, and deleting variables.

Building on the material in chapter 4, chapter 5 covers the use of functions (mathematical, statistical, character) and control structures (looping, conditional execution) for data management. We then discuss how to write your own R functions and how to aggregate data in various ways.

Chapter 6 demonstrates methods for creating common univariate graphs, such as bar plots, pie charts, histograms, density plots, box plots, and dot plots. Each is useful for understanding the distribution of a single variable.

Chapter 7 starts by showing how to summarize data, including the use of descriptive statistics and cross-tabulations. We then look at basic methods for understanding relationships between two variables, including correlations, t-tests, chi-square tests, and nonparametric methods.

Chapter 8 introduces regression methods for modeling the relationship between a numeric outcome variable and a set of one or more numeric predictor variables. Methods for fitting these models, evaluating their appropriateness, and interpreting their meaning are discussed in detail.

Chapter 9 considers the analysis of basic experimental designs through the analysis of variance and its variants. Here we are usually interested in how treatment combinations or conditions affect a numerical outcome variable. Methods for assessing the appropriateness of the analyses and visualizing the results are also covered.

A detailed treatment of power analysis is provided in chapter 10. Starting with a discussion of hypothesis testing, the chapter focuses on how to determine the sample size necessary to detect a treatment effect of a given size with a given degree of confidence. This can help you to plan experimental and quasi-experimental studies that are likely to yield useful results.

Chapter 11 expands on the material in chapter 5, covering the creation of graphs that help you to visualize relationships among two or more variables. This includes various types of 2D and 3D scatter plots, scatter-plot matrices, line plots, correlograms, and mosaic plots.

Chapter 12 presents analytic methods that work well in cases where data are sampled from unknown or mixed distributions, where sample sizes are small, where outliers are a problem, or where devising an appropriate test based on a theoretical distribution is too complex and mathematically intractable. They include both resampling and bootstrapping approaches—computer-intensive methods that are easily implemented in R.

Chapter 13 expands on the regression methods in chapter 8 to cover data that are not normally distributed. The chapter starts with a discussion of generalized linear models and then focuses on cases where you’re trying to predict an outcome variable that is either categorical (logistic regression) or a count (Poisson regression).

One of the challenges of multivariate data problems is simplification. Chapter 14 describes methods of transforming a large number of correlated variables into a smaller set of uncorrelated variables (principal component analysis), as well as methods for uncovering the latent structure underlying a given set of variables (factor analysis). The many steps involved in an appropriate analysis are covered in detail.

In keeping with our attempt to present practical methods for analyzing data, chapter 15 considers modern approaches to the ubiquitous problem of missing data values. R supports a number of elegant approaches for analyzing datasets that are incomplete for various reasons. Several of the best are described here, along with guidance for which ones to use when and which ones to avoid.

Chapter 16 wraps up the discussion of graphics with presentations of some of R’s most advanced and useful approaches to visualizing data. This includes visual representations of very complex data using lattice graphs, an introduction to the new ggplot2 package, and a review of methods for interacting with graphs in real time.

The afterword points you to many of the best internet sites for learning more about R, joining the R community, getting questions answered, and staying current with this rapidly changing product.

Last, but not least, the eight appendices (A through H) extend the text’s coverage to include such useful topics as R graphic user interfaces, customizing and upgrading an R installation, exporting data to other applications, creating publication quality output, using R for matrix algebra (à la MATLAB), and working with very large datasets.

The examples

In order to make this book as broadly applicable as possible, I have chosen examples from a range of disciplines, including psychology, sociology, medicine, biology, business, and engineering. None of these examples require a specialized knowledge of that field.

The datasets used in these examples were selected because they pose interesting questions and because they’re small. This allows you to focus on the techniques described and quickly understand the processes involved. When you’re learning new methods, smaller is better.

The datasets are either provided with the base installation of R or available through add-on packages that are available online. The source code for each example is available from www.manning.com/RinAction. To get the most out of this book, I recommend that you try the examples as you read them.

Finally, there is a common maxim that states that if you ask two statisticians how to analyze a dataset, you’ll get three answers. The flip side of this assertion is that each answer will move you closer to an understanding of the data. I make no claim that a given analysis is the best or only approach to a given problem. Using the skills taught in this text, I invite you to play with the data and see what you can learn. R is interactive, and the best way to learn is to experiment.

Code conventions

The following typographical conventions are used throughout this book:

• A monospaced font is used for code listings that should be typed as is.
• A monospaced font is also used within the general text to denote code words or previously defined objects.
• Italics within code listings indicate placeholders. You should replace them with appropriate text and values for the problem at hand. For example, path_to_my_ file would be replaced with the actual path to a file on your computer.
• R is an interactive language that indicates readiness for the next line of user input with a prompt (> by default). Many of the listings in this book capture interactive sessions. When you see code lines that start with >, don’t type the prompt.
• Code annotations are used in place of inline comments (a common convention in Manning books). Additionally, some annotations appear with numbered bullets like that refer to explanations appearing later in the text.
• To save room or make text more legible, the output from interactive sessions may include additional white space or omit text that is extraneous to the point under discussion.

Author Online

Purchase of R in Action includes free access to a private web forum run by Manning Publications where you can make comments about the book, ask technical questions, and receive help from the author and from other users. To access the forum and subscribe to it, point your web browser to www.manning.com/RinAction. This page provides information on how to get on the forum once you’re registered, what kind of help is available, and the rules of conduct on the forum.

Manning’s commitment to our readers is to provide a venue where a meaningful dialog between individual readers and between readers and the author can take place. It isn’t a commitment to any specific amount of participation on the part of the author, whose contribution to the AO forum remains voluntary (and unpaid). We suggest you try asking the authors some challenging questions, lest his interest stray!

The AO forum and the archives of previous discussions will be accessible from the publisher’s website as long as the book is in print.

About the author

Dr. Robert Kabacoff is Vice President of Research for Management Research Group, an international organizational development and consulting firm. He has more than 20 years of experience providing research and statistical consultation to organizations in health care, financial services, manufacturing, behavioral sciences, government, and academia. Prior to joining MRG, Dr. Kabacoff was a professor of psychology at Nova Southeastern University in Florida, where he taught graduate courses in quantitative methods and statistical programming. For the past two years, he has managed Quick-R, an R tutorial website.