# R语言实战 (R in Action)英文版

MANNING Robert I. Kabacoff Data analysis and graphics with R IN ACTION R in Action Download from Wow! eBook R in Action Data analysis and graphics with R ROBERT I. KABACOFF MANNING Shelter Island Download from Wow! eBook For online information and ordering of this and other Manning books, please visit www.manning.com. The publisher offers discounts on this book when ordered in quantity. For more information, please contact Special Sales Department Manning Publications Co. 20 Baldwin Road PO Box 261 Shelter Island, NY 11964 Email: orders@manning.com ©2011 by Manning Publications Co. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by means electronic, mechanical, photocopying, or otherwise, without prior written permission of the publisher. Many of the designations used by manufacturers and sellers to distinguish their products are claimed as trademarks. Where those designations appear in the book, and Manning Publications was aware of a trademark claim, the designations have been printed in initial caps or all caps. Recognizing the importance of preserving what has been written, it is Manning’s policy to have the books we publish printed on acid-free paper, and we exert our best efforts to that end. Recognizing also our responsibility to conserve the resources of our planet, Manning books are printed on paper that is at least 15 percent recycled and processed without the use of elemental chlorine. Manning Publications Co. Development editor: Sebastian Stirling 20 Baldwin Road Copyeditor: Liz Welch PO Box 261 Typesetter: Composure Graphics Shelter Island, NY 11964 Cover designer: Marija Tudor ISBN: 9781935182399 Printed in the United States of America 1 2 3 4 5 6 7 8 9 10 -- MAL -- 16 15 14 13 12 11 Download from Wow! eBook v brief contents Part I Getting started ..........................................1 1 ■ Introduction to R 3 2 ■ Creating a dataset 21 3 ■ Getting started with graphs 45 4 ■ Basic data management 73 5 ■ Advanced data management 91 Part II Basic methods ........................................ 117 6 ■ Basic graphs 119 7 ■ Basic statistics 141 Part III Intermediate methods ......................... 171 8 ■ Regression 173 9 ■ Analysis of variance 219 10 ■ Power analysis 246 11 ■ Intermediate graphs 263 12 ■ Resampling statistics and bootstrapping 291 Download from Wow! eBook vi BRIEF CONTENTS Part IV Advanced methods ...................................311 13 ■ Generalized linear models 313 14 ■ Principal components and factor analysis 331 15 ■ Advanced methods for missing data 352 16 ■ Advanced graphics 373 Download from Wow! eBook vii contents preface xv acknowledgments xvii about this book xix about the cover illustration xxiv Part I Getting started .............................................1 1 Introduction to R 3 1.1 Why use R? 5 1.2 Obtaining and installing R 7 1.3 Working with R 7 Getting started 8 ■ Getting help 11 ■ The workspace 11 Input and output 13 1.4 Packages 14 What are packages? 15 ■ Installing a package 16 Loading a package 16 ■ Learning about a package 16 1.5 Batch processing 17 1.6 Using output as input—reusing results 18 1.7 Working with large datasets 18 Download from Wow! eBook viii CONTENTS 1.8 Working through an example 18 1.9 Summary 20 2 Creating a dataset 21 2.1 Understanding datasets 22 2.2 Data structures 23 Vectors 24 ■ Matrices 24 ■ Arrays 26 ■ Data frames 27 Factors 30 ■ Lists 32 2.3 Data input 33 Entering data from the keyboard 34 ■ Importing data from a delimited text file 35 ■ Importing data from Excel 36 ■ Importing data from XML 37 Webscraping 37 ■ Importing data from SPSS 38 ■ Importing data from SAS 38 Importing data from Stata 38 ■ Importing data from netCDF 39 Importing data from HDF5 39 ■ Accessing database management systems (DBMSs) 39 ■ Importing data via Stat/Transfer 41 2.4 Annotating datasets 42 Variable labels 42 ■ Value labels 42 2.5 Useful functions for working with data objects 42 2.6 Summary 43 3 Getting started with graphs 45 3.1 Working with graphs 46 3.2 A simple example 48 3.3 Graphical parameters 49 Symbols and lines 50 ■ Colors 52 ■ Text characteristics 53 Graph and margin dimensions 54 3.4 Adding text, customized axes, and legends 56 Titles 57 ■ Axes 57 ■ Reference lines 60 ■ Legend 60 Text annotations 62 3.5 Combining graphs 65 Creating a figure arrangement with fine control 69 3.6 Summary 71 4 Basic data management 73 4.1 A working example 73 4.2 Creating new variables 75 4.3 Recoding variables 76 Download from Wow! eBook CONTENTS ix 4.4 Renaming variables 78 4.5 Missing values 79 Recoding values to missing 80 ■ Excluding missing values from analyses 80 4.6 Date values 81 Converting dates to character variables 83 ■ Going further 83 4.7 Type conversions 83 4.8 Sorting data 84 4.9 Merging datasets 85 Adding columns 85 ■ Adding rows 85 4.10 Subsetting datasets 86 Selecting (keeping) variables 86 ■ Excluding (dropping) variables 86 Selecting observations 87 ■ The subset() function 88 ■ Random samples 89 4.11 Using SQL statements to manipulate data frames 89 4.12 Summary 90 5 Advanced data management 91 5.1 A data management challenge 92 5.2 Numerical and character functions 93 Mathematical functions 93 ■ Statistical functions 94 ■ Probability functions 96 Character functions 99 ■ Other useful functions 101 ■ Applying functions to matrices and data frames 102 5.3 A solution for our data management challenge 103 5.4 Control ﬂow 107 Repetition and looping 107 ■ Conditional execution 108 5.5 User-written functions 109 5.6 Aggregation and restructuring 112 Transpose 112 ■ Aggregating data 112 ■ The reshape package 113 5.7 Summary 116 Part II Basic methods ............................................117 6 Basic graphs 119 6.1 Bar plots 120 Simple bar plots 120 ■ Stacked and grouped bar plots 121 ■ Mean bar plots 122 Tweaking bar plots 123 ■ Spinograms 124 6.2 Pie charts 125 6.3 Histograms 128 Download from Wow! eBook x CONTENTS 6.4 Kernel density plots 130 6.5 Box plots 133 Using parallel box plots to compare groups 134 ■ Violin plots 137 6.6 Dot plots 138 6.7 Summary 140 7 Basic statistics 141 7.1 Descriptive statistics 142 A menagerie of methods 142 ■ Descriptive statistics by group 146 Visualizing results 149 7.2 Frequency and contingency tables 149 Generating frequency tables 150 ■ Tests of independence 156 Measures of association 157 ■ Visualizing results 158 Converting tables to flat files 158 7.3 Correlations 159 Types of correlations 160 ■ Testing correlations for significance 162 Visualizing correlations 164 7.4 t-tests 164 Independent t-test 164 ■ Dependent t-test 165 ■ When there are more than two groups 166 7.5 Nonparametric tests of group differences 166 Comparing two groups 166 ■ Comparing more than two groups 168 7.6 Visualizing group differences 170 7.7 Summary 170 Part III Intermediate methods ............................171 8 Regression 173 8.1 The many faces of regression 174 Scenarios for using OLS regression 175 ■ What you need to know 176 8.2 OLS regression 177 Fitting regression models with lm() 178 ■ Simple linear regression 179 Polynomial regression 181 ■ Multiple linear regression 184 Multiple linear regression with interactions 186 8.3 Regression diagnostics 188 A typical approach 189 ■ An enhanced approach 192 ■ Global validation of linear model assumption 199 ■ Multicollinearity 199 8.4 Unusual observations 200 Outliers 200 ■ High leverage points 201 ■ Influential observations 202 Download from Wow! eBook CONTENTS xi 8.5 Corrective measures 205 Deleting observations 205 ■ Transforming variables 205 ■ Adding or deleting variables 207 ■ Trying a different approach 207 8.6 Selecting the “best” regression model 207 Comparing models 208 ■ Variable selection 209 8.7 Taking the analysis further 213 Cross-validation 213 ■ Relative importance 215 8.8 Summary 218 9 Analysis of variance 219 9.1 A crash course on terminology 220 9.2 Fitting ANOVA models 222 The aov() function 222 ■ The order of formula terms 223 9.3 One-way ANOVA 225 Multiple comparisons 227 ■ Assessing test assumptions 229 9.4 One-way ANCOVA 230 Assessing test assumptions 232 ■ Visualizing the results 232 9.5 Two-way factorial ANOVA 234 9.6 Repeated measures ANOVA 237 9.7 Multivariate analysis of variance (MANOVA) 239 Assessing test assumptions 241 ■ Robust MANOVA 242 9.8 ANOVA as regression 243 9.9 Summary 245 10 Power analysis 246 10.1 A quick review of hypothesis testing 247 10.2 Implementing power analysis with the pwr package 249 t-tests 250 ■ ANOVA 252 ■ Correlations 253 ■ Linear models 253 Tests of proportions 254 ■ Chi-square tests 255 ■ Choosing an appropriate effect size in novel situations 257 10.3 Creating power analysis plots 258 10.4 Other packages 260 10.5 Summary 261 11 Intermediate graphs 263 11.1 Scatter plots 264 Scatter plot matrices 267 ■ High-density scatter plots 271 ■ 3D scatter plots 274 Bubble plots 278 Download from Wow! eBook xii CONTENTS 11.2 Line charts 280 11.3 Correlograms 283 11.4 Mosaic plots 288 11.5 Summary 290 12 Resampling statistics and bootstrapping 291 12.1 Permutation tests 292 12.2 Permutation test with the coin package 294 Independent two-sample and k-sample tests 295 ■ Independence in contingency tables 296 ■ Independence between numeric variables 297 Dependent two-sample and k-sample tests 297 ■ Going further 298 12.3 Permutation tests with the lmPerm package 298 Simple and polynomial regression 299 ■ Multiple regression 300 One-way ANOVA and ANCOVA 301 ■ Two-way ANOVA 302 12.4 Additional comments on permutation tests 302 12.5 Bootstrapping 303 12.6 Bootstrapping with the boot package 304 Bootstrapping a single statistic 305 ■ Bootstrapping several statistics 307 12.7 Summary 309 Part IV Advanced methods ...................................311 13 Generalized linear models 313 13.1 Generalized linear models and the glm() function 314 The glm() function 315 ■ Supporting functions 316 ■ Model fit and regression diagnostics 317 13.2 Logistic regression 317 Interpreting the model parameters 320 ■ Assessing the impact of predictors on the probability of an outcome 321 ■ Overdispersion 322 ■ Extensions 323 13.3 Poisson regression 324 Interpreting the model parameters 326 ■ Overdispersion 327 ■ Extensions 328 13.4 Summary 330 14 Principal components and factor analysis 331 14.1 Principal components and factor analysis in R 333 14.2 Principal components 334 Selecting the number of components to extract 335 Download from Wow! eBook CONTENTS xiii Extracting principal components 336 ■ Rotating principal components 339 Obtaining principal components scores 341 14.3 Exploratory factor analysis 342 Deciding how many common factors to extract 343 ■ Extracting common factors 344 ■ Rotating factors 345 ■ Factor scores 349 ■ Other EFA-related packages 349 14.4 Other latent variable models 349 14.5 Summary 350 15 Advanced methods for missing data 352 15.1 Steps in dealing with missing data 353 15.2 Identifying missing values 355 15.3 Exploring missing values patterns 356 Tabulating missing values 357 ■ Exploring missing data visually 357 ■ Using correlations to explore missing values 360 15.4 Understanding the sources and impact of missing data 362 15.5 Rational approaches for dealing with incomplete data 363 15.6 Complete-case analysis (listwise deletion) 364 15.7 Multiple imputation 365 15.8 Other approaches to missing data 370 Pairwise deletion 370 ■ Simple (nonstochastic) imputation 371 15.9 Summary 371 16 Advanced graphics 373 16.1 The four graphic systems in R 374 16.2 The lattice package 375 Conditioning variables 379 ■ Panel functions 381 ■ Grouping variables 383 Graphic parameters 387 ■ Page arrangement 388 16.3 The ggplot2 package 390 16.4 Interactive graphs 394 Interacting with graphs: identifying points 394 ■ playwith 394 latticist 396 ■ Interactive graphics with the iplots package 397 ■ rggobi 399 16.5 Summary 399 afterword Into the rabbit hole 400 Download from Wow! eBook xiv CONTENTS appendix A Graphic user interfaces 403 appendix B Customizing the startup environment 406 appendix C Exporting data from R 408 appendix D Creating publication-quality output 410 appendix E Matrix Algebra in R 419 appendix F Packages used in this book 421 appendix G Working with large datasets 429 appendix H Updating an R installation 432 index 435 Download from Wow! eBook xv preface What is the use of a book, without pictures or conversations? —Alice, Alice in Wonderland It’s wondrous, with treasures to satiate desires both subtle and gross; but it’s not for the timid. —Q, “Q Who?” Stark Trek: The Next Generation When I began writing this book, I spent quite a bit of time searching for a good quote to start things off. I ended up with two. R is a wonderfully flexible platform and language for exploring, visualizing, and understanding data. I chose the quote from Alice in Wonderland to capture the flavor of statistical analysis today—an in- teractive process of exploration, visualization, and interpretation. The second quote reflects the generally held notion that R is difficult to learn. What I hope to show you is that is doesn’t have to be. R is broad and powerful, with so many analytic and graphic functions available (more than 50,000 at last count) that it easily intimidates both novice and experienced users alike. But there is rhyme and reason to the apparent madness. With guidelines and instructions, you can navigate the tremendous resources available, selecting the tools you need to accomplish your work with style, elegance, efficiency—and more than a little coolness. I first encountered R several years ago, when applying for a new statistical consulting position. The prospective employer asked in the pre-interview material if I was conversant in R. Following the standard advice of recruiters, I immediately said yes, and set off to learn it. I was an experienced statistician and researcher, had Download from Wow! eBook xvi PREFACE 25 years experience as an SAS and SPSS programmer, and was fluent in a half dozen programming languages. How hard could it be? Famous last words. As I tried to learn the language (as fast as possible, with an interview looming), I found either tomes on the underlying structure of the language or dense treatises on specific advanced statistical methods, written by and for subject-matter experts. The online help was written in a Spartan style that was more reference than tutorial. Every time I thought I had a handle on the overall organization and capabilities of R, I found something new that made me feel ignorant and small. To make sense of it all, I approached R as a data scientist. I thought about what it takes to successfully process, analyze, and understand data, including ■ Accessing the data (getting the data into the application from multiple sources) ■ Cleaning the data (coding missing data, fixing or deleting miscoded data, trans- forming variables into more useful formats) ■ Annotating the data (in order to remember what each piece represents) ■ Summarizing the data (getting descriptive statistics to help characterize the data) ■ Visualizing the data (because a picture really is worth a thousand words) ■ Preparing the results (creating publication-quality tables and graphs) Modeling the data (uncovering relationships and testing hypotheses) ■ Then I tried to understand how I could use R to accomplish each of these tasks. Be- cause I learn best by teaching, I eventually created a website (www.statmethods.net) to document what I had learned. Then, about a year ago, Marjan Bace (the publisher) called and asked if I would like to write a book on R. I had already written 50 journal articles, 4 technical manuals, numerous book chapters, and a book on research methodology, so how hard could it be? At the risk of sounding repetitive—famous last words. The book you’re holding is the one that I wished I had so many years ago. I have tried to provide you with a guide to R that will allow you to quickly access the power of this great open source endeavor, without all the frustration and angst. I hope you enjoy it. P.S. I was offered the job but didn’t take it. However, learning R has taken my career in directions that I could never have anticipated. Life can be funny. Download from Wow! eBook xvii acknowledgments A number of people worked hard to make this a better book. They include ■ Marjan Bace, Manning publisher, who asked me to write this book in the first place. ■ Sebastian Stirling, development editor, who spent many hours on the phone with me, helping me organize the material, clarify concepts, and generally make the text more interesting. He also helped me through the many steps to publication. ■ Karen Tegtmeyer, review editor, who helped obtain reviewers and coordinate the review process. ■ Mary Piergies, who helped shepherd this book through the production pro- cess, and her team of Liz Welch, Susan Harkins, and Rachel Schroeder. ■ Pablo Domínguez Vaselli, technical proofreader, who helped uncover areas of confusion and provided an independent and expert eye for testing code. ■ The peer reviewers who spent hours of their own time carefully reading through the material, finding typos and making valuable substantive sug- gestions: Chris Williams, Charles Malpas, Angela Staples, PhD, Daniel Reis Pereira, Dr. D. H. van Rijn, Dr. Christian Marquardt, Amos Folarin, Stuart Jefferys, Dror Berel, Patrick Breen, Elizabeth Ostrowski, PhD, Atef Ouni, Carles Fenollosa, Ricardo Pietrobon, Samuel McQuillin, Landon Cox, Austin Ziegler, Rick Wagner, Ryan Cox, Sumit Pal, Philipp K. Janert, Deepak Vohra, and Sophie Mormede. Download from Wow! eBook ACKNOWLEDGMENTS xviii ■ The many Manning Early Access Program (MEAP) participants who bought the book before it was finished, asked great questions, pointed out errors, and made helpful suggestions. Each contributor has made this a better and more comprehensive book. I would also like to acknowledge the many software authors that have contributed to making R such a powerful data-analytic platform. They include not only the core developers, but also the selfless individuals who have created and maintain contributed packages, extending R’s capabilities greatly. Appendix F provides a list of the authors of contributed packages described in this book. In particular, I would like to mention John Fox, Hadley Wickham, Frank E. Harrell, Jr., Deepayan Sarkar, and William Revelle, whose works I greatly admire. I have tried to represent their contributions accurately, and I remain solely responsible for any errors or distortions inadvertently included in this book. I really should have started this book by thanking my wife and partner, Carol Lynn. Although she has no intrinsic interest in statistics or programming, she read each chapter multiple times and made countless corrections and suggestions. No greater love has any person than to read multivariate statistics for another. Just as important, she suffered the long nights and weekends that I spent writing this book, with grace, support, and affection. There is no logical explanation why I should be this lucky. There are two other people I would like to thank. One is my father, whose love of science was inspiring and who gave me an appreciation of the value of data. The other is Gary K. Burger, my mentor in graduate school. Gary got me interested in a career in statistics and teaching when I thought I wanted to be a clinician. This is all his fault. Download from Wow! eBook xix 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 understand- ing 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 Download from Wow! eBook ABOUT THIS BOOK xx 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 nov- ices, 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 under- standing 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. Download from Wow! eBook ABOUT THIS BOOK xxi 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 Download from Wow! eBook xxii ABOUT THIS BOOK 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, busi- ness, 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. Download from Wow! eBook ABOUT THIS BOOK xxiii ■ 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 q 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 sub- scribe to it, point your web browser to www.manning.com/RinAction. This page pro- vides 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. Download from Wow! eBook xxiv about the cover illustration The figure on the cover of R in Action is captioned “A man from Zadar.” The illustra- tion is taken from a reproduction of an album of Croatian traditional costumes from the mid-nineteenth century by Nikola Arsenovic, published by the Ethnographic Mu- seum in Split, Croatia, in 2003. The illustrations were obtained from a helpful librarian at the Ethnographic Museum in Split, itself situated in the Roman core of the medieval center of the town: the ruins of Emperor Diocletian’s retirement palace from around AD 304. The book includes finely colored illustrations of figures from different regions of Croatia, accompanied by descriptions of the costumes and of everyday life. Zadar is an old Roman-era town on the northern Dalmatian coast of Croatia. It’s over 2,000 years old and served for hundreds of years as an important port on the trading route from Constantinople to the West. Situated on a peninsula framed by small Adriatic islands, the city is picturesque and has become a popular tourist destination with its architectural treasures of Roman ruins, moats, and old stone walls. The figure on the cover wears blue woolen trousers and a white linen shirt, over which he dons a blue vest and jacket trimmed with the colorful embroidery typical for this region. A red woolen belt and cap complete the costume. Dress codes and lifestyles have changed over the last 200 years, and the diversity by region, so rich at the time, has faded away. It’s now hard to tell apart the inhabitants of different continents, let alone of different hamlets or towns separated by only a few miles. Perhaps we have traded cultural diversity for a more varied personal life—certainly for a more varied and fast-paced technological life. Manning celebrates the inventiveness and initiative of the computer business with book covers based on the rich diversity of regional life of two centuries ago, brought back to life by illustrations from old books and collections like this one. Download from Wow! eBook Part 1 Getting started Welcome to R in Action! R is one of the most popular platforms for data analysis and visualization currently available. It is free, open-source software, with versions for Windows, Mac OS X, and Linux operating systems. This book will provide you with the skills needed to master this comprehensive software, and apply it effectively to your own data. The book is divided into four sections. Part I covers the basics of installing the software, learning to navigate the interface, importing data, and massaging it into a useful format for further analysis. Chapter 1 will familiarize you with the R environment. The chapter begins with an overview of R and the features that make it such a powerful platform for modern data analysis. After briefly describing how to obtain and install the software, the user interface is explored through a series of simple examples. Next, you’ll learn how to enhance the functionality of the basic installation with extensions (called contributed packages), that can be freely downloaded from online repositories. The chapter ends with an example that allows you to test your new skills. Once you’re familiar with the R interface, the next challenge is to get your data into the program. In today’s information-rich world, data can come from many sources and in many formats. Chapter 2 covers the wide variety of methods available for importing data into R. The first half of the chapter introduces the data structures R uses to hold data and describes how to input data manually. The second half discusses methods for importing data from text files, web pages, spreadsheets, statistical packages, and databases. Download from Wow! eBook From a workflow point of view, it would probably make sense to discuss data management and data cleaning next. However, many users approach R for the first time out of an interest in its powerful graphics capabilities. Rather than frustrating that interest and keeping you waiting, we dive right into graphics in chapter 3. The chapter reviews methods for creating graphs, customizing them, and saving them in a variety of formats. The chapter describes how to specify the colors, symbols, lines, fonts, axes, titles, labels, and legends used in a graph, and ends with a description of how to combine several graphs into a single plot. Once you’ve had a chance to try out R’s graphics capabilities, it is time to get back to the business of analyzing data. Data rarely comes in a readily usable format. Significant time must often be spent combining data from different sources, cleaning messy data (miscoded data, mismatched data, missing data), and creating new variables (combined variables, transformed variables, recoded variables) before the questions of interest can be addressed. Chapter 4 covers basic data management tasks in R, including sorting, merging, and subsetting datasets, and transforming, recoding, and deleting variables. Chapter 5 builds on the material in chapter 4. It covers the use of numeric (arithmetic, trigonometric, and statistical) and character functions (string subsetting, concatenation, and substitution) in data management. A comprehensive example is used throughout this section to illustrate many of the functions described. Next, control structures (looping, conditional execution) are discussed and you will learn how to write your own R functions. Writing custom functions allows you to extend R’s capabilities by encapsulating many programming steps into a single, flexible function call. Finally, powerful methods for reorganizing (reshaping) and aggregating data are discussed. Reshaping and aggregation are often useful in preparing data for further analyses. After having completed part 1, you will be thoroughly familiar with programming in the R environment. You will have the skills needed to enter and access data, clean it up, and prepare it for further analyses. You will also have experience creating, customizing, and saving a variety of graphs. Download from Wow! eBook 1 3 Introduction to R This chapter covers Installing R■ ■ Understanding the R language Running programs■ How we analyze data has changed dramatically in recent years. With the advent of personal computers and the internet, the sheer volume of data we have available has grown enormously. Companies have terabytes of data on the consumers they interact with, and governmental, academic, and private research institutions have extensive archival and survey data on every manner of research topic. Gleaning information (let alone wisdom) from these massive stores of data has become an industry in itself. At the same time, presenting the information in easily accessible and digestible ways has become increasingly challenging. The science of data analysis (statistics, psychometrics, econometrics, machine learning) has kept pace with this explosion of data. Before personal computers and the internet, new statistical methods were developed by academic researchers who published their results as theoretical papers in professional journals. It could take years for these methods to be adapted by programmers and incorporated into the statistical packages widely available to data analysts. Today, new methodologies appear daily. Statistical researchers publish new and improved methods, along with the code to produce them, on easily accessible websites. Download from Wow! eBook 4 CHAPTER 1 Introduction to R Prepare, explore, and clean data Import Data Fit a stascal model Cross-validate the model Evaluate the model ﬁt Evaluate model predicon on new data Produce report Figure 1.1 Steps in a typical data analysis The advent of personal computers had another effect on the way we analyze data. When data analysis was carried out on mainframe computers, computer time was pre- cious and difficult to come by. Analysts would carefully set up a computer run with all the parameters and options thought to be needed. When the procedure ran, the resulting output could be dozens or hundreds of pages long. The analyst would sift through this output, extracting useful material and discarding the rest. Many popular statistical packages were originally developed during this period and still follow this approach to some degree. With the cheap and easy access afforded by personal computers, modern data analysis has shifted to a different paradigm. Rather than setting up a complete data analysis at once, the process has become highly interactive, with the output from each stage serving as the input for the next stage. An example of a typical analysis is shown in figure 1.1. At any point, the cycles may include transforming the data, imputing missing values, adding or deleting variables, and looping back through the whole process again. The process stops when the analyst believes he or she understands the data intimately and has answered all the relevant questions that can be answered. The advent of personal computers (and especially the availability of high-resolution monitors) has also had an impact on how results are understood and presented. A picture really can be worth a thousand words, and human beings are very adept at extracting useful information from visual presentations. Modern data analysis increasingly relies on graphical presentations to uncover meaning and convey results. To summarize, today’s data analysts need to be able to access data from a wide range of sources (database management systems, text files, statistical packages, and spreadsheets), merge the pieces of data together, clean and annotate them, analyze them with the latest methods, present the findings in meaningful and graphically Download from Wow! eBook Why use R? 5 appealing ways, and incorporate the results into attractive reports that can be distributed to stakeholders and the public. As you’ll see in the following pages, R is a comprehensive software package that’s ideally suited to accomplish these goals. 1.1 Why use R? R is a language and environment for statistical computing and graphics, similar to the S language originally developed at Bell Labs. It’s an open source solution to data analy- sis that’s supported by a large and active worldwide research community. But there are many popular statistical and graphing packages available (such as Microsoft Excel, SAS, IBM SPSS, Stata, and Minitab). Why turn to R? R has many features to recommend it: ■ Most commercial statistical software platforms cost thousands, if not tens of thousands of dollars. R is free! If you’re a teacher or a student, the benefits are obvious. ■ R is a comprehensive statistical platform, offering all manner of data analytic techniques. Just about any type of data analysis can be done in R. ■ R has state-of-the-art graphics capabilities. If you want to visualize complex data, R has the most comprehensive and powerful feature set available. ■ R is a powerful platform for interactive data analysis and exploration. From its inception it was designed to support the approach outlined in figure 1.1. For example, the results of any analytic step can easily be saved, manipulated, and used as input for additional analyses. ■ Getting data into a usable form from multiple sources can be a challenging propo- sition. R can easily import data from a wide variety of sources, including text files, database management systems, statistical packages, and specialized data reposito- ries. It can write data out to these systems as well. ■ R provides an unparalleled platform for programming new statistical methods in an easy and straightforward manner. It’s easily extensible and provides a natural language for quickly programming recently published methods. ■ R contains advanced statistical routines not yet available in other packages. In fact, new methods become available for download on a weekly basis. If you’re a SAS user, imagine getting a new SAS PROC every few days. ■ If you don’t want to learn a new language, a variety of graphic user interfaces (GUIs) are available, offering the power of R through menus and dialogs. ■ R runs on a wide array of platforms, including Windows, Unix, and Mac OS X. It’s likely to run on any computer you might have (I’ve even come across guides for installing R on an iPhone, which is impressive but probably not a good idea). You can see an example of R’s graphic capabilities in figure 1.2. This graph, created with a single line of code, describes the relationships between income, education, and prestige for blue-collar, white-collar, and professional jobs. Technically, it’s a scatter plot matrix with groups displayed by color and symbol, two types of fit lines (linear and Download from Wow! eBook 6 CHAPTER 1 Introduction to R loess), confidence ellipses, and two types of density display (kernel density estimation , and rug plots ). Additionally, the largest outlier in each scatter plot has been automati- cally labeled. If these terms are unfamiliar to you, don’t worry. We’ll cover them in later chapters. For now, trust me that they’re really cool (and that the statisticians reading this are salivating). Basically, this graph indicates the following: ■ Education, income, and job prestige are linearly related. ■ In general, blue-collar jobs involve lower education, income, and prestige, where- as professional jobs involve higher education, income, and prestige. White-collar jobs fall in between. bc prof wc income 20 40 60 80 100 RR.engineer 2 0 4 0 6 0 8 0 minister 2 0 4 0 6 0 8 0 1 0 0 RR.engineer education RR.engineer 20 40 60 80 minister RR.engineer 0 20 40 60 80 100 0 2 0 4 0 6 0 8 0 1 0 0 prestige Figure 1.2 Relationships between income, education, and prestige for blue-collar (bc), white-collar (wc), and professional jobs (prof). Source: car package (scatterplotMatrix function ) written by John Fox. Graphs like this are difficult to create in other statistical programming languages but can be created with a line or two of code in R. Download from Wow! eBook Working with R 7 ■ There are some interesting exceptions. Railroad Engineers have high income and low education. Ministers have high prestige and low income. ■ Education and (to lesser extent) prestige are distributed bi-modally, with more scores in the high and low ends than in the middle. Chapter 8 will have much more to say about this type of graph. The important point is that R allows you to create elegant, informative, and highly customized graphs in a simple and straightforward fashion. Creating similar plots in other statistical languages would be difficult, time consuming, or impossible. Unfortunately, R can have a steep learning curve. Because it can do so much, the documentation and help files available are voluminous. Additionally, because much of the functionality comes from optional modules created by independent contributors, this documentation can be scattered and difficult to locate. In fact, getting a handle on all that R can do is a challenge. The goal of this book is to make access to R quick and easy. We’ll tour the many features of R, covering enough material to get you started on your data, with pointers on where to go when you need to learn more. Let’s begin by installing the program. 1.2 Obtaining and installing R R is freely available from the Comprehensive R Archive Network (CRAN) at http:// cran.r-project.org. Precompiled binaries are available for Linux, Mac OS X, and Win- dows. Follow the directions for installing the base product on the platform of your choice. Later we’ll talk about adding functionality through optional modules called packages (also available from CRAN). Appendix H describes how to update an existing R installation to a newer version. 1.3 Working with R R is a case-sensitive, interpreted language. You can enter commands one at a time at the command prompt (>) or run a set of commands from a source file. There are a wide variety of data types, including vectors, matrices, data frames (similar to datasets), and lists (collections of objects). We’ll discuss each of these data types in chapter 2. Most functionality is provided through built-in and user-created functions, and all data objects are kept in memory during an interactive session. Basic functions are available by default. Other functions are contained in packages that can be attached to a current session as needed. Statements consist of functions and assignments. R uses the symbol <- for assignments, rather than the typical = sign. For example, the statement x <- rnorm(5) creates a vector object named x containing five random deviates from a standard nor- mal distribution. Download from Wow! eBook 8 CHAPTER 1 Introduction to R NOTE R allows the = sign to be used for object assignments. However, you won’t find many programs written that way, because it’s not standard syntax, there are some situations in which it won’t work, and R programmers will make fun of you. You can also reverse the assignment direction. For instance, rnorm(5) -> x is equivalent to the previous statement. Again, doing so is uncommon and isn’t recommended in this book. Comments are preceded by the # symbol . Any text appearing after the # is ignored by the R interpreter. 1.3.1 Getting started If you’re using Windows, launch R from the Start Menu. On a Mac, double-click the R icon in the Applications folder. For Linux, type R at the command prompt of a termi- nal window. Any of these will start the R interface (see figure 1.3 for an example). To get a feel for the interface, let’s work through a simple contrived example. Say that you’re studying physical development and you’ve collected the ages and weights of 10 infants in their first year of life (see table 1.1). You’re interested in the distribution of the weights and their relationship to age. Figure 1.3 Example of the R interface on WindowsFFFFiFFFigFF 11 3 E3 E ll ff thth RR ii tt ff WWidid Download from Wow! eBook Working with R 9 Table 1.1 The age and weights of ten infants Age (mo.)Weight (kg.)Age (mo.)Weight (kg.) 01 4.4 09 7.3 03 5.3 03 6.0 05 7.2 09 10.4 02 5.2 12 10.2 11 8.5 03 6.1 Note: These are fictional data. You’ll enter the age and weight data as vectors, using the function c() , which com- bines its arguments into a vector or list. Then you’ll get the mean and standard de- viation of the weights, along with the correlation between age and weight, and plot the relationship between age and weight so that you can inspect any trend visually. The q() function , as shown in the following listing, will end the session and allow you to quit. Listing 1.1 A sample R session > age <- c(1,3,5,2,11,9,3,9,12,3) > weight <- c(4.4,5.3,7.2,5.2,8.5,7.3,6.0,10.4,10.2,6.1) > mean(weight) [1] 7.06 > sd(weight) [1] 2.077498 > cor(age,weight) [1] 0.9075655 > plot(age,weight) > q() You can see from listing 1.1 that the mean weight for these 10 infants is 7.06 kilograms, that the standard deviation is 2.08 kilograms, and that there is strong linear relation- ship between age in months and weight in kilograms (correlation = 0.91). The rela- tionship can also be seen in the scatter plot in figure 1.4. Not surprisingly, as infants get older, they tend to weigh more. The scatter plot in figure 1.4 is informative but somewhat utilitarian and unattractive. In later chapters, you’ll see how to customize graphs to suit your needs. TIP To get a sense of what R can do graphically, enter demo(graphics) at the command prompt. A sample of the graphs produced is included in figure 1.5. Other demonstrations include demo(Hershey) , demo(persp) , and demo(image) . To see a complete list of demonstrations, enter demo() without parameters. Download from Wow! eBook 10 CHAPTER 1 Introduction to R 2 4 6 8 10 12 56789 1 0 age w e i g h t Figure 1.4 Scatter plot of infant weight (kg) by age (mo) Figure 1.5 A sample of the graphs created with the demo() function Download from Wow! eBook Working with R 11 1.3.2 Getting help R provides extensive help facilities, and learning to navigate them will help you signifi- cantly in your programming efforts. The built-in help system provides details, refer- ences, and examples of any function contained in a currently installed package. Help is obtained using the functions listed in table 1.2. Table 1.2 R help functions Function Action help.start()General help. help("foo") or ?foo Help on function foo (the quotation marks are optional). help.search("foo") or ??foo Search the help system for instances of the string foo. example("foo") Examples of function foo (the quotation marks are optional). RSiteSearch("foo") Search for the string foo in online help manuals and archived mailing lists. apropos("foo", mode="function") List all available functions with foo in their name. data() List all available example datasets contained in currently loaded packages. vignette() List all available vignettes for currently installed packages. vignette("foo") Display specific vignettes for topic foo. The function help.start() opens a browser window with access to introductory and advanced manuals, FAQs, and reference materials. The RSiteSearch() function searches for a given topic in online help manuals and archives of the R-Help discus- sion list and returns the results in a browser window. The vignettes returned by the vignette() function are practical introductory articles provided in PDF format. Not all packages will have vignettes. As you can see, R provides extensive help facilities, and learning to navigate them will definitely aid your programming efforts. It’s a rare ses- sion that I don’t use the ? to look up the features (such as options or return values) of some function. 1.3.3 The workspace The workspace is your current R working environment and includes any user-defined objects (vectors, matrices, functions, data frames, or lists). At the end of an R session, you can save an image of the current workspace that’s automatically reloaded the next time R starts. Commands are entered interactively at the R user prompt. You can use the Download from Wow! eBook 12 CHAPTER 1 Introduction to R up and down arrow keys to scroll through your command history. Doing so allows you to select a previous command, edit it if desired, and resubmit it using the Enter key. The current working directory is the directory R will read files from and save results to by default. You can find out what the current working directory is by using the getwd() function . You can set the current working directory by using the setwd() function . If you need to input a file that isn’t in the current working directory, use the full pathname in the call. Always enclose the names of files and directories from the operating system in quote marks. Some standard commands for managing your workspace are listed in table 1.3. Table 1.3 Functions for managing the R workspace Function Action getwd() List the current working directory. setwd("mydirectory") Change the current working directory to mydirectory. ls() List the objects in the current workspace. rm(objectlist) Remove (delete) one or more objects. help(options) Learn about available options. options() View or set current options. history(#) Display your last # commands (default = 25). savehistory("myfile") Save the commands history to myfile ( default = .Rhistory). loadhistory("myfile") Reload a command’s history (default = .Rhistory). save.image("myfile") Save the workspace to myfile (default = .RData). save(objectlist, file="myfile") Save specific objects to a file. load("myfile") Load a workspace into the current session (default = .RData). q() Quit R. You’ll be prompted to save the workspace. To see these commands in action, take a look at the following listing. Listing 1.2 An example of commands used to manage the R workspace setwd("C:/myprojects/project1") options() options(digits=3) x <- runif(20) summary(x) hist(x) savehistory() save.image() q() Download from Wow! eBook Working with R 13 First, the current working directory is set to C:/myprojects/project1, the current op- tion settings are displayed, and numbers are formatted to print with three digits after the decimal place. Next, a vector with 20 uniform random variates is created, and sum- mary statistics and a histogram based on this data are generated. Finally, the command history is saved to the file .Rhistory , the workspace (including vector x) is saved to the file .RData , and the session is ended. Note the forward slashes in the pathname of the setwd() command . R treats the backslash (\) as an escape character . Even when using R on a Windows platform, use forward slashes in pathnames. Also note that the setwd() function won’t create a directory that doesn’t exist. If necessary, you can use the dir.create() function to create a directory, and then use setwd() to change to its location. It’s a good idea to keep your projects in separate directories. I typically start an R session by issuing the setwd() command with the appropriate path to a project, followed by the load() command without options. This lets me start up where I left off in my last session and keeps the data and settings separate between projects. On Windows and Mac OS X platforms, it’s even easier. Just navigate to the project directory and double-click on the saved image file. Doing so will start R, load the saved workspace, and set the current working directory to this location. 1.3.4 Input and output By default, launching R starts an interactive session with input from the keyboard and output to the screen. But you can also process commands from a script file (a file con- taining R statements) and direct output to a variety of destinations. INPUT The source("filename") function submits a script to the current session. If the file- name doesn’t include a path, the file is assumed to be in the current working directory. For example, source("myscript.R") runs a set of R statements contained in file myscript.R. By convention, script file names end with an .R extension, but this isn’t required. TEXT OUTPUT The sink("filename") function redirects output to the file filename. By default, if the file already exists, its contents are overwritten. Include the option append=TRUE to append text to the file rather than overwriting it. Including the option split=TRUE will send output to both the screen and the output file. Issuing the command sink() without options will return output to the screen alone. GRAPHIC OUTPUT Although sink() redirects text output, it has no effect on graphic output. To redirect graphic output, use one of the functions listed in table 1.4. Use dev.off() to return output to the terminal. Download from Wow! eBook 14 CHAPTER 1 Introduction to R Table 1.4 Functions for saving graphic output Function Output pdf("filename.pdf")PDF file win.metafile("filename.wmf")Windows metafile png("filename.png")PBG file jpeg("filename.jpg")JPEG file bmp("filename.bmp")BMP file postscript("filename.ps")PostScript file Let’s put it all together with an example. Assume that you have three script files con- taining R code (script1.R, script2.R, and script3.R). Issuing the statement source("script1.R") will submit the R code from script1.R to the current session and the results will appear on the screen. If you then issue the statements sink("myoutput", append=TRUE, split=TRUE) pdf("mygraphs.pdf") source("script2.R") the R code from file script2.R will be submitted, and the results will again appear on the screen. In addition, the text output will be appended to the file myoutput , and the graphic output will be saved to the file mygraphs.pdf . Finally, if you issue the statements sink() dev.off() source("script3.R") the R code from script3.R will be submitted, and the results will appear on the screen. This time, no text or graphic output is saved to files. The sequence is outlined in figure 1.6. R provides quite a bit of flexibility and control over where input comes from and where it goes. In section 1.5 you’ll learn how to run a program in batch mode. 1.4 Packages R comes with extensive capabilities right out of the box. But some of its most exciting features are available as optional modules that you can download and install. There are over 2,500 user-contributed modules called packages that you can download from http://cran.r-project.org/web/packages. They provide a tremendous range of new capabilities, from the analysis of geostatistical data to protein mass spectra process- ing to the analysis of psychological tests! You’ll use many of these optional packages in this book. Download from Wow! eBook Packages 15 myoutput Output added to the ﬁle Current Session sink("myoutput", append=TRUE, split=TRUE) pdf("mygraphs.pdf") Current Session source("script1.R") source("script2.R") Current Session sink(), dev.oﬀ() script2.R script3.R source("script3.R") script1.R Figure 1.6 Input with the source() function and output with the sink() function 1.4.1 What are packages? Packages are collections of R functions, data, and compiled code in a well-defined for- mat. The directory where packages are stored on your computer is called the library. The function .libPaths() shows you where your library is located, and the function library() shows you what packages you’ve saved in your library. Download from Wow! eBook 16 CHAPTER 1 Introduction to R R comes with a standard set of packages (including base, datasets, utils, grDevices, graphics, stats, and methods). They provide a wide range of functions and datasets that are available by default. Other packages are available for download and installation. Once installed, they have to be loaded into the session in order to be used. The command search() tells you which packages are loaded and ready to use. 1.4.2 Installing a package There are a number of R functions that let you manipulate packages. To install a pack- age for the first time, use the install.packages() command . For example, in- stall.packages() without options brings up a list of CRAN mirror sites. Once you select a site, you’ll be presented with a list of all available packages. Selecting one will download and install it. If you know what package you want to install, you can do so di- rectly by providing it as an argument to the function. For example, the gclus package contains functions for creating enhanced scatter plots. You can download and install the package with the command install.packages("gclus") . You only need to install a package once. But like any software, packages are often updated by their authors. Use the command update.packages() to update any packages that you’ve installed. To see details on your packages, you can use the installed.packages() command . It lists the packages you have, along with their version numbers, dependencies, and other information. 1.4.3 Loading a package Installing a package downloads it from a CRAN mirror site and places it in your library. To use it in an R session, you need to load the package using the library() com- mand . For example, to use the packaged gclus issue the command library(gclus) . Of course, you must have installed a package before you can load it. You’ll only have to load the package once within a given session. If desired, you can customize your startup environment to automatically load the packages you use most often. Custom- izing your startup is covered in appendix B. 1.4.4 Learning about a package When you load a package, a new set of functions and datasets becomes available. Small illustrative datasets are provided along with sample code, allowing you to try out the new functionalities. The help system contains a description of each func- tion (along with examples), and information on each dataset included. Entering help(package="package_name") provides a brief description of the package and an index of the functions and datasets included. Using help() with any of these function or dataset names will provide further details. The same information can be downloaded as a PDF manual from CRAN. Download from Wow! eBook Batch processing 17 1.5 Batch processing Most of the time, you’ll be running R interactively, entering commands at the com- mand prompt and seeing the results of each statement as it’s processed. Occasionally, you may want to run an R program in a repeated, standard, and possibly unattended fashion. For example, you may need to generate the same report once a month. You can write your program in R and run it in batch mode. How you run R in batch mode depends on your operating system. On Linux or Mac OS X systems, you can use the following command in a terminal window: R CMD BATCH options infile outfile where infile is the name of the file containing R code to be executed, outfile is the name of the file receiving the output, and options lists options that control execu- tion. By convention, infile is given the extension .R and outfile is given extension .Rout . For Windows, use "C:\Program Files\R\R-2.13.0\bin\R.exe" CMD BATCH ➥--vanilla --slave "c:\my projects\myscript.R" adjusting the paths to match the location of your R.exe binary and your script file. For additional details on how to invoke R, including the use of command-line options, see the “Introduction to R” documentation available from CRAN (http://cran.r-project.org). Common mistakes in R programming There are some common mistakes made frequently by both beginning and experienced R programmers. If your program generates an error, be sure the check for the following: ■ Using the wrong case —help(), Help(), and HELP() are three different functions (only the first will work). ■ Forgetting to use quote marks when they’re needed —install.packages- ("gclus") works, whereas install.packages(gclus) generates an error. ■ Forgetting to include the parentheses in a function call —for example, help() rather than help. Even if there are no options, you still need the (). ■ Using the \ in a pathname on Windows —R sees the backslash character as an escape character. setwd("c:\mydata") generates an error. Use setwd("c:/mydata") or setwd("c:\\mydata") instead. ■ Using a function from a package that’s not loaded —The function order. clusters() is contained in the gclus package. If you try to use it before loading the package, you’ll get an error. The error messages in R can be cryptic, but if you’re careful to follow these points, you should avoid seeing many of them. Download from Wow! eBook 18 CHAPTER 1 Introduction to R 1.6 Using output as input—reusing results One of the most useful design features of R is that the output of analyses can easily be saved and used as input to additional analyses. Let’s walk through an example, using one of the datasets that comes pre-installed with R. If you don’t understand the statis- tics involved, don’t worry. We’re focusing on the general principle here. First, run a simple linear regression predicting miles per gallon (mpg) from car weight (wt), using the automotive dataset mtcars. This is accomplished with the function call: lm(mpg~wt, data=mtcars) The results are displayed on the screen and no information is saved. Next, run the regression, but store the results in an object: lmfit <- lm(mpg~wt, data=mtcars) The assignment has created a list object called lmfit that contains extensive infor- mation from the analysis (including the predicted values, residuals, regression coef- ficients, and more). Although no output has been sent to the screen, the results can be both displayed and manipulated further. Typing summary(lmfit) displays a summary of the results, and plot(lmfit) produces diagnostic plots. The statement cook<-cooks.distance(lmfit) generates influence statistics and plot(cook) graphs them. To predict miles per gallon from car weight in a new set of data, you’d use predict(lmfit, mynewdata). To see what a function returns, look at the Value section of the online help for that function. Here you’d look at help(lm) or ?lm. This tells you what’s saved when you assign the results of that function to an object. 1.7 Working with large datasets Programmers frequently ask me if R can handle large data problems. Typically, they work with massive amounts of data gathered from web research, climatology, or genet- ics. Because R holds objects in memory, you’re typically limited by the amount of RAM available. For example, on my 5-year-old Windows PC with 2 GB of RAM, I can easily han- dle datasets with 10 million elements (100 variables by 100,000 observations). On an iMac with 4 GB of RAM, I can usually handle 100 million elements without difficulty. But there are two issues to consider: the size of the dataset and the statistical methods that will be applied. R can handle data analysis problems in the gigabyte to terabyte range, but specialized procedures are required. The management and analysis of very large datasets is discussed in appendix G. 1.8 Working through an example We’ll finish this chapter with an example that ties many of these ideas together. Here’s the task: 1 Open the general help and look at the “Introduction to R” section. 2 Install the vcd package (a package for visualizing categorical data that we’ll be using in chapter 11). Download from Wow! eBook Working through an example 19 3 List the functions and datasets available in this package. 4 Load the package and read the description of the dataset Arthritis. 5 Print out the Arthritis dataset (entering the name of an object will list it). 6 Run the example that comes with the Arthritis dataset . Don’t worry if you don’t understand the results. It basically shows that arthritis patients receiving treatment improved much more than patients receiving a placebo. 7 Quit. The code required is provided in the following listing, with a sample of the results displayed in figure 1.7. Listing 1.3 Working with a new package help.start() install.packages("vcd") help(package="vcd") library(vcd) help(Arthritis) Arthritis example(Arthritis) q() Figure 1.7 Output from listing 1.3 including (left to right) output from the arthritis example, general help, information on the vcd package , information on the Arthritis dataset , and a graph displaying the relationship between arthritis treatment and outcome Download from Wow! eBook 20 CHAPTER 1 Introduction to R As this short exercise demonstrates, you can accomplish a great deal with a small amount of code. 1.9 Summary In this chapter, we looked at some of the strengths that make R an attractive option for students, researchers, statisticians, and data analysts trying to understand the meaning of their data. We walked through the program’s installation and talked about how to enhance R’s capabilities by downloading additional packages. We explored the basic interface, running programs interactively and in batches, and produced a few sample graphs. You also learned how to save your work to both text and graphic files. Because R can be a complex program, we spent some time looking at how to access the exten- sive help that’s available. We hope you’re getting a sense of how powerful this freely available software can be. Now that you have R up and running, it’s time to get your data into the mix. In the next chapter, we’ll look at the types of data R can handle and how to import them into R from text files, other programs, and database management systems. Download from Wow! eBook 2 21 Creating a dataset This chapter covers ■ Exploring R data structures ■ Using data entry ■ Importing data ■ Annotating datasets The first step in any data analysis is the creation of a dataset containing the infor- mation to be studied, in a format that meets your needs. In R, this task involves the following: ■ Selecting a data structure to hold your data ■ Entering or importing your data into the data structure The first part of this chapter (sections 2.1–2.2) describes the wealth of structures that R can use for holding data. In particular, section 2.2 describes vectors, fac- tors, matrices, data frames, and lists. Familiarizing yourself with these structures (and the notation used to access elements within them) will help you tremendously in understanding how R works. You might want to take your time working through this section. The second part of this chapter (section 2.3) covers the many methods available for importing data into R. Data can be entered manually, or imported from an Download from Wow! eBook 22 CHAPTER 2 Creating a dataset external source. These data sources can include text files, spreadsheets, statistical packages, and database management systems. For example, the data that I work with typically comes from SQL databases. On occasion, though, I receive data from legacy DOS systems, and from current SAS and SPSS databases. It’s likely that you’ll only have to use one or two of the methods described in this section, so feel free to choose those that fit your situation. Once a dataset is created, you’ll typically annotate it, adding descriptive labels for variables and variable codes. The third portion of this chapter (section 2.4) looks at annotating datasets and reviews some useful functions for working with datasets (section 2.5). Let’s start with the basics. 2.1 Understanding datasets A dataset is usually a rectangular array of data with rows representing observations and columns representing variables. Table 2.1 provides an example of a hypothetical patient dataset. Table 2.1 A patient dataset PatientIDAdmDate Age Diabetes Status 1 10/15/2009 25 Type1 Poor 2 11/01/2009 34 Type2 Improved 3 10/21/2009 28 Type1 Excellent 4 10/28/2009 52 Type1 Poor Different traditions have different names for the rows and columns of a dataset. Statisti- cians refer to them as observations and variables, database analysts call them records and fields, and those from the data mining/machine learning disciplines call them examples and attributes. We’ll use the terms observations and variables throughout this book. You can distinguish between the structure of the dataset (in this case a rectangular array) and the contents or data types included. In the dataset shown in table 2.1, PatientID is a row or case identifier, AdmDate is a date variable, Age is a continuous variable, Diabetes is a nominal variable, and Status is an ordinal variable. R contains a wide variety of structures for holding data, including scalars, vectors, arrays, data frames, and lists. Table 2.1 corresponds to a data frame in R. This diversity of structures provides the R language with a great deal of flexibility in dealing with data. The data types or modes that R can handle include numeric, character, logical (TRUE/FALSE), complex (imaginary numbers), and raw (bytes). In R, PatientID, AdmDate, and Age would be numeric variables, whereas Diabetes and Status would be character variables. Additionally, you’ll need to tell R that PatientID is a case identifier, that AdmDate contains dates, and that Diabetes and Status are nominal Download from Wow! eBook Data structures 23 and ordinal variables, respectively. R refers to case identifiers as rownames and categorical variables (nominal, ordinal) as factors . We’ll cover each of these in the next section. You’ll learn about dates in chapter 3. 2.2 Data structures R has a wide variety of objects for holding data, including scalars, vectors, matrices, arrays, data frames, and lists. They differ in terms of the type of data they can hold, how they’re created, their structural complexity, and the notation used to identify and access individual elements. Figure 2.1 shows a diagram of these data structures. Let’s look at each structure in turn, starting with vectors. Some definitions There are several terms that are idiosyncratic to R, and thus confusing to new users. In R, an object is anything that can be assigned to a variable. This includes constants, data structures, functions, and even graphs. Objects have a mode (which describes how the object is stored) and a class (which tells generic functions like print how to handle it). A data frame is a structure in R that holds data and is similar to the datasets found in standard statistical packages (for example, SAS, SPSS, and Stata). The columns are variables and the rows are observations. You can have variables of different types (for example, numeric, character) in the same data frame. Data frames are the main structures you’ll use to store datasets. (continued) (a) Vector (b) Matrix (c) Array (d) Data frame Columns can be different modes (e) List Vectors Arrays Data frames Lists Figure 2.1 R data structures Download from Wow! eBook Factors are nominal or ordinal variables. They’re stored and treated specially in R. You’ll learn about factors in section 2.2.5. Most other terms should be familiar to you and follow the terminology used in statistics and computing in general. 2.2.1 Vectors Vectors are one-dimensional arrays that can hold numeric data, character data, or logi- cal data. The combine function c() is used to form the vector. Here are examples of each type of vector: a <- c(1, 2, 5, 3, 6, -2, 4) b <- c("one", "two", "three") c <- c(TRUE, TRUE, TRUE, FALSE, TRUE, FALSE) Here, a is numeric vector, b is a character vector, and c is a logical vector. Note that the data in a vector must only be one type or mode (numeric, character, or logical). You can’t mix modes in the same vector. NOTE Scalars are one-element vectors. Examples include f <- 3, g <- "US" and h <- TRUE. They’re used to hold constants. You can refer to elements of a vector using a numeric vector of positions within brack- ets. For example, a[c(2, 4)] refers to the 2nd and 4th element of vector a. Here are additional examples: > a <- c(1, 2, 5, 3, 6, -2, 4) > a[3] [1] 5 > a[c(1, 3, 5)] [1] 1 5 6 > a[2:6] [1] 2 5 3 6 -2 The colon operator used in the last statement is used to generate a sequence of num- bers. For example, a <- c(2:6) is equivalent to a <- c(2, 3, 4, 5, 6). 2.2.2 Matrices A matrix is a two-dimensional array where each element has the same mode (numeric, character, or logical). Matrices are created with the matrix function . The general for- mat is myymatrix <- matrix(vector, nrow=number_of_rows, ncol=number_of_columns, byrow=logical_value, dimnames=list( char_vector_rownames, char_vector_colnames)) where vector contains the elements for the matrix, nrow and ncol specify the row and column dimensions, and dimnames contains optional row and column labels stored in 24 CHAPTER 2 Creating a dataset Download from Wow! eBook Data structures 25 character vectors. The option byrow indicates whether the matrix should be filled in by row (byrow=TRUE) or by column (byrow=FALSE). The default is by column. The following listing demonstrates the matrix function . Listing 2.1 Creating matrices > y <- matrix(1:20, nrow=5, ncol=4) q> y [,1] [,2] [,3] [,4] [1,] 1 6 11 16 [2,] 2 7 12 17 [3,] 3 8 13 18 [4,] 4 9 14 19 [5,] 5 10 15 20 > cells <- c(1,26,24,68) > rnames <- c("R1", "R2") > cnames <- c("C1", "C2") w > mymatrix <- matrix(cells, nrow=2, ncol=2, byrow=TRUE, dimnames=list(rnames, cnames)) > mymatrix C1 C2 R1 1 26 R2 24 68 > mymatrix <- matrix(cells, nrow=2, ncol=2, byrow=FALSE, dimnames=list(rnames, cnames)) > mymatrix e C1 C2 R1 1 24 R2 26 68 First, you create a 5x4 matrix q. Then you create a 2x2 matrix with labels and fill the matrix by rows w. Finally, you create a 2x2 matrix and fill the matrix by columns e. You can identify rows, columns, or elements of a matrix by using subscripts and brackets. X[i,] refers to the ith row of matrix X, X[,j] refers to jth column, and X[i, j] refers to the ijth element, respectively. The subscripts i and j can be numeric vectors in order to select multiple rows or columns, as shown in the following listing. Listing 2.2 Using matrix subscripts > x <- matrix(1:10, nrow=2) > x [,1] [,2] [,3] [,4] [,5] [1,] 1 3 5 7 9 [2,] 2 4 6 8 10 > x[2,] [1] 2 4 6 8 10 > x[,2] [1] 3 4 > x[1,4] [1] 7 > x[1, c(4,5)] [1] 7 9 Create a 5x4 matrix 2x2 matrix filled by rows 2x2 matrix filled by columns Download from Wow! eBook First a 2 x 5 matrix is created containing numbers 1 to 10. By default, the matrix is filled by column. Then the elements in the 2nd row are selected, followed by the ele- ments in the 2nd column. Next, the element in the 1st row and 4th column is selected. Finally, the elements in the 1st row and the 4th and 5th columns are selected. Matrices are two-dimensional and, like vectors, can contain only one data type. When there are more than two dimensions, you’ll use arrays (section 2.2.3). When there are multiple modes of data, you’ll use data frames (section 2.2.4). 2.2.3 Arrays Arrays are similar to matrices but can have more than two dimensions. They’re created with an array function of the following form: myarray <- array(vector, dimensions, dimnames) where vector contains the data for the array, dimensions is a numeric vector giving the maximal index for each dimension, and dimnames is an optional list of dimension labels. The following listing gives an example of creating a three-dimensional (2x3x4) array of numbers. Listing 2.3 Creating an array > dim1 <- c("A1", "A2") > dim2 <- c("B1", "B2", "B3") > dim3 <- c("C1", "C2", "C3", "C4") > z <- array(1:24, c(2, 3, 4), dimnames=list(dim1, dim2, dim3)) > z , , C1 B1 B2 B3 A1 1 3 5 A2 2 4 6 , , C2 B1 B2 B3 A1 7 9 11 A2 8 10 12 , , C3 B1 B2 B3 A1 13 15 17 A2 14 16 18 , , C4 B1 B2 B3 A1 19 21 23 A2 20 22 24 As you can see, arrays are a natural extension of matrices. They can be useful in programming new statistical methods. Like matrices, they must be a single mode. 26 CHAPTER 2 Creating a dataset Download from Wow! eBook Data structures 27 Identifying elements follows what you’ve seen for matrices. In the previous example, the z[1,2,3] element is 15. 2.2.4 Data frames A data frame is more general than a matrix in that different columns can contain different modes of data (numeric, character, etc.). It’s similar to the datasets you’d typically see in SAS, SPSS, and Stata. Data frames are the most common data structure you’ll deal with in R. The patient dataset in table 2.1 consists of numeric and character data. Because there are multiple modes of data, you can’t contain this data in a matrix. In this case, a data frame would be the structure of choice. A data frame is created with the data.frame() function : mydata <- data.frame(col1, col2, col3,…) where col1, col2, col3, … are column vectors of any type (such as character, nu- meric, or logical). Names for each column can be provided with the names function. The following listing makes this clear. Listing 2.4 Creating a data frame > patientID <- c(1, 2, 3, 4) > age <- c(25, 34, 28, 52) > diabetes <- c("Type1", "Type2", "Type1", "Type1") > status <- c("Poor", "Improved", "Excellent", "Poor") > patientdata <- data.frame(patientID, age, diabetes, status) > patientdata patientID age diabetes status 1 1 25 Type1 Poor 2 2 34 Type2 Improved 3 3 28 Type1 Excellent 4 4 52 Type1 Poor Each column must have only one mode, but you can put columns of different modes together to form the data frame. Because data frames are close to what analysts typi- cally think of as datasets, we’ll use the terms columns and variables interchangeably when discussing data frames. There are several ways to identify the elements of a data frame. You can use the subscript notation you used before (for example, with matrices) or you can specify column names. Using the patientdata data frame created earlier, the following listing demonstrates these approaches. Listing 2.5 Specifying elements of a data frame > patientdata[1:2] patientID age 1 1 25 2 2 34 3 3 28 4 4 52 > patientdata[c("diabetes", "status")] Download from Wow! eBook diabetes status 1 Type1 Poor 2 Type2 Improved 3 Type1 Excellent q 4 Type1 Poor > patientdata$age [1] 25 34 28 52 The$ notation in the third example is new q. It’s used to indicate a particular variable from a given data frame. For example, if you want to cross tabulate diabetes type by status, you could use the following code: > table(patientdata$diabetes, patientdata$status) Excellent Improved Poor Type1 1 0 2 Type2 0 1 0 It can get tiresome typing patientdata$at the beginning of every variable name, so shortcuts are available. You can use either the attach() and detach() or with() functions to simplify your code. ATTACH, DETACH, AND WITH The attach() function adds the data frame to the R search path. When a variable name is encountered, data frames in the search path are checked in order to locate the variable. Using the mtcars data frame from chapter 1 as an example, you could use the following code to obtain summary statistics for automobile mileage (mpg), and plot this variable against engine displacement (disp), and weight (wt): summary(mtcars$mpg) plot(mtcars$mpg, mtcars$disp) plot(mtcars$mpg, mtcars$wt) This could also be written as attach(mtcars) summary(mpg) plot(mpg, disp) plot(mpg, wt) detach(mtcars) The detach() function removes the data frame from the search path. Note that detach() does nothing to the data frame itself. The statement is optional but is good programming practice and should be included routinely. (I’ll sometimes ignore this sage advice in later chapters in order to keep code fragments simple and short.) The limitations with this approach are evident when more than one object can have the same name. Consider the following code: > mpg <- c(25, 36, 47) > attach(mtcars) The following object(s) are masked _by_ ‘.GlobalEnv’: mpg Indicates age variable in patient data frame 28 CHAPTER 2 Creating a dataset Download from Wow! eBook Data structures 29 > plot(mpg, wt) Error in xy.coords(x, y, xlabel, ylabel, log) : ‘x’ and ‘y’ lengths differ > mpg [1] 25 36 47 Here we already have an object named mpg in our environment when the mtcars data frame is attached. In such cases, the original object takes precedence, which isn’t what you want. The plot statement fails because mpg has 3 elements and disp has 32 ele- ments. The attach() and detach() functions are best used when you’re analyzing a single data frame and you’re unlikely to have multiple objects with the same name. In any case, be vigilant for warnings that say that objects are being masked. An alternative approach is to use the with() function. You could write the previous example as with(mtcars, { summary(mpg, disp, wt) plot(mpg, disp) plot(mpg, wt) }) In this case, the statements within the {} brackets are evaluated with reference to the mtcars data frame. You don’t have to worry about name conflicts here. If there’s only one statement (for example, summary(mpg)), the {} brackets are optional. The limitation of the with() function is that assignments will only exist within the function brackets. Consider the following: > with(mtcars, { stats <- summary(mpg) stats }) Min. 1st Qu. Median Mean 3rd Qu. Max. 10.40 15.43 19.20 20.09 22.80 33.90 > stats Error: object ‘stats’ not found If you need to create objects that will exist outside of the with() construct, use the special assignment operator <<- instead of the standard one (<-). It will save the object to the global environment outside of the with() call. This can be demonstrated with the following code: > with(mtcars, { nokeepstats <- summary(mpg) keepstats <<- summary(mpg) }) > nokeepstats Error: object ‘nokeepstats’ not found > keepstats Min. 1st Qu. Median Mean 3rd Qu. Max. 10.40 15.43 19.20 20.09 22.80 33.90 Download from Wow! eBook Most books on R recommend using with() over attach(). I think that ultimately the choice is a matter of preference and should be based on what you’re trying to achieve and your understanding of the implications. We’ll use both in this book. CASE IDENTIFIERS In the patient data example, patientID is used to identify individuals in the dataset. In R, case identifiers can be specified with a rowname option in the data frame function. For example, the statement patientdata <- data.frame(patientID, age, diabetes, status, row.names=patientID) specifies patientID as the variable to use in labeling cases on various printouts and graphs produced by R. 2.2.5 Factors As you’ve seen, variables can be described as nominal, ordinal, or continuous. Nomi- nal variables are categorical, without an implied order. Diabetes (Type1, Type2) is an example of a nominal variable. Even if Type1 is coded as a 1 and Type2 is coded as a 2 in the data, no order is implied. Ordinal variables imply order but not amount. Status (poor, improved, excellent) is a good example of an ordinal variable. You know that a patient with a poor status isn’t doing as well as a patient with an improved status, but not by how much. Continuous variables can take on any value within some range, and both order and amount are implied. Age in years is a continuous variable and can take on values such as 14.5 or 22.8 and any value in between. You know that someone who is 15 is one year older than someone who is 14. Categorical (nominal) and ordered categorical (ordinal) variables in R are called factors. Factors are crucial in R because they determine how data will be analyzed and presented visually. You’ll see examples of this throughout the book. The function factor() stores the categorical values as a vector of integers in the range [1... k] (where k is the number of unique values in the nominal variable), and an internal vector of character strings (the original values) mapped to these integers. For example, assume that you have the vector diabetes <- c("Type1", "Type2", "Type1", "Type1") The statement diabetes <- factor(diabetes) stores this vector as (1, 2, 1, 1) and associates it with 1=Type1 and 2=Type2 internally (the assignment is alphabetical). Any analyses performed on the vector diabetes will treat the variable as nominal and select the statistical methods appropriate for this level of measurement. For vectors representing ordinal variables, you add the parameter ordered=TRUE to the factor() function . Given the vector status <- c("Poor", "Improved", "Excellent", "Poor") the statement status <- factor(status, ordered=TRUE) will encode the vector as (3, 2, 1, 3) and associate these values internally as 1=Excellent, 2=Improved, and 30 CHAPTER 2 Creating a dataset Download from Wow! eBook Data structures 31 3=Poor. Additionally, any analyses performed on this vector will treat the variable as ordinal and select the statistical methods appropriately. By default, factor levels for character vectors are created in alphabetical order. This worked for the status factor, because the order “Excellent,” “Improved,” “Poor” made sense. There would have been a problem if “Poor” had been coded as “Ailing” instead, because the order would be “Ailing,” “Excellent,” “Improved.” A similar problem exists if the desired order was “Poor,” “Improved,” “Excellent.” For ordered factors, the alphabetical default is rarely sufficient. You can override the default by specifying a levels option. For example, status <- factor(status, order=TRUE, levels=c("Poor", "Improved", "Excellent")) would assign the levels as 1=Poor, 2=Improved, 3=Excellent. Be sure that the specified levels match your actual data values. Any data values not in the list will be set to missing. The following listing demonstrates how specifying factors and ordered factors impact data analyses. Listing 2.6 Using factors > patientID <- c(1, 2, 3, 4) q> age <- c(25, 34, 28, 52) > diabetes <- c("Type1", "Type2", "Type1", "Type1") > status <- c("Poor", "Improved", "Excellent", "Poor") > diabetes <- factor(diabetes) > status <- factor(status, order=TRUE) > patientdata <- data.frame(patientID, age, diabetes, status) > str(patientdata) ‘data.frame’: 4 obs. of 4 variables: $patientID: num 1 2 3 4 w$ age : num 25 34 28 52 $diabetes : Factor w/ 2 levels "Type1","Type2": 1 2 1 1$ status : Ord.factor w/ 3 levels "Excellent"<"Improved"<..: 3 2 1 3 > summary(patientdata) patientID age diabetes status Min. :1.00 Min. :25.00 Type1:3 Excellent:1 e 1st Qu.:1.75 1st Qu.:27.25 Type2:1 Improved :1 Median :2.50 Median :31.00 Poor :2 Mean :2.50 Mean :34.75 3rd Qu.:3.25 3rd Qu.:38.50 Max. :4.00 Max. :52.00 First, you enter the data as vectors q. Then you specify that diabetes is a factor and status is an ordered factor. Finally, you combine the data into a data frame. The function str(object) provides information on an object in R (the data frame in this case) w. It clearly shows that diabetes is a factor and status is an ordered factor, along with how it’s coded internally. Note that the summary() function treats the vari- ables differently e. It provides the minimum, maximum, mean, and quartiles for the continuous variable age, and frequency counts for the categorical variables diabetes and status. Enter data as vectors Display object structure Display object summary Download from Wow! eBook 2.2.6 Lists Lists are the most complex of the R data types. Basically, a list is an ordered collection of objects (components). A list allows you to gather a variety of (possibly unrelated) objects under one name. For example, a list may contain a combination of vectors, matrices, data frames, and even other lists. You create a list using the list() function : mylist <- list(object1, object2, …) where the objects are any of the structures seen so far. Optionally, you can name the objects in a list: mylist <- list(name1=object1, name2=object2, …) The following listing shows an example. Listing 2.7 Creating a list > g <- "My First List" > h <- c(25, 26, 18, 39) > j <- matrix(1:10, nrow=5) > k <- c("one", "two", "three") > mylist <- list(title=g, ages=h, j, k) > mylist $title [1] "My First List"$ages [1] 25 26 18 39 [[3]] [,1] [,2] [1,] 1 6 [2,] 2 7 [3,] 3 8 [4,] 4 9 [5,] 5 10 [[4]] [1] "one" "two" "three" > mylist[[2]] [1] 25 26 18 39 > mylist[["ages"]] [[1] 25 26 18 39 In this example, you create a list with four components: a string, a numeric vector, a matrix, and a character vector. You can combine any number of objects and save them as a list. You can also specify elements of the list by indicating a component number or a name within double brackets. In this example, mylist[[2]] and mylist[["ages"]] both refer to the same four-element numeric vector. Lists are important R structures Create list Print entire list Print second component 32 CHAPTER 2 Creating a dataset Download from Wow! eBook Data input 33 for two reasons. First, they allow you to organize and recall disparate information in a simple way. Second, the results of many R functions return lists. It’s up to the analyst to pull out the components that are needed. You’ll see numerous examples of functions that return lists in later chapters. A note for programmers Experienced programmers typically find several aspects of the R language unusual. Here are some features of the language you should be aware of: ■ The period (.) has no special significance in object names. But the dollar sign ($) has a somewhat analogous meaning, identifying the parts of an object. For example, A$x refers to variable x in data frame A. ■ R doesn’t provide multiline or block comments . You must start each line of a multiline comment with #. For debugging purposes, you can also surround code that you want the interpreter to ignore with the state- ment if(FALSE){…}. Changing the FALSE to TRUE allows the code to be executed. ■ Assigning a value to a nonexistent element of a vector, matrix, array, or list will expand that structure to accommodate the new value. For example, consider the following: > x <- c(8, 6, 4) > x[7] <- 10 > x [1] 8 6 4 NA NA NA 10 The vector x has expanded from three to seven elements through the assignment. x <- x[1:3] would shrink it back to three elements again. ■ R doesn’t have scalar values . Scalars are represented as one-element vectors. ■ Indices in R start at 1, not at 0. In the vector earlier, x[1] is 8. ■ Variables can’t be declared. They come into existence on first assignment. To learn more, see John Cook’s excellent blog post, R programming for those coming from other languages (www.johndcook.com/R_language_for_programmers.html). Programmers looking for stylistic guidance may also want to check out Google’s R Style Guide (http://google-styleguide.googlecode.com/svn/trunk/google-r-style .html). 2.3 Data input Now that you have data structures, you need to put some data in them! As a data ana- lyst, you’re typically faced with data that comes to you from a variety of sources and in a variety of formats. Your task is to import the data into your tools, analyze the data, Download from Wow! eBook R Stascal Packages Database Management Systems Keyboard Other Text Files SASSPSSStata Excel netCFD SQLMySQLOracle Access ASCII XML HDF5Webscraping Figure 2.2 Sources of data that can be imported into R and report on the results. R provides a wide range of tools for importing data. The definitive guide for importing data in R is the R Data Import/Export manual available at http://cran.r-project.org/doc/manuals/R-data.pdf. As you can see in figure 2.2, R can import data from the keyboard, from flat files, from Microsoft Excel and Access, from popular statistical packages, from specialty formats, and from a variety of relational database management systems. Because you never know where your data will come from, we’ll cover each of them here. You only need to read about the ones you’re going to be using. 2.3.1 Entering data from the keyboard Perhaps the simplest method of data entry is from the keyboard. The edit() function in R will invoke a text editor that will allow you to enter your data manually. Here are the steps involved: 1 Create an empty data frame (or matrix) with the variable names and modes you want to have in the final dataset. 2 Invoke the text editor on this data object, enter your data, and save the results back to the data object. In the following example, you’ll create a data frame named mydata with three vari- ables: age (numeric) , gender (character) , and weight (numeric) . You’ll then invoke the text editor, add your data, and save the results. mydata <- data.frame(age=numeric(0), gender=character(0), weight=numeric(0)) mydata <- edit(mydata) Assignments like age=numeric(0) create a variable of a specific mode, but without actual data. Note that the result of the editing is assigned back to the object itself. The edit() function operates on a copy of the object. If you don’t assign it a destination, all of your edits will be lost! 34 CHAPTER 2 Creating a dataset Download from Wow! eBook Data input 35 Figure 2.3 Entering data via the built-in editor on a Windows platform The results of invoking the edit() function on a Windows platform can be seen in figure 2.3. In this figure, I’ve taken the liberty of adding some data. If you click on a column title, the editor gives you the option of changing the variable name and type (numeric, character). You can add additional variables by clicking on the titles of unused columns. When the text editor is closed, the results are saved to the object assigned (mydata in this case). Invoking mydata <- edit(mydata) again allows you to edit the data you’ve entered and to add new data. A shortcut for mydata <- edit(mydata) is simply fix(mydata) . This method of data entry works well for small datasets. For larger datasets, you’ll probably want to use the methods we’ll describe next: importing data from existing text files, Excel spreadsheets, statistical packages, or database management systems. 2.3.2 Importing data from a delimited text file You can import data from delimited text files using read.table() , a function that reads a file in table format and saves it as a data frame. Here’s the syntax: mydataframe <- read.table(file, header=logical_value, sep="delimiter", row.names="name") where file is a delimited ASCII file , header is a logical value indicating whether the first row contains variable names (TRUE or FALSE), sep specifies the delimiter Download from Wow! eBook separating data values, and row.names is an optional parameter specifying one or more variables to represent row identifiers. For example, the statement grades <- read.table("studentgrades.csv", header=TRUE, sep=",", row.names="STUDENTID") reads a comma-delimited file named studentgrades.csv from the current working directory, gets the variable names from the first line of the file, specifies the variable STUDENTID as the row identifier, and saves the results as a data frame named grades. Note that the sep parameter allows you to import files that use a symbol other than a comma to delimit the data values. You could read tab-delimited files with sep="\t". The default is sep="", which denotes one or more spaces, tabs, new lines, or carriage returns. By default, character variables are converted to factors. This behavior may not always be desirable (for example, a variable containing respondents’ comments). You can suppress this behavior in a number of ways. Including the option stringsAs Factors=FALSE will turn this behavior off for all character variables. Alternatively, you can use the colClasses option to specify a class (for example, logical, numeric, character, factor) for each column. The read.table() function has many additional options for fine-tuning the data import. See help(read.table) for details. NOTE Many of the examples in this chapter import data from files that exist on the user’s computer. R provides several mechanisms for accessing data via connections as well. For example, the functions file() , gzfile() , bzfile() , xzfile() , unz() , and url() can be used in place of the filename. The file() function allows the user to access files, the clipboard, and C-level standard input. The gzfile() , bzfile() , xzfile() , and unz() function s let the user read compressed files. The url() function lets you access internet files through a complete URL that includes http://, ftp://, or file://. For HTTP and FTP, proxies can be specified. For convenience, complete URLs (surrounded by "" marks) can usually be used directly in place of filenames as well. See help(file) for details. 2.3.3 Importing data from Excel The best way to read an Excel file is to export it to a comma-delimited file from within Excel and import it to R using the method described earlier. On Windows systems you can also use the RODBC package to access Excel files . The first row of the spreadsheet should contain variable/column names. First, download and install the RODBC package. install.packages("RODBC") 36 CHAPTER 2 Creating a dataset Download from Wow! eBook Data input 37 You can then use the following code to import the data: library(RODBC) channel <- odbcConnectExcel("myfile.xls") mydataframe <- sqlFetch(channel, "mysheet") odbcClose(channel) Here, myfile.xls is an Excel file, mysheet is the name of the Excel worksheet to read from the workbook, channel is an RODBC connection object returned by odbcConnectExcel() , and mydataframe is the resulting data frame. RODBC can also be used to import data from Microsoft Access. See help(RODBC) for details. Excel 2007 uses an XLSX file format, which is essentially a zipped set of XML files. The xlsx package can be used to access spreadsheets in this format. Be sure to download and install it before first use. The read.xlsx() function imports a worksheet from an XLSX file into a data frame. The simplest format is read.xlsx(file, n) where file is the path to an Excel 2007 workbook and n is the number of the worksheet to be imported. For example, on a Windows platform, the code library(xlsx) workbook <- "c:/myworkbook.xlsx" mydataframe <- read.xlsx(workbook, 1) imports the first worksheet from the workbook myworkbook.xlsx stored on the C: drive and saves it as the data frame mydataframe. The xlsx package can do more than import worksheets. It can create and manipulate Excel XLSX files as well. Program- mers who need to develop an interface between R and Excel should check out this relatively new package. 2.3.4 Importing data from XML Increasingly, data is provided in the form of files encoded in XML. R has several pack- ages for handling XML files. For example, the XML package written by Duncan Temple Lang allows users to read, write, and manipulate XML files. Coverage of XML is beyond the scope of this text. Readers interested in the accessing XML documents from within R are referred to the excellent package documentation at www.omegahat.org/RSXML. 2.3.5 Webscraping In webscraping, the user extracts information embedded in a web page available over the internet and saves it into R structures for further analysis. One way to accomplish this is to download the web page using the readLines() function and manipulate it with functions such as grep() and gsub() . For complex web pages, the RCurl and XML packages can be used to extract the information desired. For more information, including examples, see “Webscraping using readLines and RCurl,” available from the website Programming with R (www.programmingr.com). Download from Wow! eBook 2.3.6 Importing data from SPSS SPSS datasets can be imported into R via the read.spss() function in the foreign package . Alternatively, you can use the spss.get() function in the Hmisc package . spss.get() is a wrapper function that automatically sets many parameters of read. spss() for you, making the transfer easier and more consistent with what data analysts expect as a result. First, download and install the Hmisc package (the foreign package is already installed by default): install.packages("Hmisc") Then use the following code to import the data: library(Hmisc) mydataframe <- spss.get("mydata.sav", use.value.labels=TRUE) In this code, mydata.sav is the SPSS data file to be imported, use.value. labels=TRUE tells the function to convert variables with value labels into R factors with those same levels, and mydataframe is the resulting R data frame. 2.3.7 Importing data from SAS A number of functions in R are designed to import SAS datasets, including read. ssd() in the foreign package and sas.get() in the Hmisc package . Unfortunately, if you’re using a recent version of SAS (SAS 9.1 or higher), you’re likely to find that these functions don’t work for you because R hasn’t caught up with changes in SAS file structures. There are two solutions that I recommend. You can save the SAS dataset as a comma-delimited text file from within SAS using PROC EXPORT, and read the resulting file into R using the method described in section 2.3.2. Here’s an example: SAS program: proc export data=mydata outfile="mydata.csv" dbms=csv; run; R program: mydata <- read.table("mydata.csv", header=TRUE, sep=",") Alternatively, a commercial product called Stat Transfer (described in section 2.3.12) does an excellent job of saving SAS datasets (including any existing variable formats) as R data frames. 2.3.8 Importing data from Stata Importing data from Stata to R is straightforward. The necessary code looks like this: 38 CHAPTER 2 Creating a dataset Download from Wow! eBook Data input 39 library(foreign) mydataframe <- read.dta("mydata.dta") Here, mydata.dta is the Stata dataset and mydataframe is the resulting R data frame. 2.3.9 Importing data from netCDF Unidata’s netCDF (network Common Data Form) open source software contains ma- chine-independent data formats for the creation and distribution of array-oriented sci- entific data. netCDF is commonly used to store geophysical data. The ncdf and ncdf4 packages provide high-level R interfaces to netCDF data files. The ncdf package provides support for data files created with Unidata’s netCDF library (version 3 or earlier) and is available for Windows, Mac OS X, and Linux platforms. The ncdf4 package supports version 4 or earlier, but isn’t yet available for Windows. Consider this code: library(ncdf) nc <- nc_open("mynetCDFfile") myarray <- get.var.ncdf(nc, myvar) In this example, all the data from the variable myvar , contained in the netCDF file mynetCDFfile , is read and saved into an R array called myarray . Note that both ncdf and ncdf4 packages have received major recent upgrades and may operate differently than previous versions. Additionally, function names in the two packages differ. Read the online documentation for details. 2.3.10 Importing data from HDF5 HDF5 (Hierarchical Data Format) is a software technology suite for the management of extremely large and complex data collections. The hdf5 package can be used to write R objects into a file in a form that can be read by software that understands the HDF5 format. These files can be read back into R at a later time. The package is experimental and assumes that the user has the HDF5 library (version 1.2 or higher) installed. At present, support for the HDF5 format in R is extremely limited. 2.3.11 Accessing database management systems (DBMSs) R can interface with a wide variety of relational database management systems (DBMSs), including Microsoft SQL Server, Microsoft Access, MySQL, Oracle, PostgreSQL, DB2, Sybase, Teradata, and SQLite. Some packages provide access through native database drivers, whereas others offer access via ODBC or JDBC. Using R to access data stored in external DMBSs can be an efficient way to analyze large datasets (see appendix G), and leverages the power of both SQL and R. THE ODBC INTERFACE Perhaps the most popular method of accessing a DBMS in R is through the RODBC pack- age, which allows R to connect to any DBMS that has an ODBC driver. This includes all of the DBMSs listed. Download from Wow! eBook The first step is to install and configure the appropriate ODBC driver for your platform and database—they’re not part of R. If the requisite drivers aren’t already installed on your machine, an internet search should provide you with options. Once the drivers are installed and configured for the database(s) of your choice, install the RODBC package. You can do so by using the install.packages("RODBC") command . The primary functions included with the RODBC package are listed in table 2.2. Table 2.2 RODBC functions Function Description odbcConnect(dsn,uid="",pwd="") Open a connection to an ODBC database sqlFetch(channel,sqltable) Read a table from an ODBC database into a data frame sqlQuery(channel,query) Submit a query to an ODBC database and return the results sqlSave(channel,mydf,tablename = sqtable,append=FALSE) Write or update (append=TRUE) a data frame to a table in the ODBC database sqlDrop(channel,sqtable) Remove a table from the ODBC database close(channel) Close the connection The RODBC package allows two-way communication between R and an ODBC-connect- ed SQL database. This means that you can not only read data from a connected data- base into R, but you can use R to alter the contents of the database itself. Assume that you want to import two tables (Crime and Punishment) from a DBMS into two R data frames called crimedat and pundat , respectively. You can accomplish this with code similar to the following: library(RODBC) myconn <-odbcConnect("mydsn", uid="Rob", pwd="aardvark") crimedat <- sqlFetch(myconn, Crime) pundat <- sqlQuery(myconn, "select * from Punishment") close(myconn) Here, you load the RODBC package and open a connection to the ODBC database through a registered data source name (mydsn) with a security UID (rob) and pass- word (aardvark). The connection string is passed to sqlFetch, which copies the table Crime into the R data frame crimedat . You then run the SQL select statement against the table Punishment and save the results to the data frame pundat . Finally, you close the connection. The sqlQuery() function is very powerful because any valid SQL statement can be inserted. This flexibility allows you to select specific variables, subset the data, create new variables, and recode and rename existing variables. 40 CHAPTER 2 Creating a dataset Download from Wow! eBook Data input 41 DBI-RELATED PACKAGES The DBI package provides a general and consistent client-side interface to DBMS. Build- ing on this framework, the RJDBC package provides access to DBMS via a JDBC driver. Be sure to install the necessary JDBC drivers for your platform and database. Other use- ful DBI-based packages include RMySQL , ROracle , RPostgreSQL , and RSQLite . These packages provide native database drivers for their respective databases but may not be available on all platforms. Check the documentation on CRAN (http://cran.r-project. org) for details. 2.3.12 Importing data via Stat/Transfer Before we end our discussion of importing data, it’s worth mentioning a commercial product that can make the task significantly easier. Stat/Transfer (www.stattransfer. com) is a stand-alone application that can transfer data between 34 data formats, in- cluding R (see figure 2.4). Figure 2.4 Stat/Transfer’s main dialog on Windows Download from Wow! eBook It’s available for Windows, Mac, and Unix platforms and supports the latest versions of the statistical packages we’ve discussed so far, as well as ODBC-accessed DBMSs such as Oracle, Sybase, Informix, and DB/2. 2.4 Annotating datasets Data analysts typically annotate datasets to make the results easier to interpret. Typi- cally annotation includes adding descriptive labels to variable names and value labels to the codes used for categorical variables. For example, for the variable age, you might want to attach the more descriptive label “Age at hospitalization (in years).” For the variable gender coded 1 or 2, you might want to associate the labels “male” and “female.” 2.4.1 Variable labels Unfortunately, R’s ability to handle variable labels is limited. One approach is to use the variable label as the variable’s name and then refer to the variable by its position index. Consider our earlier example, where you have a data frame containing patient data. The second column, named age, contains the ages at which individuals were first hospitalized. The code names(patientdata)[2] <- "Age at hospitalization (in years)" renames age to "Age at hospitalization (in years)". Clearly this new name is too long to type repeatedly. Instead, you can refer to this variable as patientdata[2] and the string "Age at hospitalization (in years)" will print wherever age would’ve originally. Obviously, this isn’t an ideal approach, and you may be better off trying to come up with better names (for example, admissionAge). 2.4.2 Value labels The factor() function can be used to create value labels for categorical variables. Continuing our example, say that you have a variable named gender, which is coded 1 for male and 2 for female. You could create value labels with the code patientdata$gender <- factor(patientdata$gender, levels = c(1,2), labels = c("male", "female")) Here levels indicate the actual values of the variable, and labels refer to a character vector containing the desired labels. 2.5 Useful functions for working with data objects We’ll end this chapter with a brief summary of useful functions for working with data objects (see table 2.3). 42 CHAPTER 2 Creating a dataset Download from Wow! eBook Summary 43 Table 2.3 Useful functions for working with data objects Function Purpose length(object) Number of elements/components. dim(object) Dimensions of an object. str(object) Structure of an object. class(object) Class or type of an object. mode(object) How an object is stored. names(object) Names of components in an object. c(object, object,...) Combines objects into a vector. cbind(object, object, ...) Combines objects as columns. rbind(object, object, ...) Combines objects as rows. object Prints the object. head(object) Lists the first part of the object. tail(object) Lists the last part of the object. ls() Lists current objects. rm(object, object, ...) Deletes one or more objects. The statement rm(list = ls()) will remove most objects from the working environment. newobject <- edit(object) Edits object and saves as newobject. fix(object) Edits in place. We’ve already discussed most of these functions. The functions head() and tail() are useful for quickly scanning large datasets. For example, head(patientdata) lists the first six rows of the data frame, whereas tail(patientdata) lists the last six. We’ll cover functions such as length(), cbind(), and rbind() in the next chapter. They’re gathered here as a reference. 2.6 Summary One of the most challenging tasks in data analysis is data preparation. We’ve made a good start in this chapter by outlining the various structures that R provides for hold- ing data and the many methods available for importing data from both keyboard and external sources. In particular, we’ll use the definitions of a vector, matrix, data frame, and list again and again in later chapters. Your ability to specify elements of these struc- tures via the bracket notation will be particularly important in selecting, subsetting, and transforming data. Download from Wow! eBook As you’ve seen, R offers a wealth of functions for accessing external data. This includes data from flat files, web files, statistical packages, spreadsheets, and databases. Although the focus of this chapter has been on importing data into R, you can also export data from R into these external formats. Exporting data is covered in appendix C, and methods of working with large datasets (in the gigabyte to terabyte range) are covered in appendix G. Once you get your datasets into R, it’s likely that you’ll have to manipulate them into a more conducive format (actually, I find guilt works well). In chapter 4, we’ll explore ways of creating new variables, transforming and recoding existing variables, merging datasets, and selecting observations. But before turning to data management tasks, let’s spend some time with R graphics. Many readers have turned to R out of an interest in its graphing capabilities, and I don’t want to make you wait any longer. In the next chapter, we’ll jump directly into the creation of graphs. Our emphasis will be on general methods for managing and customizing graphs that can be applied throughout the remainder of this book. 44 CHAPTER 2 Creating a dataset Download from Wow! eBook 3 45 Getting started with graphs This chapter covers .n Creating and saving graphs .n Customizing symbols, lines, colors, and axes .n Annotating with text and titles .n Controlling a graph’s dimensions .n Combining multiple graphs into one On many occasions, I’ve presented clients with carefully crafted statistical results in the form of numbers and text, only to have their eyes glaze over while the chirping of crickets permeated the room. Yet those same clients had enthusiastic “Ah-ha!” moments when I presented the same information to them in the form of graphs. Many times I was able to see patterns in data or detect anomalies in data values by looking at graphs—patterns or anomalies that I completely missed when conduct- ing more formal statistical analyses. Human beings are remarkably adept at discerning relationships from visual representations. A well-crafted graph can help you make meaningful comparisons among thousands of pieces of information, extracting patterns not easily found through other methods. This is one reason why advances in the field of statistical graphics have had such a major impact on data analysis. Data analysts need to look at their data, and this is one area where R shines. Download from Wow! eBook 6 Chapter 3 Getting started with graphs In this chapter, we’ll review general methods for working with graphs. We’ll start with how to create and save graphs. Then we’ll look at how to modify the features that are found in any graph. These features include graph titles, axes, labels, colors, lines, symbols, and text annotations. Our focus will be on generic techniques that apply across graphs. (In later chapters, we’ll focus on specific types of graphs.) Finally, we’ll investigate ways to combine multiple graphs into one overall graph. 3.1 Working with graphs R is an amazing platform for building graphs. I’m using the term “building” intention- ally. In a typical interactive session, you build a graph one statement at a time, adding features, until you have what you want. Consider the following five lines: attach(mtcars) plot(wt, mpg) abline(lm(mpg~wt)) title("Regression of MPG on Weight") detach(mtcars) The first statement attaches the data frame mtcars. The second statement opens a graphics window and generates a scatter plot between automobile weight on the hori- zontal axis and miles per gallon on the vertical axis. The third statement adds a line of best fit. The fourth statement adds a title. The final statement detaches the data frame. In R, graphs are typically created in this interactive fashion (see figure 3.1). You can save your graphs via code or through GUI menus. To save a graph via code, sandwich the statements that produce the graph between a statement that sets a destination and a statement that closes that destination. For example, the following Figure 3.1 Creating a graph Download from Wow! eBook orking with graphs 47 will save the graph as a PDF document named mygraph.pdf in the current working directory: pdf("mygraph.pdf") attach(mtcars) plot(wt, mpg) abline(lm(mpg~wt)) title("Regression of MPG on Weight") detach(mtcars) dev.off() In addition to pdf(), you can use the functions win.metafile(), png(), jpeg(), bmp(), tiff(), xfig(), and postscript() to save graphs in other formats. (Note: The Windows metafile format is only available on Windows platforms.) See chapter 1, section 1.3.4 for more details on sending graphic output to files. Saving graphs via the GUI will be platform specific. On a Windows platform, select File > Save As from the graphics window, and choose the format and location desired in the resulting dialog. On a Mac, choose File > Save As from the menu bar when the Quartz graphics window is highlighted. The only output format provided is PDF. On a Unix platform, the graphs must be saved via code. In appendix A, we’ll consider alternative GUIs for each platform that will give you more options. Creating a new graph by issuing a high-level plotting command such as plot(), hist() (for histograms), or boxplot() will typically overwrite a previous graph. How can you create more than one graph and still have access to each? There are several methods. First, you can open a new graph window before creating a new graph: dev.new() statements to create graph 1 dev.new() statements to create a graph 2 etc. Each new graph will appear in the most recently opened window. Second, you can access multiple graphs via the GUI. On a Mac platform, you can step through the graphs at any time using Back and Forward on the Quartz menu. On a Windows platform, you must use a two-step process. After opening the first graph window, choose History > Recording. Then use the Previous and Next menu items to step through the graphs that are created. Third and finally, you can use the functions dev.new(), dev.next(), dev.prev(), dev.set(), and dev.off() to have multiple graph windows open at one time and choose which output are sent to which windows. This approach works on any platform. See help(dev.cur) for details on this approach. R will create attractive graphs with a minimum of input on our part. But you can also use graphical parameters to specify fonts, colors, line styles, axes, reference lines, and annotations. This flexibility allows for a wide degree of customization. Download from Wow! eBook 8 Chapter 3 Getting started with graphs In this chapter, we’ll start with a simple graph and explore the ways you can modify and enhance it to meet your needs. Then we’ll look at more complex examples that illustrate additional customization methods. The focus will be on techniques that you can apply to a wide range of the graphs that you’ll create in R. The methods discussed here will work on all the graphs described in this book, with the exception of those created with the lattice package in chapter 16. (The lattice package has its own methods for customizing a graph’s appearance.) In other chapters, we’ll explore each specific type of graph and discuss where and when they’re most useful. 3.2 A simple example Let’s start with the simple fictitious dataset given in table 3.1. It describes patient re- sponse to two drugs at five dosage levels. Table 3.1 Patient response to two drugs at five dosage levels Dosage Response to Drug AResponse to Drug B 20 16 15 30 20 18 40 27 25 45 40 31 60 60 40 You can input this data using this code: dose <- c(20, 30, 40, 45, 60) drugA <- c(16, 20, 27, 40, 60) drugB <- c(15, 18, 25, 31, 40) A simple line graph relating dose to response for drug A can be created using plot(dose, drugA, type="b") plot() is a generic function that plots objects in R (its output will vary according to the type of object being plotted). In this case, plot(x, y, type="b") places x on the horizontal axis and y on the vertical axis, plots the (x, y) data points, and connects them with line segments. The option type="b" indicates that both points and lines should be plotted. Use help(plot) to view other options. The graph is displayed in figure 3.2. Line plots are covered in detail in chapter 11. Now let’s modify the appearance of this graph. Download from Wow! eBook raphical parameters 49 20 30 40 50 60 2 0 3 0 4 0 5 0 6 0 dose d r u g A Figure 3.2 Line plot of dose vs. response for drug A 3.3 Graphical parameters You can customize many features of a graph (fonts, colors, axes, titles) through options called graphical parameters. One way is to specify these options through the par() function. Values set in this manner will be in effect for the rest of the session or until they’re changed. The format is par(optionname=value, optionname=value, ...). Specifying par() without parameters produces a list of the current graphical settings. Adding the no.readonly=TRUE option produces a list of current graphical settings that can be modified. Continuing our example, let’s say that you’d like to use a solid triangle rather than an open circle as your plotting symbol, and connect points using a dashed line rather than a solid line. You can do so with the following code: opar <- par(no.readonly=TRUE) par(lty=2, pch=17) plot(dose, drugA, type="b") par(opar) The resulting graph is shown in figure 3.3. The first statement makes a copy of the current settings. The second statement changes the default line type to dashed (lty=2) and the default symbol for plotting Download from Wow! eBook 0 Chapter 3 Getting started with graphs points to a solid triangle (pch=17). You then generate the plot and restore the original settings. Line types and symbols are covered in section 3.3.1. You can have as many par() functions as desired, so par(lty=2, pch=17) could also have been written as par(lty=2) par(pch=17) A second way to specify graphical parameters is by providing the optionname=value pairs directly to a high-level plotting function. In this case, the options are only in ef- fect for that specific graph. You could’ve generated the same graph with the code plot(dose, drugA, type="b", lty=2, pch=17) Not all high-level plotting functions allow you to specify all possible graphical parame- ters. See the help for a specific plotting function (such as ?plot, ?hist, or ?boxplot) to determine which graphical parameters can be set in this way. The remainder of sec- tion 3.3 describes many of the important graphical parameters that you can set. 3.3.1 Symbols and lines As you’ve seen, you can use graphical parameters to specify the plotting symbols and lines used in your graphs. The relevant parameters are shown in table 3.2. 20 30 40 50 60 2 0 3 0 4 0 5 0 6 0 dose d r u g A Figure 3.3 Line plot of dose vs. response for drug A with modified line type and symbol Download from Wow! eBook raphical parameters 51 Table 3.2 Parameters for specifying symbols and lines Parameter Description pch Specifies the symbol to use when plotting points (see figure 3.4). cex Specifies the symbol size. cex is a number indicating the amount by which plotting symbols should be scaled relative to the default. 1=default, 1.5 is 50% larger, 0.5 is 50% smaller, and so forth. lty Specifies the line type (see figure 3.5). lwd Specifies the line width. lwd is expressed relative to the default (default=1). For example, lwd=2 generates a line twice as wide as the default. The pch= option specifies the symbols to use when plotting points. Possible values are shown in figure 3.4. For symbols 21 through 25 you can also specify the border (col=) and fill (bg=) colors. Use lty= to specify the type of line desired. The option values are shown in figure 3.5. Taking these options together, the code plot(dose, drugA, type="b", lty=3, lwd=3, pch=15, cex=2) would produce a plot with a dotted line that was three times wider than the default width, connecting points displayed as filled squares that are twice as large as the default symbol size. The results are displayed in figure 3.6. Next, let’s look at specifying colors. plot symbols: pch= 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Figure 3.4 Plotting symbols specified with the pch parameter Figure 3.5 Line types specified with the lty parameter line types: lty= 1 2 3 4 5 6 Download from Wow! eBook 2 Chapter 3 Getting started with graphs 3.3.2 Colors There are several color-related parameters in R. Table 3.3 shows some of the common ones. Table 3.3 Parameters for specifying color Parameter Description col Default plotting color. Some functions (such as lines and pie) accept a vector of values that are recycled. For example, if col=c(“red”, “blue”)and three lines are plotted, the first line will be red, the second blue, and the third red. col.axis Color for axis text. col.lab Color for axis labels. col.main Color for titles. col.sub Color for subtitles. fg The plot’s foreground color. bg The plot’s background color. 20 30 40 50 60 2 0 3 0 4 0 5 0 6 0 dose d r u g A Figure 3.6 Line plot of dose vs. response for drug A with modified line type, line width, symbol, and symbol width Download from Wow! eBook raphical parameters 53 You can specify colors in R by index, name, hexadecimal, RGB, or HSV. For example, col=1, col="white", col="#FFFFFF", col=rgb(1,1,1), and col=hsv(0,0,1) are equivalent ways of specifying the color white. The function rgb()creates colors based on red-green-blue values, whereas hsv() creates colors based on hue-saturation values. See the help feature on these functions for more details. The function colors() returns all available color names. Earl F. Glynn has created an excellent online chart of R colors, available at http://research.stowers-institute. org/efg/R/Color/Chart. R also has a number of functions that can be used to create vectors of contiguous colors. These include rainbow(), heat.colors(), terrain. colors(), topo.colors(), and cm.colors(). For example, rainbow(10) produces 10 contiguous “rainbow" colors. Gray levels are generated with the gray() function. In this case, you specify gray levels as a vector of numbers between 0 and 1. gray(0:10/10) would produce 10 gray levels. Try the code n <- 10 mycolors <- rainbow(n) pie(rep(1, n), labels=mycolors, col=mycolors) mygrays <- gray(0:n/n) pie(rep(1, n), labels=mygrays, col=mygrays) to see how this works. You’ll see examples that use color parameters throughout this chapter. 3.3.3 Text characteristics Graphic parameters are also used to specify text size, font, and style. Parameters con- trolling text size are explained in table 3.4. Font family and style can be controlled with font options (see table 3.5). Table 3.4 Parameters specifying text size Parameter Description cex Number indicating the amount by which plotted text should be scaled relative to the default. 1=default, 1.5 is 50% larger, 0.5 is 50% smaller, etc. cex.axis Magnification of axis text relative to cex. cex.lab Magnification of axis labels relative to cex. cex.main Magnification of titles relative to cex. cex.sub Magnification of subtitles relative to cex. For example, all graphs created after the statement par(font.lab=3, cex.lab=1.5, font.main=4, cex.main=2) will have italic axis labels that are 1.5 times the default text size, and bold italic titles that are twice the default text size. Download from Wow! eBook 4 Chapter 3 Getting started with graphs Table 3.5 Parameters specifying font family, size, and style Parameter Description font Integer specifying font to use for plotted text.. 1=plain, 2=bold, 3=italic, 4=bold italic, 5=symbol (in Adobe symbol encoding). font.axis Font for axis text. font.lab Font for axis labels. font.main Font for titles. font.sub Font for subtitles. ps Font point size (roughly 1/72 inch). The text size = ps*cex. family Font family for drawing text. Standard values are serif, sans, and mono. Whereas font size and style are easily set, font family is a bit more complicated. This is because the mapping of serif, sans, and mono are device dependent. For example, on Windows platforms, mono is mapped to TT Courier New, serif is mapped to TT Times New Roman, and sans is mapped to TT Arial (TT stands for True Type). If you’re satis- fied with this mapping, you can use parameters like family="serif" to get the results you want. If not, you need to create a new mapping. On Windows, you can create this mapping via the windowsFont() function. For example, after issuing the statement windowsFonts( A=windowsFont("Arial Black"), B=windowsFont("Bookman Old Style"), C=windowsFont("Comic Sans MS") ) you can use A, B, and C as family values. In this case, par(family="A") will specify an Arial Black font. (Listing 3.2 in section 3.4.2 provides an example of modifying text parameters.) Note that the windowsFont() function only works for Windows. On a Mac, use quartzFonts() instead. If graphs will be output in PDF or PostScript format, changing the font family is relatively straightforward. For PDFs, use names(pdfFonts())to find out which fonts are available on your system and pdf(file="myplot.pdf", family="fontname") to generate the plots. For graphs that are output in PostScript format, use names(postscriptFonts()) and postscript(file="myplot.ps", family="fontname"). See the online help for more information. 3.3.4 Graph and margin dimensions Finally, you can control the plot dimensions and margin sizes using the parameters listed in table 3.6. Download from Wow! eBook raphical parameters 55 Table 3.6 Parameters for graph and margin dimensions Parameter Description pin Plot dimensions (width, height) in inches. mai Numerical vector indicating margin size where c(bottom, left, top, right) is expressed in inches. mar Numerical vector indicating margin size where c(bottom, left, top, right) is expressed in lines. The default is c(5, 4, 4, 2) + 0.1. The code par(pin=c(4,3), mai=c(1,.5, 1, .2)) produces graphs that are 4 inches wide by 3 inches tall, with a 1-inch margin on the bottom and top, a 0.5-inch margin on the left, and a 0.2-inch margin on the right. For a complete tutorial on margins, see Earl F. Glynn’s comprehensive online tutorial (http://research.stowers-institute.org/efg/R/Graphics/Basics/mar-oma/). Let’s use the options we’ve covered so far to enhance our simple example. The code in the following listing produces the graphs in figure 3.7. Listing 3.1 Using graphical parameters to control graph appearance dose <- c(20, 30, 40, 45, 60) drugA <- c(16, 20, 27, 40, 60) drugB <- c(15, 18, 25, 31, 40) opar <- par(no.readonly=TRUE) par(pin=c(2, 3)) par(lwd=2, cex=1.5) par(cex.axis=.75, font.axis=3) plot(dose, drugA, type="b", pch=19, lty=2, col="red") plot(dose, drugB, type="b", pch=23, lty=6, col="blue", bg="green") par(opar) First you enter your data as vectors, then save the current graphical parameter settings (so that you can restore them later). You modify the default graphical parameters so that graphs will be 2 inches wide by 3 inches tall. Additionally, lines will be twice the default width and symbols will be 1.5 times the default size. Axis text will be set to italic and scaled to 75 percent of the default. The first plot is then created using filled red circles and dashed lines. The second plot is created using filled green filled diamonds and a blue border and blue dashed lines. Finally, you restore the original graphical parameter settings. Note that parameters set with the par() function apply to both graphs, whereas parameters specified in the plot functions only apply to that specific graph. Looking at figure 3.7 you can see some limitations in your presentation. The graphs lack titles and the vertical axes are not on the same scale, limiting your ability to compare the two drugs directly. The axis labels could also be more informative. Download from Wow! eBook 6 Chapter 3 Getting started with graphs 20 30 40 50 60 2 0 3 0 4 0 5 0 6 0 dose d r u g A 20 30 40 50 60 1 5 2 0 2 5 3 0 3 5 4 0 dose d r u g B Figure 3.7 Line plot of dose vs. response for both drug A and drug B In the next section, we’ll turn to the customization of text annotations (such as titles and labels) and axes. For more information on the graphical parameters that are avail- able, take a look at help(par). 3.4 Adding text, customized axes, and legends Many high-level plotting functions (for example, plot, hist, boxplot) allow you to include axis and text options, as well as graphical parameters. For example, the follow- ing adds a title (main), subtitle (sub), axis labels (xlab, ylab), and axis ranges (xlim, ylim). The results are presented in figure 3.8: plot(dose, drugA, type="b", col="red", lty=2, pch=2, lwd=2, main="Clinical Trials for Drug A", sub="This is hypothetical data", xlab="Dosage", ylab="Drug Response", xlim=c(0, 60), ylim=c(0, 70)) Again, not all functions allow you to add these options. See the help for the function of interest to see what options are accepted. For finer control and for modularization, you can use the functions described in the remainder of this section to control titles, axes, legends, and text annotations. NoTe Some high-level plotting functions include default titles and labels. You can remove them by adding ann=FALSE in the plot() statement or in a separate par() statement. Download from Wow! eBook dding text, customized axes, and legends 57 0 10 20 30 40 50 60 0 1 0 2 0 3 0 4 0 5 0 6 0 70 Clinical Trials for Drug A This is hypothetical data Dosage D r u g R e s p o n s e Figure 3.8 Line plot of dose versus response for drug A with title, subtitle, and modified axes 3.4.1 Titles Use the title() function to add title and axis labels to a plot. The format is title(main="main title", sub="sub-title", xlab="x-axis label", ylab="y-axis label") Graphical parameters (such as text size, font, rotation, and color) can also be specified in the title() function. For example, the following produces a red title and a blue subtitle, and creates green x and y labels that are 25 percent smaller than the default text size: title(main="My Title", col.main="red", sub="My Sub-title", col.sub="blue", xlab="My X label", ylab="My Y label", col.lab="green", cex.lab=0.75) 3.4.2 Axes Rather than using R’s default axes, you can create custom axes with the axis() func- tion. The format is axis(side, at=, labels=, pos=, lty=, col=, las=, tck=, ...) where each parameter is described in table 3.7. When creating a custom axis, you should suppress the axis automatically generated by the high-level plotting function. The option axes=FALSE suppresses all axes (including all axis frame lines, unless you add the option frame.plot=TRUE). The options xaxt=”n” and yaxt=”n” suppress the x- and y-axis, respectively (leaving the frame Download from Wow! eBook 8 Chapter 3 Getting started with graphs Table 3.7 Axis options option Description side An integer indicating the side of the graph to draw the axis (1=bottom, 2=left, 3=top, 4=right). at A numeric vector indicating where tick marks should be drawn. labels A character vector of labels to be placed at the tick marks (if NULL, the at values will be used). pos The coordinate at which the axis line is to be drawn (that is, the value on the other axis where it crosses). lty Line type. col The line and tick mark color. las Labels are parallel (=0) or perpendicular (=2) to the axis. tck Length of tick mark as a fraction of the plotting region (a negative number is outside the graph, a positive number is inside, 0 suppresses ticks, 1 creates gridlines); the default is –0.01. (...)Other graphical parameters. lines, without ticks). The following listing is a somewhat silly and overblown example that demonstrates each of the features we’ve discussed so far. The resulting graph is presented in figure 3.9. 2 4 6 8 10 123456789 10 11.111.25 1.43 1.67 2 2.5 3.33 5 10 y=10/x An Example of Creative Axes X values Y = X Figure 3.9 A demonstration of axis options Download from Wow! eBook dding text, customized axes, and legends 59 Listing 3.2 An example of custom axes x <- c(1:10) y <- x z <- 10/x opar <- par(no.readonly=TRUE) par(mar=c(5, 4, 4, 8) + 0.1) plot(x, y, type="b", pch=21, col="red", yaxt="n", lty=3, ann=FALSE) lines(x, z, type="b", pch=22, col="blue", lty=2) axis(2, at=x, labels=x, col.axis="red", las=2) axis(4, at=z, labels=round(z, digits=2), col.axis="blue", las=2, cex.axis=0.7, tck=-.01) mtext("y=1/x", side=4, line=3, cex.lab=1, las=2, col="blue") title("An Example of Creative Axes", xlab="X values", ylab="Y=X") par(opar) At this point, we’ve covered everything in listing 3.2 except for the line()and the mtext() statements. A plot() statement starts a new graph. By using the line() statement instead, you can add new graph elements to an existing graph. You’ll use it again when you plot the response of drug A and drug B on the same graph in sec- tion 3.4.4. The mtext() function is used to add text to the margins of the plot. The mtext()function is covered in section 3.4.5, and the line() function is covered more fully in chapter 11. MiNoR TiCk MARks Notice that each of the graphs you’ve created so far have major tick marks but not mi- nor tick marks. To create minor tick marks, you’ll need the minor.tick() function in the Hmisc package. If you don’t already have Hmisc installed, be sure to install it first (see chapter 1, section 1.4.2). You can add minor tick marks with the code library(Hmisc) minor.tick(nx=n, ny=n, tick.ratio=n) where nx and ny specify the number of intervals in which to divide the area between major tick marks on the x-axis and y-axis, respectively. tick.ratio is the size of the minor tick mark relative to the major tick mark. The current length of the major tick mark can be retrieved using par("tck"). For example, the following statement will add one tick mark between each major tick mark on the x-axis and two tick marks be- tween each major tick mark on the y-axis: Specify data Increase margins Plot x versus y Add x versus 1/x line Draw your axes Add titles and text Download from Wow! eBook 0 Chapter 3 Getting started with graphs minor.tick(nx=2, ny=3, tick.ratio=0.5) The length of the tick marks will be 50 percent as long as the major tick marks. An example of minor tick marks is given in the next section (listing 3.3 and figure 3.10). 3.4.3 Reference lines The abline() function is used to add reference lines to our graph. The format is abline(h=yvalues, v=xvalues) Other graphical parameters (such as line type, color, and width) can also be specified in the abline() function. For example: abline(h=c(1,5,7)) adds solid horizontal lines at y = 1, 5, and 7, whereas the code abline(v=seq(1, 10, 2), lty=2, col="blue") adds dashed blue vertical lines at x = 1, 3, 5, 7, and 9. Listing 3.3 creates a reference line for our drug example at y = 30. The resulting graph is displayed in figure 3.10. 3.4.4 Legend When more than one set of data or group is incorporated into a graph, a legend can help you to identify what’s being represented by each bar, pie slice, or line. A legend can be added (not surprisingly) with the legend() function. The format is legend(location, title, legend, ...) The common options are described in table 3.8. Table 3.8 Legend options option Description location There are several ways to indicate the location of the legend. You can give an x,y coordinate for the upper-left corner of the legend. You can use locator(1), in which case you use the mouse to indicate the location of the legend. You can also use the keywords bottom, bottomleft, left, topleft, top, topright, right, bottomright, or center to place the legend in the graph. If you use one of these keywords, you can also use inset= to specify an amount to move the legend into the graph (as fraction of plot region). title A character string for the legend title (optional). legend A character vector with the labels. Download from Wow! eBook dding text, customized axes, and legends 61 Table 3.8 Legend options (continued ) option Description ...Other options. If the legend labels colored lines, specify col= and a vector of colors. If the legend labels point symbols, specify pch= and a vector of point symbols. If the legend labels line width or line style, use lwd= or lty= and a vector of widths or styles. To create colored boxes for the legend (common in bar, box, or pie charts), use fill= and a vector of colors. Other common legend options include bty for box type, bg for background color, cex for size, and text.col for text color. Specifying horiz=TRUE sets the legend horizon- tally rather than vertically. For more on legends, see help(legend). The examples in the help file are particularly informative. Let’s take a look at an example using our drug data (listing 3.3). Again, you’ll use a number of the features that we’ve covered up to this point. The resulting graph is presented in figure 3.10. Listing 3.3 Comparing Drug A and Drug B response by dose dose <- c(20, 30, 40, 45, 60) drugA <- c(16, 20, 27, 40, 60) drugB <- c(15, 18, 25, 31, 40) opar <- par(no.readonly=TRUE) par(lwd=2, cex=1.5, font.lab=2) plot(dose, drugA, type="b", pch=15, lty=1, col="red", ylim=c(0, 60), main="Drug A vs. Drug B", xlab="Drug Dosage", ylab="Drug Response") lines(dose, drugB, type="b", pch=17, lty=2, col="blue") abline(h=c(30), lwd=1.5, lty=2, col="gray") library(Hmisc) minor.tick(nx=3, ny=3, tick.ratio=0.5) legend("topleft", inset=.05, title="Drug Type", c("A","B"), lty=c(1, 2), pch=c(15, 17), col=c("red", "blue")) par(opar) Increase line, text, symbol, label size Generate graph Add minor tick marks Add legend Download from Wow! eBook 2 Chapter 3 Getting started with graphs 20 30 40 50 60 0 1 0 2 0 3 0 4 0 5 0 6 0 Drug A vs. Drug B Drug Dosage Drug Type A B D r u g R e s p o n s e Figure 3.10 An annotated comparison of Drug A and Drug B Almost all aspects of the graph in figure 3.10 can be modified using the options dis- cussed in this chapter. Additionally, there are many ways to specify the options desired. The final annotation to consider is the addition of text to the plot itself. This topic is covered in the next section. 3.4.5 Text annotations Text can be added to graphs using the text() and mtext() functions. text() places text within the graph whereas mtext() places text in one of the four margins. The formats are text(location, "text to place", pos, ...) mtext("text to place", side, line=n, ...) and the common options are described in table 3.9. Table 3.9 options for the text() and mtext() functions option Description location Location can be an x,y coordinate. Alternatively, the text can be placed interactively via mouse by specifying location as locator(1). pos Position relative to location. 1 = below, 2 = left, 3 = above, 4 = right. If you specify pos, you can specify offset= in percent of character width. side Which margin to place text in, where 1 = bottom, 2 = left, 3 = top, 4 = right. You can specify line= to indicate the line in the margin starting with 0 (closest to the plot area) and moving out. You can also specify adj=0 for left/bottom alignment or adj=1 for top/right alignment. Download from Wow! eBook dding text, customized axes, and legends 63 Other common options are cex, col, and font (for size, color, and font style, respectively). The text() function is typically used for labeling points as well as for adding other text annotations. Specify location as a set of x, y coordinates and specify the text to place as a vector of labels. The x, y, and label vectors should all be the same length. An example is given next and the resulting graph is shown in figure 3.11. attach(mtcars) plot(wt, mpg, main="Mileage vs. Car Weight", xlab="Weight", ylab="Mileage", pch=18, col="blue") text(wt, mpg, row.names(mtcars), cex=0.6, pos=4, col="red") detach(mtcars) 2 3 4 5 1 0 1 5 2 0 2 5 3 0 Mileage vs. Car Weight Weight M i l e a g e Mazda RX4Mazda RX4 Wag Datsun 710 Hornet 4 Drive Hornet Sportabout Valiant Duster 360 Merc 240D Merc 230 Merc 280 Merc 280C Merc 450SE Merc 450SL Merc 450SLC CadillacLin Chrys Fiat 128 Honda Civic Toyota Corolla Toyota Corona Dodge ChallengerAMC Javelin Camaro Z28 Pontiac Firebird Fiat X1−9 Porsche 914−2 Lotus Europa Ford Pantera L Ferrari Dino Maserati Bora Volvo 142E Figure 3.11 example of a scatter plot (car weight vs. mileage) with labeled points (car make) Download from Wow! eBook 4 Chapter 3 Getting started with graphs Here we’ve plotted car mileage versus car weight for the 32 automobile makes pro- vided in the mtcars data frame. The text() function is used to add the car makes to the right of each data point. The point labels are shrunk by 40 percent and presented in red. As a second example, the following code can be used to display font families: opar <- par(no.readonly=TRUE) par(cex=1.5) plot(1:7,1:7,type="n") text(3,3,"Example of default text") text(4,4,family="mono","Example of mono-spaced text") text(5,5,family="serif","Example of serif text") par(opar) The results, produced on a Windows platform, are shown in figure 3.12. Here the par() function was used to increase the font size to produce a better display. The resulting plot will differ from platform to platform, because plain, mono, and serif text are mapped to different font families on different systems. What does it look like on yours? MATh ANNoTATioNs Finally, you can add mathematical symbols and formulas to a graph using TEX-like rules. See help(plotmath) for details and examples. You can also try demo(plotmath) to see this in action. A portion of the results is presented in figure 3.13. The plotmath() function can be used to add mathematical symbols to titles, axis labels, or text annota- tion in the body or margins of the graph. You can often gain greater insight into your data by comparing several graphs at one time. So, we’ll end this chapter by looking at ways to combine more than one graph into a single image. 1 2 3 4 5 6 7 1234567 1:7 1 : 7 Example of default text Example of mono−spaced text Example of serif text Figure 3.12 examples of font families on a Windows platform Download from Wow! eBook ombining graphs 65 Arithmetic Operators x + y x + y x − y x − y x * y xy x/y x y x %+−% y x ± y x%/%y x √ y x %*% y x × y x %.% y x ⋅ y −x −x +x +x Sub/Superscripts x[i] xi x^2 x2 Juxtaposition x * y xy paste(x, y, z) xyz Lists list(x, y, z) x, y, z Radicals sqrt(x) x sqrt(x, y) y x Relations x == y x = y x != y x ↑ y x < y x < y x <= y x ʺ y x > y x > y x >= y x ≥ y x %~~% y x ⊕y x %=~% y x ≅ y x %==% y x ≡ y x %prop% y x ∝ y Typeface plain(x) x italic(x) x bold(x) x bolditalic(x) x underline(x) x Figure 3.13 Partial results from demo(plotmath) 3.5 Combining graphs R makes it easy to combine several graphs into one overall graph, using either the par() or layout() function. At this point, don’t worry about the specific types of graphs being combined; our focus here is on the general methods used to com- bine them. The creation and interpretation of each graph type is covered in later chapters. With the par() function, you can include the graphical parameter mfrow=c(nrows, ncols) to create a matrix of nrows x ncols plots that are filled in by row. Alternatively, you can use mfcol=c(nrows, ncols) to fill the matrix by columns. For example, the following code creates four plots and arranges them into two rows and two columns: attach(mtcars) opar <- par(no.readonly=TRUE) par(mfrow=c(2,2)) plot(wt,mpg, main="Scatterplot of wt vs. mpg") plot(wt,disp, main="Scatterplot of wt vs disp") hist(wt, main="Histogram of wt") Download from Wow! eBook 6 Chapter 3 Getting started with graphs boxplot(wt, main="Boxplot of wt") par(opar) detach(mtcars) The results are presented in figure 3.14. As a second example, let’s arrange 3 plots in 3 rows and 1 column. Here’s the code: attach(mtcars) opar <- par(no.readonly=TRUE) par(mfrow=c(3,1)) hist(wt) hist(mpg) hist(disp) par(opar) detach(mtcars) The graph is displayed in figure 3.15. Note that the high-level function hist()includes a default title (use main="" to suppress it, or ann=FALSE to suppress all titles and labels). 2 3 4 5 1 0 1 5 2 0 2 5 3 0 Scatterplot of wt vs. mpg wt m p g 2 3 4 5 1 0 0 2 0 0 3 0 0 4 0 0 Scatterplot of wt vs disp wt d i s p Histogram of wt wt F r e q u e n c y 2 3 4 5 02468 2345 Boxplot of wt Figure 3.14 Graph combining four figures through par(mfrow=c(2,2)) Download from Wow! eBook ombining graphs 67 Histogram of wt wt F r e q u e n c y 2 3 4 5 02468 Histogram of mpg mpg F r e q u e n c y 10 15 20 25 30 35 02468 1 2 Histogram of disp disp F r e q u e n c y 100 200 300 400 500 0246 Figure 3.15 Graph combining with three figures through par(mfrow=c(3,1)) The layout() function has the form layout(mat) where mat is a matrix object speci- fying the location of the multiple plots to combine. In the following code, one figure is placed in row 1 and two figures are placed in row 2: attach(mtcars) layout(matrix(c(1,1,2,3), 2, 2, byrow = TRUE)) hist(wt) hist(mpg) hist(disp) detach(mtcars) The resulting graph is presented in figure 3.16. Optionally, you can include widths= and heights= options in the layout() function to control the size of each figure more precisely. These options have the form widths = a vector of values for the widths of columns heights = a vector of values for the heights of rows Relative widths are specified with numeric values. Absolute widths (in centimeters) are specified with the lcm() function. Download from Wow! eBook 8 Chapter 3 Getting started with graphs Histogram of wt wt F r e q u e n c y 2 3 4 5 02468 Histogram of mpg mpg F r e q u e n c y 10 15 20 25 30 35 02468 1 0 1 2 Histogram of disp disp F r e q u e n c y 100 200 300 400 500 01234567 Figure 3.16 Graph combining three figures using the layout() function with default widths In the following code, one figure is again placed in row 1 and two figures are placed in row 2. But the figure in row 1 is one-third the height of the figures in row 2. Addi- tionally, the figure in the bottom-right cell is one-fourth the width of the figure in the bottom-left cell: attach(mtcars) layout(matrix(c(1, 1, 2, 3), 2, 2, byrow = TRUE), widths=c(3, 1), heights=c(1, 2)) hist(wt) hist(mpg) hist(disp) detach(mtcars) The graph is presented in figure 3.17. As you can see, the layout() function gives you easy control over both the number and placement of graphs in a final image and the relative sizes of these graphs. See help(layout) for more details. Download from Wow! eBook ombining graphs 69 Histogram of wt wt F r e q u e n c y 2 3 4 5 048 Histogram of mpg mpg F r e q u e n c y 10 15 20 25 30 35 02468 1 0 1 2 Histogram of disp disp F r e q u e n c y 100 400 01234567 Figure 3.17 Graph combining three figures using the layout() function with specified widths 3.5.1 Creating a figure arrangement with fine control There are times when you want to arrange or superimpose several figures to create a single meaningful plot. Doing so requires fine control over the placement of the figures. You can accomplish this with the fig= graphical parameter. In the following listing, two box plots are added to a scatter plot to create a single enhanced graph. The resulting graph is shown in figure 3.18. Listing 3.4 Fine placement of figures in a graph par <- par(no.readonly=TRUE) par(fig=c(0, 0.8, 0, 0.8)) plot(mtcars$wt, mtcars$mpg, xlab="Miles Per Gallon", ylab="Car Weight") par(fig=c(0, 0.8, 0.55, 1), new=TRUE) boxplot(mtcars$wt, horizontal=TRUE, axes=FALSE) Set up scatter plot Add box plot above Download from Wow! eBook 0 Chapter 3 Getting started with graphs par(fig=c(0.65, 1, 0, 0.8), new=TRUE) boxplot(mtcars$mpg, axes=FALSE) mtext("Enhanced Scatterplot", side=3, outer=TRUE, line=-3) par(opar) To understand how this graph was created, think of the full graph area as going from (0,0) in the lower-left corner to (1,1) in the upper-right corner. Figure 3.19 will help you visualize this. The format of the fig= parameter is a numerical vector of the form c(x1, x2, y1, y2). The first fig= sets up the scatter plot going from 0 to 0.8 on the x-axis and 0 to 0.8 on the y-axis. The top box plot goes from 0 to 0.8 on the x-axis and 0.55 to 1 on the y-axis. The right-hand box plot goes from 0.65 to 1 on the x-axis and 0 to 0.8 on the y-axis. fig= starts a new plot, so when adding a figure to an existing graph, include the new=TRUE option. I chose 0.55 rather than 0.8 so that the top figure would be pulled closer to the scatter plot. Similarly, I chose 0.65 to pull the right-hand box plot closer to the scatter plot. You have to experiment to get the placement right. 2 3 4 5 1 0 1 5 2 0 2 5 3 0 Miles Per Gallon C a r W e i g h t Enhanced Scatterplot Figure 3.18 A scatter plot with two box plots added to the margins Add box plot to right Download from Wow! eBook ummary 71 (0,0) (1,1) x1 x2 y1 y2 Figure 3.19 specifying locations using the fig= graphical parameter NoTe The amount of space needed for individual subplots can be device dependent. If you get “Error in plot.new(): figure margins too large,” try varying the area given for each portion of the overall graph. You can use fig= graphical parameter to combine several plots into any arrangement within a single graph. With a little practice, this approach gives you a great deal of flexibility when creating complex visual presentations. 3.6 Summary In this chapter, we reviewed methods for creating graphs and saving them in a variety of formats. The majority of the chapter was concerned with modifying the default graphs produced by R, in order to arrive at more useful or attractive plots. You learned how to modify a graph’s axes, fonts, symbols, lines, and colors, as well as how to add titles, subtitles, labels, plotted text, legends, and reference lines. You saw how to specify the size of the graph and margins, and how to combine multiple graphs into a single useful image. Our focus in this chapter was on general techniques that you can apply to all graphs (with the exception of lattice graphs in chapter 16). Later chapters look at specific types of graphs. For example, chapter 7 covers methods for graphing a single variable. Graphing relationships between variables will be described in chapter 11. In chapter 16, we discuss advanced graphic methods, including lattice graphs (graphs that display the relationship between variables, for each level of other variables) and interactive graphs. Interactive graphs let you use the mouse to dynamically explore the plotted relationships. In other chapters, we’ll discuss methods of visualizing data that are particularly useful for the statistical approaches under consideration. Graphs are a central part of Download from Wow! eBook 2 Chapter 3 Getting started with graphs modern data analysis, and I’ll endeavor to incorporate them into each of the statistical approaches we discuss. In the previous chapter we discussed a range of methods for inputting or importing data into R. Unfortunately, in the real world your data is rarely usable in the format in which you first get it. In the next chapter we look at ways to transform and massage our data into a state that’s more useful and conducive to analysis. Download from Wow! eBook 4 73 Basic data management This chapter covers ■ Manipulating dates and missing values ■ Understanding data type conversions ■ Creating and recoding variables ■ Selecting and dropping variables Sorting, merging, and subsetting datasets ■ In chapter 2, we covered a variety of methods for importing data into R. Unfortu- nately, getting our data in the rectangular arrangement of a matrix or data frame is the first step in preparing it for analysis. To paraphrase Captain Kirk in the Star Trek episode “A Taste of Armageddon” (and proving my geekiness once and for all): “Data is a messy business—a very, very messy business.” In my own work, as much as 60 percent of the time I spend on data analysis is focused on preparing the data for analysis. I’ll go out a limb and say that the same is probably true in one form or another for most real-world data analysts. Let’s take a look at an example. 4.1 A working example One of the topics that I study in my current job is how men and women differ in the ways they lead their organizations. Typical questions might be ■ Do men and women in management positions differ in the degree to which they defer to superiors? Download from Wow! eBook 74 CHAPTER 4 Basic data management Does this vary from country to country, or are these gender differences universal?■ One way to address these questions is to have bosses in multiple countries rate their managers on deferential behavior, using questions like the following: This manager asks my opinion before making personnel decisions. 1 2 3 4 5 strongly disagree disagree neither agree nor disagree agree strongly agree The resulting data might resemble those in table 4.1. Each row represents the ratings given to a manager by his or her boss. Table 4.1 Gender differences in leadership behavior Manager Date Country Gender Age q1 q2 q3 q4 q5 1 10/24/08 USM 32 5 4 5 5 5 2 10/28/08 USF 45 3 5 2 5 5 3 10/01/08 UKF 25 3 5 5 5 2 4 10/12/08 UKM 39 3 3 4 5 05/01/09 UKF 99 2 2 1 2 1 Here, each manager is rated by their boss on five statements (q1 to q5) related to def- erence to authority. For example, manager 1 is a 32-year-old male working in the US and is rated deferential by his boss, while manager 5 is a female of unknown age (99 probably indicates missing) working in the UK and is rated low on deferential behavior. The date column captures when the ratings were made. Although a dataset might have dozens of variables and thousands of observations, we’ve only included 10 columns and 5 rows to simplify the examples. Additionally, we’ve limited the number of items pertaining to the managers’ deferential behavior to 5. In a real-world study, you’d probably use 10–20 such items to improve the reliability and validity of the results. You can create a data frame containing the data in table 4.1 using the following code. Listing 4.1 Creating the leadership data frame manager <- c(1, 2, 3, 4, 5) date <- c("10/24/08", "10/28/08", "10/1/08", "10/12/08", "5/1/09") country <- c("US", "US", "UK", "UK", "UK") gender <- c("M", "F", "F", "M", "F") age <- c(32, 45, 25, 39, 99) q1 <- c(5, 3, 3, 3, 2) q2 <- c(4, 5, 5, 3, 2) q3 <- c(5, 2, 5, 4, 1) q4 <- c(5, 5, 5, NA, 2) q5 <- c(5, 5, 2, NA, 1) leadership <- data.frame(manager, date, country, gender, age, q1, q2, q3, q4, q5, stringsAsFactors=FALSE) Download from Wow! eBook Creating new variables 75 In order to address the questions of interest, we must first address several data manage- ment issues. Here’s a partial list: ■ The five ratings (q1 to q5) will need to be combined, yielding a single mean deferential score from each manager. ■ In surveys, respondents often skip questions. For example, the boss rating man- ager 4 skipped questions 4 and 5. We’ll need a method of handling incomplete data. We’ll also need to recode values like 99 for age to missing. ■ There may be hundreds of variables in a dataset, but we may only be interested in a few. To simplify matters, we’ll want to create a new dataset with only the vari- ables of interest. ■ Past research suggests that leadership behavior may change as a function of the manager’s age. To examine this, we may want to recode the current values of age into a new categorical age grouping (for example, young, middle-aged, elder). ■ Leadership behavior may change over time. We might want to focus on deferen- tial behavior during the recent global financial crisis. To do so, we may want to limit the study to data gathered during a specific period of time (say, January 1, 2009 to December 31, 2009). We’ll work through each of these issues in the current chapter, as well as other basic data management tasks such as combining and sorting datasets. Then in chapter 5 we’ll look at some advanced topics. 4.2 Creating new variables In a typical research project, you’ll need to create new variables and transform existing ones. This is accomplished with statements of the form variable <- expression A wide array of operators and functions can be included in the expression portion of the statement. Table 4.2 lists R’s arithmetic operators . Arithmetic operators are used when developing formulas. Table 4.2 Arithmetic operators Operator Description + Addition - Subtraction * Multiplication / Division ^ or ** Exponentiation x%%y Modulus (x mod y) 5%%2 is 1 x%/%y Integer division 5%/%2 is 2 Download from Wow! eBook 76 CHAPTER 4 Basic data management Let’s say that you have a data frame named mydata, with variables x1 and x2, and you want to create a new variable sumx that adds these two variables and a new variable called meanx that averages the two variables. If you use the code sumx <- x1 + x2 meanx <- (x1 + x2)/2 you’ll get an error, because R doesn’t know that x1 and x2 are from data frame mydata. If you use this code instead sumx <- mydata$x1 + mydata$x2 meanx <- (mydata$x1 + mydata$x2)/2 the statements will succeed but you’ll end up with a data frame (mydata) and two separate vectors (sumx and meanx). This is probably not what you want. Ultimately, you want to incorporate new variables into the original data frame. The following listing provides three separate ways to accomplish this goal. The one you choose is up to you; the results will be the same. Listing 4.2 Creating new variables mydata<-data.frame(x1 = c(2, 2, 6, 4), x2 = c(3, 4, 2, 8)) mydata$sumx <- mydata$x1 + mydata$x2 mydata$meanx <- (mydata$x1 + mydata$x2)/2 attach(mydata) mydata$sumx <- x1 + x2 mydata$meanx <- (x1 + x2)/2 detach(mydata) mydata <- transform(mydata, sumx = x1 + x2, meanx = (x1 + x2)/2) Personally, I prefer the third method, exemplified by the use of the transform() func- tion . It simplifies inclusion of as many new variables as desired and saves the results to the data frame. 4.3 Recoding variables Recoding involves creating new values of a variable conditional on the existing values of the same and/or other variables. For example, you may want to ■ Change a continuous variable into a set of categories ■ Create a pass/fail variable based on a set of cutoff scores Replace miscoded values with correct values ■ To recode data, you can use one or more of R’s logical operators (see table 4.3). Logi- cal operators are expressions that return TRUE or FALSE. Download from Wow! eBook Recoding variables 77 Table 4.3 Logical operators Operator Description < Less than <= Less than or equal to > Greater than >= Greater than or equal to == Exactly equal to != Not equal to !x Not x x | y x or y x & y x and y isTRUE(x) Test if x is TRUE Let’s say that you want to recode the ages of the managers in our leadership dataset from the continuous variable age to the categorical variable agecat (Young, Middle Aged, Elder). First, you must recode the value 99 for age to missing with code such as leadership$age[leadership$age == 99] <- NA The statement variable[condition] <- expression will only make the assignment when condition is TRUE. Once missing values for age have been specified, you can then use the following code to create the agecat variable: leadership$agecat[leadership$age > 75] <- "Elder" leadership$agecat[leadership$age >= 55 & leadership$age <= 75] <- "Middle Aged" leadership$agecat[leadership$age < 55] <- "Young" You include the data frame names in leadership$agecat to ensure that the new variable is saved back to the data frame. You define middle aged as 55 to 75 so that I won’t feel so old. Note that if you hadn’t recoded 99 as missing for age first, manager 5 would’ve erroneously been given the value “Elder” for agecat. This code can be written more compactly as leadership <- within(leadership,{ agecat <- NA agecat[age > 75] <- "Elder" agecat[age >= 55 & age <= 75] <- "Middle Aged" agecat[age < 55] <- "Young" }) The within() function is similar to the with() function (section 2.2.4), but allows you to modify the data frame. First, the variable agecat variable is created and set to missing for each row of the data frame. Then the remaining statements within the Download from Wow! eBook 78 CHAPTER 4 Basic data management braces are executed in order. Remember that agecat is a character variable; you’re likely to want to turn it into an ordered factor, as explained in section 2.2.5. Several packages offer useful recoding functions; in particular, the car package’s recode() function recodes numeric and character vectors and factors very simply. The package doBy offers recodevar() , another popular function. Finally, R ships with cut() , which allows you to divide the range of a numeric variable into intervals, returning a factor. 4.4 Renaming variables If you’re not happy with your variable names, you can change them interactively or pro- grammatically. Let’s say that you want to change the variables manager to managerID and date to testDate. You can use the statement fix(leadership) to invoke an interactive editor, click on the variable names, and rename them in the dialogs that are presented (see figure 4.1). Programmatically, the reshape package has a rename() function that’s useful for altering the names of variables. The format of the rename() function is rename(dataframe, c(oldname="newname", oldname="newname",…)) Here’s an example: library(reshape) leadership <- rename(leadership, c(manager="managerID", date="testDate") ) Figure 4.1 Renaming variables interactively using the fix() function Download from Wow! eBook Missing values 79 The reshape package isn’t installed by default, so you’ll need to install it on first use using the install.packages("reshape") command . The reshape package has a powerful set of functions for altering the structure of a dataset. We’ll explore several in chapter 5. Finally, you can rename variables via the names() function . For example: names(leadership)[2] <- "testDate" would rename date to testDate as demonstrated in the following code: > names(leadership) [1] "manager" "date" "country" "gender" "age" "q1" "q2" [8] "q3" "q4" "q5" > names(leadership)[2] <- "testDate" > leadership manager testDate country gender age q1 q2 q3 q4 q5 1 1 10/24/08 US M 32 5 4 5 5 5 2 2 10/28/08 US F 45 3 5 2 5 5 3 3 10/1/08 UK F 25 3 5 5 5 2 4 4 10/12/08 UK M 39 3 3 4 NA NA 5 5 5/1/09 UK F 99 2 2 1 2 1 In a similar fashion, names(leadership)[6:10] <- c("item1", "item2", "item3", "item4", "item5") would rename q1 through q5 to item1 through item5. 4.5 Missing values In a project of any size, data is likely to be incomplete because of missed questions, faulty equipment, or improperly coded data. In R, missing values are represented by the symbol NA (not available) . Impossible values (for example, dividing by 0) are rep- resented by the symbol NaN (not a number) . Unlike programs such as SAS, R uses the same missing values symbol for character and numeric data. R provides a number of functions for identifying observations that contain missing values. The function is.na() allows you to test for the presence of missing values. Assume that you have a vector: y <- c(1, 2, 3, NA) then the function is.na(y) returns c(FALSE, FALSE, FALSE, TRUE). Notice how the is.na() function works on an object. It returns an object of the same size, with the entries replaced by TRUE if the element is a missing value, and FALSE if the element is not a missing value. Listing 4.3 applies this to our leadership example. Download from Wow! eBook 80 CHAPTER 4 Basic data management Listing 4.3 Applying the is.na() function > is.na(leadership[,6:10]) q1 q2 q3 q4 q5 [1,] FALSE FALSE FALSE FALSE FALSE [2,] FALSE FALSE FALSE FALSE FALSE [3,] FALSE FALSE FALSE FALSE FALSE [4,] FALSE FALSE FALSE TRUE TRUE [5,] FALSE FALSE FALSE FALSE FALSE Here, leadership[,6:10] limited the data frame to columns 6 to 10, and is.na() identified which values are missing. NOTE Missing values are considered noncomparable, even to themselves. This means that you can’t use comparison operators to test for the presence of missing values. For example, the logical test myvar == NA is never TRUE. Instead, you have to use missing values functions, like those in this section, to identify the missing values in R data objects. 4.5.1 Recoding values to missing As demonstrated in section 4.3, you can use assignments to recode values to missing. In our leadership example, missing age values were coded as 99. Before analyzing this dataset, you must let R know that the value 99 means missing in this case (otherwise the mean age for this sample of bosses will be way off!). You can accomplish this by recoding the variable: leadership$age[leadership$age == 99] <- NA Any value of age that’s equal to 99 is changed to NA. Be sure that any missing data is properly coded as missing before analyzing the data or the results will be meaningless. 4.5.2 Excluding missing values from analyses Once you’ve identified the missing values, you need to eliminate them in some way before analyzing your data further. The reason is that arithmetic expressions and func- tions that contain missing values yield missing values. For example, consider the fol- lowing code: x <- c(1, 2, NA, 3) y <- x[1] + x[2] + x[3] + x[4] z <- sum(x) Both y and z will be NA (missing) because the third element of x is missing. Luckily, most numeric functions have a na.rm=TRUE option that removes missing values prior to calculations and applies the function to the remaining values: x <- c(1, 2, NA, 3) y <- sum(x, na.rm=TRUE) Here, y is equal to 6. When using functions with incomplete data, be sure to check how that function handles missing data by looking at its online help (for example, help(sum)). The Download from Wow! eBook Date values 81 sum() function is only one of many functions we’ll consider in chapter 5. Functions allow you to transform data with flexibility and ease. You can remove any observation with missing data by using the na.omit() function . na.omit() deletes any rows with missing data. Let’s apply this to our leadership dataset in the following listing. Listing 4.4 Using na.omit() to delete incomplete observations > leadership manager date country gender age q1 q2 q3 q4 q5 1 1 10/24/08 US M 32 5 4 5 5 5 2 2 10/28/08 US F 40 3 5 2 5 5 3 3 10/01/08 UK F 25 3 5 5 5 2 4 4 10/12/08 UK M 39 3 3 4 NA NA 5 5 05/01/09 UK F 99 2 2 1 2 1 > newdata <- na.omit(leadership) > newdata manager date country gender age q1 q2 q3 q4 q5 1 1 10/24/08 US M 32 5 4 5 5 5 2 2 10/28/08 US F 40 3 5 2 5 5 3 3 10/01/08 UK F 25 3 5 5 5 2 5 5 05/01/09 UK F 99 2 2 1 2 1 Any rows containing missing data are deleted from leadership before the results are saved to newdata. Deleting all observations with missing data (called listwise deletion ) is one of several methods of handling incomplete datasets. If there are only a few missing values or they’re concentrated in a small number of observations, listwise deletion can provide a good solution to the missing values problem. But if missing values are spread throughout the data, or there’s a great deal of missing data in a small number of variables, listwise deletion can exclude a substantial percentage of your data. We’ll explore several more sophisticated methods of dealing with missing values in chapter 15. Next, let’s take a look at dates. 4.6 Date values Dates are typically entered into R as character strings and then translated into date vari- ables that are stored numerically. The function as.Date() is used to make this transla- tion. The syntax is as.Date(x, "input_format") , where x is the character data and input_format gives the appropriate format for reading the date (see table 4.4). Table 4.4 Date formats Symbol Meaning Example %d Day as a number (0–31) 01–31 %a %A Abbreviated weekday Unabbreviated weekday Mon Monday %m Month (00–12) 00–12 Data frame with missing data Data frame with complete cases only Download from Wow! eBook 82 CHAPTER 4 Basic data management Table 4.4 Date formats (continued) Symbol Meaning Example %b %B Abbreviated month Unabbreviated month Jan January %y %Y 2-digit year 4-digit year 07 2007 The default format for inputting dates is yyyy-mm-dd. The statement mydates <- as.Date(c("2007-06-22", "2004-02-13")) converts the character data to dates using this default format. In contrast, strDates <- c("01/05/1965", "08/16/1975") dates <- as.Date(strDates, "%m/%d/%Y") reads the data using a mm/dd/yyyy format. In our leadership dataset, date is coded as a character variable in mm/dd/yy format. Therefore: myformat <- "%m/%d/%y" leadership$date <- as.Date(leadership$date, myformat) uses the specified format to read the character variable and replace it in the data frame as a date variable. Once the variable is in date format, you can analyze and plot the dates using the wide range of analytic techniques covered in later chapters. Two functions are especially useful for time-stamping data . Sys.Date() returns today’s date and date() returns the current date and time. As I write this, it’s December 12, 2010 at 4:28pm. So executing those functions produces > Sys.Date() [1] "2010-12-01" > date() [1] "Wed Dec 01 16:28:21 2010" You can use the format(x, format="output_format") function to output dates in a specified format, and to extract portions of dates: > today <- Sys.Date() > format(today, format="%B %d %Y") [1] "December 01 2010" > format(today, format="%A") [1] "Wednesday" The format() function takes an argument (a date in this case) and applies an output format (in this case, assembled from the symbols in table 4.4). The important result here is that there are only two more days until the weekend! When R stores dates internally, they’re represented as the number of days since January 1, 1970, with negative values for earlier dates. That means you can perform arithmetic operations on them. For example: > startdate <- as.Date("2004-02-13") > enddate <- as.Date("2011-01-22") Download from Wow! eBook Type conversions 83 > days <- enddate - startdate > days Time difference of 2535 days displays the number of days between February 13, 2004 and January 22, 2011. Finally, you can also use the function difftime() to calculate a time interval and express it as seconds, minutes, hours, days, or weeks. Let’s assume that I was born on October 12, 1956. How old am I? > today <- Sys.Date() > dob <- as.Date("1956-10-12") > difftime(today, dob, units="weeks") Time difference of 2825 weeks Apparently, I am 2825 weeks old. Who knew? Final test: On which day of the week was I born? 4.6.1 Converting dates to character variables Although less commonly used, you can also convert date variables to character vari- ables. Date values can be converted to character values using the as.character() function : strDates <- as.character(dates) The conversion allows you to apply a range of character functions to the data values (subsetting, replacement, concatenation, etc.). We’ll cover character functions in de- tail in chapter 5. 4.6.2 Going further To learn more about converting character data to dates, take a look at help(as. Date) and help(strftime) . To learn more about formatting dates and times, see help(ISOdatetime) . The lubridate package contains a number of functions that simplify working with dates, including functions to identify and parse date-time data, extract date-time components (for example, years, months, days, etc.), and perform arithmetic calculations on date-times. If you need to do complex calculations with dates, the fCalendar package can also help. It provides a myriad of functions for deal- ing with dates, can handle multiple time zones at once, and provides sophisticated calendar manipulations that recognize business days, weekends, and holidays. 4.7 Type conversions In the previous section, we discussed how to convert character data to date values, and vice versa. R provides a set of functions to identify an object’s data type and convert it to a different data type. Type conversions in R work in a similar fashion to those in other statistical programming languages. For example, adding a character string to a numeric vector converts all the elements in the vector to character values. You can use the functions listed in table 4.5 to test for a data type and to convert it to a given type. Download from Wow! eBook 84 CHAPTER 4 Basic data management Table 4.5 Type conversion functions Test Convert is.numeric() as.numeric() is.character() as.character() is.vector() as.vector() is.matrix() as.matrix() is.data.frame() as.data.frame() is.factor() as.factor() is.logical() as.logical() Functions of the form is.datatype()return TRUE or FALSE, whereas as.datatype() converts the argument to that type. The following listing provides an example. Listing 4.5 Converting from one data type to another > a <- c(1,2,3) > a [1] 1 2 3 > is.numeric(a) [1] TRUE > is.vector(a) [1] TRUE > a <- as.character(a) > a [1] "1" "2" "3" > is.numeric(a) [1] FALSE > is.vector(a) [1] TRUE > is.character(a) [1] TRUE When combined with the flow controls (such as if-then) that we’ll discuss in chapter 5, the is.datatype() function can be a powerful tool, allowing you to handle data in different ways, depending on its type. Additionally, some R functions require data of a specific type (character or numeric, matrix or data frame) and the as.datatype() will let you transform your data into the format required prior to analyses. 4.8 Sorting data Sometimes, viewing a dataset in a sorted order can tell you quite a bit about the data. For example, which managers are most deferential? To sort a data frame in R, use the order() function . By default, the sorting order is ascending. Prepend the sorting variable with a minus sign to indicate a descending order. The following examples il- lustrate sorting with the leadership data frame. Download from Wow! eBook Merging datasets 85 The statement newdata <- leadership[order(leadership$age),] creates a new dataset containing rows sorted from youngest manager to oldest man- ager. The statement attach(leadership) newdata <- leadership[order(gender, age),] detach(leadership) sorts the rows into female followed by male, and youngest to oldest within each gender. Finally, attach(leadership) newdata <-leadership[order(gender, -age),] detach(leadership) sorts the rows by gender, and then from oldest to youngest manager within each gender. 4.9 Merging datasets If your data exist in multiple locations, you’ll need to combine them before moving forward. This section shows you how to add columns (variables) and rows (observa- tions) to a data frame. 4.9.1 Adding columns To merge two data frames (datasets) horizontally, you use the merge() function. In most cases, two data frames are joined by one or more common key variables (that is an inner join). For example: total <- merge(dataframeA, dataframeB, by="ID") merges dataframeA and dataframeB by ID. Similarly, total <- merge(dataframeA, dataframeB, by=c("ID","Country")) merges the two data frames by ID and Country. Horizontal joins like this are typically used to add variables to a data frame. NOTE If you’re joining two matrices or data frames horizontally and don’t need to specify a common key, you can use the cbind() function : total <- cbind(A, B) This function will horizontally concatenate the objects A and B. For the function to work properly, each object has to have the same number of rows and be sorted in the same order. 4.9.2 Adding rows To join two data frames (datasets) vertically, use the rbind() function : Download from Wow! eBook 86 CHAPTER 4 Basic data management total <- rbind(dataframeA, dataframeB) The two data frames must have the same variables, but they don’t have to be in the same order. If dataframeA has variables that dataframeB doesn’t, then before joining them do one of the following: ■ Delete the extra variables in dataframeA ■ Create the additional variables in dataframeB and set them to NA (missing) Vertical concatenation is typically used to add observations to a data frame. 4.10 Subsetting datasets R has powerful indexing features for accessing the elements of an object. These features can be used to select and exclude variables, observations, or both. The following sec- tions demonstrate several methods for keeping or deleting variables and observations. 4.10.1 Selecting (keeping) variables It’s a common practice to create a new dataset from a limited number of variables cho- sen from a larger dataset. In chapter 2, you saw that the elements of a data frame are accessed using the notation dataframe[row indices, column indices] . You can use this to select variables. For example: newdata <- leadership[, c(6:10)] selects variables q1, q2, q3, q4, and q5 from the leadership data frame and saves them to the data frame newdata . Leaving the row indices blank (,) selects all the rows by default. The statements myvars <- c("q1", "q2", "q3", "q4", "q5") newdata <-leadership[myvars] accomplish the same variable selection. Here, variable names (in quotes) have been entered as column indices, thereby selecting the same columns. Finally, you could’ve used myvars <- paste("q", 1:5, sep="") newdata <- leadership[myvars] This example uses the paste() function to create the same character vector as in the previous example. The paste() function will be covered in chapter 5. 4.10.2 Excluding (dropping) variables There are many reasons to exclude variables. For example, if a variable has several missing values, you may want to drop it prior to further analyses. Let’s look at some methods of excluding variables. You could exclude variables q3 and q4 with the statements myvars <- names(leadership) %in% c("q3", "q4") newdata <- leadership[!myvars] Download from Wow! eBook Subsetting datasets 87 In order to understand why this works, you need to break it down: 1 names(leadership) produces a character vector containing the variable names. c("managerID","testDate","country","gender","age","q1", "q2","q3","q4","q5"). 2 names(leadership) %in% c("q3", "q4") returns a logical vector with TRUE for each element in names(leadership)that matches q3 or q4 and FALSE otherwise. c(FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, TRUE, TRUE, FALSE). 3 The not (!) operator reverses the logical values c(TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, TRUE). 4 leadership[c(TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, TRUE)] selects columns with TRUE logical values, so q3 and q4 are excluded. Knowing that q3 and q4 are the 8th and 9th variable, you could exclude them with the statement newdata <- leadership[c(-8,-9)] This works because prepending a column index with a minus sign (-) excludes that column. Finally, the same deletion can be accomplished via leadership$q3 <- leadership$q4 <- NULL Here you set columns q3 and q4 to undefined (NULL). Note that NULL isn’t the same as NA (missing). Dropping variables is the converse of keeping variables. The choice will depend on which is easier to code. If there are many variables to drop, it may be easier to keep the ones that remain, or vice versa. 4.10.3 Selecting observations Selecting or excluding observations (rows) is typically a key aspect of successful data preparation and analysis. Several examples are given in the following listing. Listing 4.6 Selecting observations newdata <- leadership[1:3,] newdata <- leadership[which(leadership$gender=="M" & leadership$age > 30),] attach(leadership) newdata <- leadership[which(gender=='M' & age > 30),] detach(leadership) In each of these examples, you provide the row indices and leave the column indi- ces blank (therefore choosing all columns). In the first example, you ask for rows 1 through 3 (the first three observations). Download from Wow! eBook 88 CHAPTER 4 Basic data management In the second example, you select all men over 30. Let’s break down this line of code in order to understand it: 1 The logical comparison leadership$gender=="M" produces the vector c(TRUE, FALSE, FALSE, TRUE, FALSE). 2 The logical comparison leadership$age > 30 produces the vector c(TRUE, TRUE, FALSE, TRUE, TRUE). 3 The logical comparison c(TRUE, FALSE, FALSE, TRUE, TRUE) & c(TRUE, TRUE, FALSE, TRUE, TRUE) produces the vector c(TRUE, FALSE, FALSE, TRUE, FALSE). 4 The function which() gives the indices of a vector that are TRUE. Thus, which(c(TRUE, FALSE, FALSE, TRUE, FALSE)) produces the vector c(1, 4). 5 leadership[c(1,4),] selects the first and fourth observations from the data frame. This meets our selection criteria (men over 30). In the third example, the attach() function is used so that you don’t have to prepend the variable names with the data frame names. At the beginning of this chapter, I suggested that you might want to limit your analyses to observations collected between January 1, 2009 and December 31, 2009. How can you do this? Here’s one solution: leadership$date <- as.Date(leadership$date, "%m/%d/%y") startdate <- as.Date("2009-01-01") enddate <- as.Date("2009-10-31") newdata <- leadership[which(leadership$date >= startdate & leadership$date <= enddate),] Convert the date values read in originally as character values to date values using the format mm/dd/yy. Then, create starting and ending dates. Because the default for the as.Date() function is yyyy-mm-dd, you don’t have to supply it here. Finally, select cases meeting your desired criteria as you did in the previous example. 4.10.4 The subset() function The examples in the previous two sections are important because they help describe the ways in which logical vectors and comparison operators are interpreted within R. Understanding how these examples work will help you to interpret R code in general. Now that you’ve done things the hard way, let’s look at a shortcut. The subset function is probably the easiest way to select variables and observations. Here are two examples: newdata <- subset(leadership, age >= 35 | age < 24, select=c(q1, q2, q3, q4)) newdata <- subset(leadership, gender=="M" & age > 25, select=gender:q4) In the first example, you select all rows that have a value of age greater than or equal to 35 or age less than 24. You keep the variables q1 through q4. In the second example, Download from Wow! eBook Using SQL statements to manipulate data frames 89 you select all men over the age of 25 and you keep variables gender through q4 (gen- der, q4, and all columns between them). You’ve seen the colon operator from:to in chapter 2. Here, it provides all variables in a data frame between the from variable and the to variable, inclusive. 4.10.5 Random samples Sampling from larger datasets is a common practice in data mining and machine learn- ing. For example, you may want to select two random samples, creating a predictive model from one and validating its effectiveness on the other. The sample() function enables you to take a random sample (with or without replacement) of size n from a dataset. You could take a random sample of size 3 from the leadership dataset using the statement mysample <- leadership[sample(1:nrow(leadership), 3, replace=FALSE),] The first argument to the sample() function is a vector of elements to choose from. Here, the vector is 1 to the number of observations in the data frame. The second argument is the number of elements to be selected, and the third argument indicates sampling without replacement. The sample() function returns the randomly sampled elements, which are then used to select rows from the data frame. GOING FURTHER R has extensive facilities for sampling, including drawing and calibrating survey sam- ples (see the sampling package) and analyzing complex survey data (see the survey package). Other methods that rely on sampling, including bootstrapping and resam- pling statistics , are described in chapter 11. 4.11 Using SQL statements to manipulate data frames Until now, you’ve been using R statements to manipulate data. But many data analysts come to R well versed in Structured Query Language (SQL). It would be a shame to lose all that accumulated knowledge. Therefore, before we end, let me briefly mention the existence of the sqldf package. (If you’re unfamiliar with SQL, please feel free to skip this section.) After downloading and installing the package (install.packages("sqldf")) , you can use the sqldf() function to apply SQL SELECT statements to data frames. Two examples are given in the following listing. Listing 4.7 Using SQL statements to manipulate data frames > library(sqldf) > newdf <- sqldf("select * from mtcars where carb=1 order by mpg", row.names=TRUE) > newdf mpg cyl disp hp drat wt qsec vs am gear carb Valiant 18.1 6 225.0 105 2.76 3.46 20.2 1 0 3 1 Download from Wow! eBook 90 CHAPTER 4 Basic data management Hornet 4 Drive 21.4 6 258.0 110 3.08 3.21 19.4 1 0 3 1 Toyota Corona 21.5 4 120.1 97 3.70 2.46 20.0 1 0 3 1 Datsun 710 22.8 4 108.0 93 3.85 2.32 18.6 1 1 4 1 Fiat X1-9 27.3 4 79.0 66 4.08 1.94 18.9 1 1 4 1 Fiat 128 32.4 4 78.7 66 4.08 2.20 19.5 1 1 4 1 Toyota Corolla 33.9 4 71.1 65 4.22 1.83 19.9 1 1 4 1 > sqldf("select avg(mpg) as avg_mpg, avg(disp) as avg_disp, gear from mtcars where cyl in (4, 6) group by gear") avg_mpg avg_disp gear 1 20.3 201 3 2 24.5 123 4 3 25.4 120 5 In the first example, you selected all the variables (columns) from the data frame mt- cars, kept only automobiles (rows) with one carburetor (carb), sorted the automo- biles in ascending order by mpg, and saved the results as the data frame newdf. The option row.names=TRUE carried the row names from the original data frame over to the new one. In the second example, you printed the mean mpg and disp within each level of gear for automobiles with four or six cylinders (cyl). Experienced SQL users will find the sqldf package a useful adjunct to data management in R. See the project home page (http://code.google.com/p/sqldf/) for more details. 4.12 Summary We covered a great deal of ground in this chapter. We looked at the way R stores miss- ing and date values and explored various ways of handling them. You learned how to determine the data type of an object and how to convert it to other types. You used simple formulas to create new variables and recode existing variables. I showed you how to sort your data and rename your variables. You learned how to merge your data with other datasets both horizontally (adding variables) and vertically (adding observa- tions). Finally, we discussed how to keep or drop variables and how to select observa- tions based on a variety of criteria. In the next chapter, we’ll look at the myriad of arithmetic, character, and statistical functions that R makes available for creating and transforming variables. After exploring ways of controlling program flow, you’ll see how to write your own functions. We’ll also explore how you can use these functions to aggregate and summarize your data. By the end of chapter 5 you’ll have most of the tools necessary to manage complex datasets. (And you’ll be the envy of data analysts everywhere!) Download from Wow! eBook 5 91 Advanced data management This chapter covers Mathematical and statistical functions■ Character functions■ ■ Looping and conditional execution User-written functions■ ■ Ways to aggregate and reshape data In chapter 4, we reviewed the basic techniques used for managing datasets within R. In this chapter, we’ll focus on advanced topics. The chapter is divided into three ba- sic parts. In the first part we’ll take a whirlwind tour of R’s many functions for math- ematical, statistical, and character manipulation. To give this section relevance, we begin with a data management problem that can be solved using these functions. After covering the functions themselves, we’ll look at one possible solution to the data management problem. Next, we cover how to write your own functions to accomplish data management and analysis tasks. First, you’ll explore ways of controlling program flow, including looping and conditional statement execution. Then we’ll investigate the structure of user-written functions and how to invoke them once created. Then, we’ll look at ways of aggregating and summarizing data, along with methods of reshaping and restructuring datasets. When aggregating data, you Download from Wow! eBook 92 CHAPTER 5 Advanced data management can specify the use of any appropriate built-in or user-written function to accomplish the summarization, so the topics you learned in the first two parts of the chapter will provide a real benefit. 5.1 A data management challenge To begin our discussion of numerical and character functions, let’s consider a data management problem. A group of students have taken exams in Math, Science, and English. You want to combine these scores in order to determine a single performance indicator for each student. Additionally, you want to assign an A to the top 20 percent of students, a B to the next 20 percent, and so on. Finally, you want to sort the students alphabetically. The data are presented in table 5.1. Table 5.1 Student exam data Student Math Science English John Davis 502 95 25 Angela Williams 600 99 22 Bullwinkle Moose 412 80 18 David Jones 358 82 15 Janice Markhammer 495 75 20 Cheryl Cushing 512 85 28 Reuven Ytzrhak 410 80 15 Greg Knox 625 95 30 Joel England 573 89 27 Mary Rayburn 522 86 18 Looking at this dataset, several obstacles are immediately evident. First, scores on the three exams aren’t comparable. They have widely different means and standard devia- tions, so averaging them doesn’t make sense. You must transform the exam scores into comparable units before combining them. Second, you’ll need a method of determin- ing a student’s percentile rank on this score in order to assign a grade. Third, there’s a single field for names, complicating the task of sorting students. You’ll need to break apart their names into first name and last name in order to sort them properly. Each of these tasks can be accomplished through the judicious use of R’s numerical and character functions. After working through the functions described in the next section, we’ll consider a possible solution to this data management challenge. Download from Wow! eBook Numerical and character functions 93 5.2 Numerical and character functions In this section, we’ll review functions in R that can be used as the basic building blocks for manipulating data. They can be divided into numerical (mathematical, statistical, probability) and character functions. After we review each type, I’ll show you how to apply functions to the columns (variables) and rows (observations) of matrices and data frames (see section 5.2.6). 5.2.1 Mathematical functions Table 5.2 lists common mathematical functions along with short examples. Table 5.2 Mathematical functions Function Description abs(x) Absolute value abs(-4) returns 4. sqrt(x) Square root sqrt(25) returns 5. This is the same as 25^(0.5). ceiling(x) Smallest integer not less than x ceiling(3.475) returns 4. floor(x) Largest integer not greater than x floor(3.475) returns 3. trunc(x) Integer formed by truncating values in x toward 0 trunc(5.99) returns 5. round(x, digits=n) Round x to the specified number of decimal places round(3.475, digits=2) returns 3.48. signif(x, digits=n ) Round x to the specified number of significant digits signif(3.475, digits=2) returns 3.5. cos(x) , sin(x) , tan(x) Cosine, sine, and tangent cos(2) returns –0.416. acos(x) , asin(x) , atan(x) Arc-cosine, arc-sine, and arc-tangent acos(-0.416) returns 2. cosh(x) , sinh(x) , tanh(x) Hyperbolic cosine, sine, and tangent sinh(2) returns 3.627. acosh(x) , asinh(x) , atanh(x) Hyperbolic arc-cosine, arc-sine, and arc-tangent asinh(3.627) returns 2. log(x,base=n) log(x) log10(x) Logarithm of x to the base n For convenience log(x) is the natural logarithm. log10(x) is the common logarithm. log(10) returns 2.3026. log10(10) returns 1. Download from Wow! eBook 94 CHAPTER 5 Advanced data management Table 5.2 Mathematical functions (continued) Function Description exp(x) Exponential function exp(2.3026) returns 10. Data transformation is one of the primary uses for these functions. For example, you often transform positively skewed variables such as income to a log scale before further analyses. Mathematical functions will also be used as components in formulas, in plot- ting functions (for example, x versus sin(x)) and in formatting numerical values prior to printing. The examples in table 5.2 apply mathematical functions to scalars (individual numbers). When these functions are applied to numeric vectors, matrices, or data frames, they operate on each individual value. For example, sqrt(c(4, 16, 25)) returns c(2, 4, 5). 5.2.2 Statistical functions Common statistical functions are presented in table 5.3. Many of these functions have optional parameters that affect the outcome. For example: y <- mean(x) provides the arithmetic mean of the elements in object x, and z <- mean(x, trim = 0.05, na.rm=TRUE) provides the trimmed mean, dropping the highest and lowest 5 percent of scores and any missing values. Use the help() function to learn more about each function and its arguments. Table 5.3 Statistical functions Function Description mean(x) Mean mean(c(1,2,3,4)) returns 2.5. median(x) Median median(c(1,2,3,4)) returns 2.5. sd(x) Standard deviation sd(c(1,2,3,4)) returns 1.29. var(x) Variance var(c(1,2,3,4)) returns 1.67. mad(x) Median absolute deviation mad(c(1,2,3,4)) returns 1.48. Download from Wow! eBook Numerical and character functions 95 Table 5.3 Statistical functions (continued) Function Description quantile(x, probs) Quantiles where x is the numeric vector where quantiles are desired and probs is a numeric vector with probabilities in [0,1]. # 30th and 84th percentiles of x y <- quantile(x, c(.3,.84)) range(x) Range x <- c(1,2,3,4) range(x) returns c(1,4). diff(range(x)) returns 3. sum(x) Sum sum(c(1,2,3,4)) returns 10. diff(x, lag=n) Lagged differences, with lag indicating which lag to use. The default lag is 1. x<- c(1, 5, 23, 29) diff(x) returns c(4, 18, 6). min(x) Minimum min(c(1,2,3,4)) returns 1. max(x) Maximum max(c(1,2,3,4)) returns 4. scale(x, center=TRUE, scale=TRUE) Column center (center=TRUE) or standardize (center=TRUE, scale=TRUE) data object x. An example is given in listing 5.6. To see these functions in action, look at the next listing. This listing demonstrates two ways to calculate the mean and standard deviation of a vector of numbers. Listing 5.1 Calculating the mean and standard deviation > x <- c(1,2,3,4,5,6,7,8) > mean(x) [1] 4.5 > sd(x) [1] 2.449490 > n <- length(x) > meanx <- sum(x)/n > css <- sum((x - meanx)^2) > sdx <- sqrt(css / (n-1)) > meanx [1] 4.5 > sdx [1] 2.449490 It’s instructive to view how the corrected sum of squares (css) is calculated in the second approach: Short way Long way Download from Wow! eBook 96 CHAPTER 5 Advanced data management 1 x equals c(1, 2, 3, 4, 5, 6, 7, 8) and mean x equals 4.5 (length(x) returns the number of elements in x). 2 (x – meanx) subtracts 4.5 from each element of x, resulting in c(-3.5, -2.5, -1.5, -0.5, 0.5, 1.5, 2.5, 3.5). 3 (x – meanx)^2 squares each element of (x - meanx), resulting in c(12.25, 6.25, 2.25, 0.25, 0.25, 2.25, 6.25, 12.25). 4 sum((x - meanx)^2) sums each of the elements of (x - meanx)^2), resulting in 42. Writing formulas in R has much in common with matrix manipulation languages such as MATLAB (we’ll look more specifically at solving matrix algebra problems in appendix E). STANDARDIZING DATA By default, the scale() function standardizes the specified columns of a matrix or data frame to a mean of 0 and a standard deviation of 1: newdata <- scale(mydata) To standardize each column to an arbitrary mean and standard deviation, you can use code similar to the following: newdata <- scale(mydata)*SD + M where M is the desired mean and SD is the desired standard deviation. Using the scale() function on non-numeric columns will produce an error. To standardize a specific column rather than an entire matrix or data frame, you can use code such as newdata <- transform(mydata, myvar = scale(myvar)*10+50) This code standardizes the variable myvar to a mean of 50 and standard deviation of 10. We’ll use the scale() function in the solution to the data management challenge in section 5.3. 5.2.3 Probability functions You may wonder why probability functions aren’t listed with the statistical functions (it was really bothering you, wasn’t it?). Although probability functions are statistical by definition, they’re unique enough to deserve their own section. Probability functions are often used to generate simulated data with known characteristics and to calculate probability values within user-written statistical functions. In R, probability functions take the form [dpqr]distribution_abbreviation() where the first letter refers to the aspect of the distribution returned: d = density p = distribution function q = quantile function r = random generation (random deviates) The common probability functions are listed in table 5.4. Download from Wow! eBook Numerical and character functions 97 Table 5.4 Probability distributions Distribution Abbreviation Distribution Abbreviation Beta beta Logistic logis Binomial binom Multinomial multinom Cauchy cauchy Negative binomial nbinom Chi-squared (noncentral) chisq Normal norm Exponential exp Poisson pois F f Wilcoxon Signed Rank signrank Gamma gamma T t Geometric geom Uniform unif Hypergeometric hyper Weibull weibull Lognormal lnorm Wilcoxon Rank Sum wilcox To see how these work, let’s look at functions related to the normal distribution. If you don’t specify a mean and a standard deviation, the standard normal distribution is as- sumed (mean=0, sd=1). Examples of the density (dnorm), distribution (pnorm), quan- tile (qnorm) and random deviate generation (rnorm) functions are given in table 5.5. Table 5.5 Normal distribution functions Problem Solution Plot the standard normal curve on the interval [–3,3] (see below) −3 −2 −1 0 1 2 3 0 . 1 0 . 2 0 . 3 Normal Deviate D e n s i t y x <- pretty(c(-3,3), 30) y <- dnorm(x) plot(x, y, type = "l", xlab = "Normal Deviate", ylab = "Density", yaxs = "i" ) What is the area under the standard normal curve to the left of z=1.96? pnorm(1.96)equals 0.975 Download from Wow! eBook 98 CHAPTER 5 Advanced data management Table 5.5 Normal distribution functions (continued) Problem Solution What is the value of the 90th percentile of a normal distribution with a mean of 500 and a standard deviation of 100? qnorm(.9, mean=500, sd=100) equals 628.16 Generate 50 random normal deviates with a mean of 50 and a standard deviation of 10. rnorm(50, mean=50, sd=10) Don’t worry if the plot function options are unfamiliar. They’re covered in detail in chapter 11; pretty() is explained in table 5.7 later in this chapter. SETTING THE SEED FOR RANDOM NUMBER GENERATION Each time you generate pseudo-random deviates, a different seed, and therefore dif- ferent results, are produced. To make your results reproducible, you can specify the seed explicitly, using the set.seed() function . An example is given in the next listing. Here, the runif() function is used to generate pseudo-random numbers from a uni- form distribution on the interval 0 to 1. Listing 5.2 Generating pseudo-random numbers from a uniform distribution > runif(5) [1] 0.8725344 0.3962501 0.6826534 0.3667821 0.9255909 > runif(5) [1] 0.4273903 0.2641101 0.3550058 0.3233044 0.6584988 > set.seed(1234) > runif(5) [1] 0.1137034 0.6222994 0.6092747 0.6233794 0.8609154 > set.seed(1234) > runif(5) [1] 0.1137034 0.6222994 0.6092747 0.6233794 0.8609154 By setting the seed manually, you’re able to reproduce your results. This ability can be helpful in creating examples you can access at a future time and share with others. GENERATING MULTIVARIATE NORMAL DATA In simulation research and Monte Carlo studies, you often want to draw data from multivariate normal distribution with a given mean vector and covariance matrix. The mvrnorm() function in the MASS package makes this easy. The function call is mvrnorm(n, mean, sigma) where n is the desired sample size, mean is the vector of means, and sigma is the vari- ance-covariance (or correlation) matrix. In listing 5.3 you’ll sample 500 observations from a three-variable multivariate normal distribution with Mean Vector 230.7 146.7 3.6 Covariance Matrix 15360.8 6721.2 -47.1 6721.2 4700.9 -16.5 -47.1 -16.5 0.3 Download from Wow! eBook Numerical and character functions 99 Listing 5.3 Generating data from a multivariate normal distribution > library(MASS) > options(digits=3) > set.seed(1234) q > mean <- c(230.7, 146.7, 3.6) > sigma <- matrix(c(15360.8, 6721.2, -47.1, w 6721.2, 4700.9, -16.5, -47.1, -16.5, 0.3), nrow=3, ncol=3) > mydata <- mvrnorm(500, mean, sigma) e > mydata <- as.data.frame(mydata) > names(mydata) <- c("y","x1","x2") > dim(mydata) r [1] 500 3 > head(mydata, n=10) y x1 x2 1 98.8 41.3 4.35 2 244.5 205.2 3.57 3 375.7 186.7 3.69 4 -59.2 11.2 4.23 5 313.0 111.0 2.91 6 288.8 185.1 4.18 7 134.8 165.0 3.68 8 171.7 97.4 3.81 9 167.3 101.0 4.01 10 121.1 94.5 3.76 In listing 5.3, you set a random number seed so that you can reproduce the results at a later time q. You specify the desired mean vector and variance-covariance matrix w, and generate 500 pseudo-random observations e. For convenience, the results are converted from a matrix to a data frame, and the variables are given names. Finally, you confirm that you have 500 observations and 3 variables, and print out the first 10 observations r. Note that because a correlation matrix is also a covariance matrix, you could’ve specified the correlations structure directly. The probability functions in R allow you to generate simulated data, sampled from distributions with known characteristics. Statistical methods that rely on simulated data have grown exponentially in recent years, and you’ll see several examples of these in later chapters. 5.2.4 Character functions Although mathematical and statistical functions operate on numerical data, character functions extract information from textual data, or reformat textual data for printing and reporting. For example, you may want to concatenate a person’s first name and last name, ensuring that the first letter of each is capitalized. Or you may want to count the instances of obscenities in open-ended feedback. Some of the most useful charac- ter functions are listed in table 5.6. Set random number seed Specify mean vector, covariance matrix Generate data View results Download from Wow! eBook 100 CHAPTER 5 Advanced data management Table 5.6 Character functions Function Description nchar(x) Counts the number of characters of x x <- c("ab", "cde", "fghij") length(x) returns 3 (see table 5.7). nchar(x[3]) returns 5. substr(x, start, stop )Extract or replace substrings in a character vector. x <- "abcdef" substr(x, 2, 4) returns “bcd”. substr(x, 2, 4) <- "22222" (x is now "a222ef"). grep(pattern, x, ignore. case=FALSE, fixed=FALSE) Search for pattern in x. If fixed=FALSE, then pattern is a regular expression. If fixed=TRUE, then pattern is a text string. Returns matching indices. grep("A", c("b","A","c"), fixed=TRUE) returns 2. sub(pattern, replacement, x, ignore.case=FALSE, fixed=FALSE) Find pattern in x and substitute with replacement text. If fixed=FALSE then pattern is a regular expression. If fixed=TRUE then pattern is a text string. sub("\\s",".","Hello There") returns Hello.There. Note "\s" is a regular expression for finding whitespace; use "\\s" instead because "\" is R’s escape character (see section 1.3.3). strsplit(x, split, fixed=FALSE) Split the elements of character vector x at split. If fixed=FALSE, then pattern is a regular expression. If fixed=TRUE, then pattern is a text string. y <- strsplit("abc", "") returns a 1-component, 3-element list containing "a" "b" "c". unlist(y)[2] and sapply(y, "[", 2) both return “b”. paste(..., sep="") Concatenate strings after using sep string to separate them. paste("x", 1:3, sep="") returns c("x1", "x2", "x3"). paste("x",1:3,sep="M") returns c("xM1","xM2" "xM3"). paste("Today is", date()) returns Today is Thu Jun 25 14:17:32 2011 (I changed the date to appear more current.) toupper(x) Uppercase toupper("abc") returns “ABC”. tolower(x) Lowercase tolower("ABC") returns “abc”. Download from Wow! eBook Numerical and character functions 101 Note that the functions grep(), sub(), and strsplit() can search for a text string (fixed=TRUE) or a regular expression (fixed=FALSE) (FALSE is the default). Regular expressions provide a clear and concise syntax for matching a pattern of text. For ex- ample, the regular expression ^[hc]?at matches any string that starts with 0 or one occurrences of h or c, followed by at. The expression therefore matches hat, cat, and at, but not bat. To learn more, see the regu- lar expression entry in Wikipedia. 5.2.5 Other useful functions The functions in table 5.7 are also quite useful for data management and manipula- tion, but they don’t fit cleanly into the other categories. Table 5.7 Other useful functions Function Description length(x) Length of object x. x <- c(2, 5, 6, 9) length(x) returns 4. seq(from, to, by) Generate a sequence. indices <- seq(1,10,2) indices is c(1, 3, 5, 7, 9). rep(x, n) Repeat x n times. y <- rep(1:3, 2) y is c(1, 2, 3, 1, 2, 3). cut(x, n) Divide continuous variable x into factor with n levels. To create an ordered factor, include the option ordered_result = TRUE. pretty(x, n) Create pretty breakpoints. Divides a continuous variable x into n intervals, by selecting n+1 equally spaced rounded values. Often used in plotting. cat(… , file = "myfile", append = FALSE) Concatenates the objects in … and outputs them to the screen or to a file (if one is declared) . firstname <- c("Jane") cat("Hello" , firstname, "\n"). The last example in the table demonstrates the use of escape characters in printing. Use \n for new lines, \t for tabs, \' for a single quote, \b for backspace, and so forth (type ?Quotes for more information). For example, the code name <- "Bob" cat( "Hello", name, "\b.\n", "Isn\'t R", "\t", "GREAT?\n") Download from Wow! eBook 102 CHAPTER 5 Advanced data management produces Hello Bob. Isn't R GREAT? Note that the second line is indented one space. When cat concatenates objects for output, it separates each by a space. That’s why you include the backspace (\b) escape character before the period. Otherwise it would have produced “Hello Bob .” How you apply the functions you’ve covered so far to numbers, strings, and vectors is intuitive and straightforward, but how do you apply them to matrices and data frames? That’s the subject of the next section. 5.2.6 Applying functions to matrices and data frames One of the interesting features of R functions is that they can be applied to a variety of data objects (scalars, vectors, matrices, arrays, and data frames). The following listing provides an example. Listing 5.4 Applying functions to data objects > a <- 5 > sqrt(a) [1] 2.236068 > b <- c(1.243, 5.654, 2.99) > round(b) [1] 1 6 3 > c <- matrix(runif(12), nrow=3) > c [,1] [,2] [,3] [,4] [1,] 0.4205 0.355 0.699 0.323 [2,] 0.0270 0.601 0.181 0.926 [3,] 0.6682 0.319 0.599 0.215 > log(c) [,1] [,2] [,3] [,4] [1,] -0.866 -1.036 -0.358 -1.130 [2,] -3.614 -0.508 -1.711 -0.077 [3,] -0.403 -1.144 -0.513 -1.538 > mean(c) [1] 0.444 Notice that the mean of matrix c in listing 5.4 results in a scalar (0.444). The mean() function took the average of all 12 elements in the matrix. But what if you wanted the 3 row means or the 4 column means? R provides a function, apply() , that allows you to apply an arbitrary function to any dimension of a matrix, array, or data frame. The format for the apply function is apply(x, MARGIN, FUN, ...) where x is the data object, MARGIN is the dimension index, FUN is a function you specify, and ... are any parameters you want to pass to FUN. In a matrix or data frame MARGIN=1 indicates rows and MARGIN=2 indicates columns. Take a look at the examples in listing 5.5. Download from Wow! eBook A solution for our data management challenge 103 Listing 5.5 Applying a function to the rows (columns) of a matrix > mydata <- matrix(rnorm(30), nrow=6) q> mydata [,1] [,2] [,3] [,4] [,5] [1,] 0.71298 1.368 -0.8320 -1.234 -0.790 [2,] -0.15096 -1.149 -1.0001 -0.725 0.506 [3,] -1.77770 0.519 -0.6675 0.721 -1.350 [4,] -0.00132 -0.308 0.9117 -1.391 1.558 [5,] -0.00543 0.378 -0.0906 -1.485 -0.350 [6,] -0.52178 -0.539 -1.7347 2.050 1.569 > apply(mydata, 1, mean) w [1] -0.155 -0.504 -0.511 0.154 -0.310 0.165 > apply(mydata, 2, mean) e [1] -0.2907 0.0449 -0.5688 -0.3442 0.1906 > apply(mydata, 2, mean, trim=0.2) [1] -0.1699 0.0127 -0.6475 -0.6575 0.2312 r You start by generating a 6 x 5 matrix containing random normal variates q. Then you calculate the 6 row means w, and 5 column means e. Finally, you calculate trimmed column means (in this case, means based on the middle 60 percent of the data, with the bottom 20 percent and top 20 percent of values discarded) r. Because FUN can be any R function, including a function that you write yourself (see section 5.4), apply() is a powerful mechanism. While apply() applies a function over the margins of an array, lapply() and sapply() apply a function over a list. You’ll see an example of sapply (which is a user-friendly version of lapply) in the next section. You now have all the tools you need to solve the data challenge in section 5.1, so let’s give it a try. 5.3 A solution for our data management challenge Your challenge from section 5.1 is to combine subject test scores into a single perfor- mance indicator for each student, grade each student from A to F based on their rela- tive standing (top 20 percent, next 20 percent, etc.), and sort the roster by students’ last name, followed by first name. A solution is given in the following listing. Listing 5.6 A solution to the learning example > options(digits=2) > Student <- c("John Davis", "Angela Williams", "Bullwinkle Moose", "David Jones", "Janice Markhammer", "Cheryl Cushing", "Reuven Ytzrhak", "Greg Knox", "Joel England", "Mary Rayburn") > Math <- c(502, 600, 412, 358, 495, 512, 410, 625, 573, 522) > Science <- c(95, 99, 80, 82, 75, 85, 80, 95, 89, 86) > English <- c(25, 22, 18, 15, 20, 28, 15, 30, 27, 18) > roster <- data.frame(Student, Math, Science, English, stringsAsFactors=FALSE) > z <- scale(roster[,2:4]) > score <- apply(z, 1, mean) > roster <- cbind(roster, score) Generate data Calculate row means Calculate column means Calculate trimmed column means Obtain performance scores Download from Wow! eBook 104 CHAPTER 5 Advanced data management > y <- quantile(score, c(.8,.6,.4,.2)) > roster$grade[score >= y[1]] <- "A" > roster$grade[score < y[1] & score >= y[2]] <- "B" > roster$grade[score < y[2] & score >= y[3]] <- "C" > roster$grade[score < y[3] & score >= y[4]] <- "D" > roster$grade[score < y[4]] <- "F" > name <- strsplit((roster$Student), " ") > lastname <- sapply(name, "[", 2) > firstname <- sapply(name, "[", 1) > roster <- cbind(firstname,lastname, roster[,-1]) > roster <- roster[order(lastname,firstname),] > roster Firstname Lastname Math Science English score grade 6 Cheryl Cushing 512 85 28 0.35 C 1 John Davis 502 95 25 0.56 B 9 Joel England 573 89 27 0.70 B 4 David Jones 358 82 15 -1.16 F 8 Greg Knox 625 95 30 1.34 A 5 Janice Markhammer 495 75 20 -0.63 D 3 Bullwinkle Moose 412 80 18 -0.86 D 10 Mary Rayburn 522 86 18 -0.18 C 2 Angela Williams 600 99 22 0.92 A 7 Reuven Ytzrhak 410 80 15 -1.05 F The code is dense so let’s walk through the solution step by step: Step 1. The original student roster is given. The options(digits=2) limits the num- ber of digits printed after the decimal place and makes the printouts easier to read. > options(digits=2) > roster Student Math Science English 1 John Davis 502 95 25 2 Angela Williams 600 99 22 3 Bullwinkle Moose 412 80 18 4 David Jones 358 82 15 5 Janice Markhammer 495 75 20 6 Cheryl Cushing 512 85 28 7 Reuven Ytzrhak 410 80 15 8 Greg Knox 625 95 30 9 Joel England 573 89 27 10 Mary Rayburn 522 86 18 Step 2. Because the Math, Science, and English tests are reported on different scales (with widely differing means and standard deviations), you need to make them compa- rable before combining them. One way to do this is to standardize the variables so that each test is reported in standard deviation units, rather than in their original scales. You can do this with the scale() function : > z <- scale(roster[,2:4]) > z Math Science English Grade students Extract last and first names Sort by last and first names Download from Wow! eBook A solution for our data management challenge 105 [1,] 0.013 1.078 0.587 [2,] 1.143 1.591 0.037 [3,] -1.026 -0.847 -0.697 [4,] -1.649 -0.590 -1.247 [5,] -0.068 -1.489 -0.330 [6,] 0.128 -0.205 1.137 [7,] -1.049 -0.847 -1.247 [8,] 1.432 1.078 1.504 [9,] 0.832 0.308 0.954 [10,] 0.243 -0.077 -0.697 Step 3. You can then get a performance score for each student by calculating the row means using the mean() function and adding it to the roster using the cbind() function : > score <- apply(z, 1, mean) > roster <- cbind(roster, score) > roster Student Math Science English score 1 John Davis 502 95 25 0.559 2 Angela Williams 600 99 22 0.924 3 Bullwinkle Moose 412 80 18 -0.857 4 David Jones 358 82 15 -1.162 5 Janice Markhammer 495 75 20 -0.629 6 Cheryl Cushing 512 85 28 0.353 7 Reuven Ytzrhak 410 80 15 -1.048 8 Greg Knox 625 95 30 1.338 9 Joel England 573 89 27 0.698 10 Mary Rayburn 522 86 18 -0.177 Step 4. The quantile() function gives you the percentile rank of each student’s per- formance score. You see that the cutoff for an A is 0.74, for a B is 0.44, and so on. > y <- quantile(roster$score, c(.8,.6,.4,.2)) > y 80% 60% 40% 20% 0.74 0.44 -0.36 -0.89 Step 5. Using logical operators, you can recode students’ percentile ranks into a new categorical grade variable. This creates the variable grade in the roster data frame. > roster$grade[score >= y[1]] <- "A" > roster$grade[score < y[1] & score >= y[2]] <- "B" > roster$grade[score < y[2] & score >= y[3]] <- "C" > roster$grade[score < y[3] & score >= y[4]] <- "D" > roster$grade[score < y[4]] <- "F" > roster Student Math Science English score grade 1 John Davis 502 95 25 0.559 B 2 Angela Williams 600 99 22 0.924 A 3 Bullwinkle Moose 412 80 18 -0.857 D 4 David Jones 358 82 15 -1.162 F 5 Janice Markhammer 495 75 20 -0.629 D 6 Cheryl Cushing 512 85 28 0.353 C 7 Reuven Ytzrhak 410 80 15 -1.048 F 8 Greg Knox 625 95 30 1.338 A Download from Wow! eBook 106 CHAPTER 5 Advanced data management 9 Joel England 573 89 27 0.698 B 10 Mary Rayburn 522 86 18 -0.177 C Step 6. You’ll use the strsplit() function to break student names into first name and last name at the space character. Applying strsplit() to a vector of strings re- turns a list: > name <- strsplit((roster$Student), " ") > name [[1]] [1] "John" "Davis" [[2]] [1] "Angela" "Williams" [[3]] [1] "Bullwinkle" "Moose" [[4]] [1] "David" "Jones" [[5]] [1] "Janice" "Markhammer" [[6]] [1] "Cheryl" "Cushing" [[7]] [1] "Reuven" "Ytzrhak" [[8]] [1] "Greg" "Knox" [[9]] [1] "Joel" "England" [[10]] [1] "Mary" "Rayburn" Step 7. You can use the sapply() function to take the first element of each compo- nent and put it in a firstname vector, and the second element of each component and put it in a lastname vector. "[" is a function that extracts part of an object—here the first or second component of the list name. You’ll use cbind() to add them to the roster. Because you no longer need the student variable, you’ll drop it (with the –1 in the roster index). > Firstname <- sapply(name, "[", 1) > Lastname <- sapply(name, "[", 2) > roster <- cbind(Firstname, Lastname, roster[,-1]) > roster Firstname Lastname Math Science English score grade 1 John Davis 502 95 25 0.559 B 2 Angela Williams 600 99 22 0.924 A 3 Bullwinkle Moose 412 80 18 -0.857 D Download from Wow! eBook Control flow 107 4 David Jones 358 82 15 -1.162 F 5 Janice Markhammer 495 75 20 -0.629 D 6 Cheryl Cushing 512 85 28 0.353 C 7 Reuven Ytzrhak 410 80 15 -1.048 F 8 Greg Knox 625 95 30 1.338 A 9 Joel England 573 89 27 0.698 B 10 Mary Rayburn 522 86 18 -0.177 C Step 8. Finally, you can sort the dataset by first and last name using the order() function : > roster[order(Lastname,Firstname),] Firstname Lastname Math Science English score grade 6 Cheryl Cushing 512 85 28 0.35 C 1 John Davis 502 95 25 0.56 B 9 Joel England 573 89 27 0.70 B 4 David Jones 358 82 15 -1.16 F 8 Greg Knox 625 95 30 1.34 A 5 Janice Markhammer 495 75 20 -0.63 D 3 Bullwinkle Moose 412 80 18 -0.86 D 10 Mary Rayburn 522 86 18 -0.18 C 2 Angela Williams 600 99 22 0.92 A 7 Reuven Ytzrhak 410 80 15 -1.05 F Voilà! Piece of cake! There are many other ways to accomplish these tasks, but this code helps capture the flavor of these functions. Now it’s time to look at control structures and user-written functions. 5.4 Control flow In the normal course of events, the statements in an R program are executed sequen- tially from the top of the program to the bottom. But there are times that you’ll want to execute some statements repetitively, while only executing other statements if certain conditions are met. This is where control-flow constructs come in. R has the standard control structures you’d expect to see in a modern programming language. First you’ll go through the constructs used for conditional execution, followed by the constructs used for looping. For the syntax examples throughout this section, keep the following in mind: ■ statement is a single R statement or a compound statement (a group of R state- ments enclosed in curly braces { } and separated by semicolons). ■ cond is an expression that resolves to true or false. ■ expr is a statement that evaluates to a number or character string. ■ seq is a sequence of numbers or character strings. After we discuss control-flow constructs, you’ll learn how to write your functions. 5.4.1 Repetition and looping Looping constructs repetitively execute a statement or series of statements until a con- dition isn’t true. These include the for and while structures. Download from Wow! eBook 108 CHAPTER 5 Advanced data management FOR The for loop executes a statement repetitively until a variable’s value is no longer con- tained in the sequence seq. The syntax is for (var in seq) statement In this example for (i in 1:10) print("Hello") the word Hello is printed 10 times. WHILE A while loop executes a statement repetitively until the condition is no longer true. The syntax is while (cond) statement In a second example, the code i <- 10 while (i > 0) {print("Hello"); i <- i - 1} once again prints the word Hello 10 times. Make sure that the statements inside the brackets modify the while condition so that sooner or later it’s no longer true—other- wise the loop will never end! In the previous example, the statement i <- i - 1 subtracts 1 from object i on each loop, so that after the tenth loop it’s no longer larger than 0. If you instead added 1 on each loop, R would never stop saying Hello. This is why while loops can be more dangerous than other looping constructs. Looping in R can be inefficient and time consuming when you’re processing the rows or columns of large datasets. Whenever possible, it’s better to use R’s built- in numerical and character functions in conjunction with the apply family of functions. 5.4.2 Conditional execution In conditional execution, a statement or statements are only executed if a specified condition is met. These constructs include if-else, ifelse, and switch. IF-ELSE The if-else control structure executes a statement if a given condition is true. Op- tionally, a different statement is executed if the condition is false. The syntax is if (cond) statement if (cond) statement1 else statement2 Here are examples: if (is.character(grade)) grade <- as.factor(grade) if (!is.factor(grade)) grade <- as.factor(grade) else print("Grade already is a factor") Download from Wow! eBook User-written functions 109 In the first instance, if grade is a character vector, it’s converted into a factor. In the second instance, one of two statements is executed. If grade isn’t a factor (note the ! symbol), it’s turned into one. If it is a factor, then the message is printed. IFELSE The ifelse construct is a compact and vectorized version of the if-else construct . The syntax is ifelse(cond, statement1, statement2) The first statement is executed if cond is TRUE. If cond is FALSE, the second statement is executed. Here are examples: ifelse(score > 0.5, print("Passed"), print("Failed")) outcome <- ifelse (score > 0.5, "Passed", "Failed") Use ifelse when you want to take a binary action or when you want to input and out- put vectors from the construct. SWITCH switch chooses statements based on the value of an expression. The syntax is switch(expr, ...) where ... represents statements tied to the possible outcome values of expr. It’s easiest to understand how switch works by looking at the example in the following listing. Listing 5.7 A switch example > feelings <- c("sad", "afraid") > for (i in feelings) print( switch(i, happy = "I am glad you are happy", afraid = "There is nothing to fear", sad = "Cheer up", angry = "Calm down now" ) ) [1] "Cheer up" [1] "There is nothing to fear" This is a silly example but shows the main features. You’ll learn how to use switch in user-written functions in the next section. 5.5 User-written functions One of R’s greatest strengths is the user’s ability to add functions. In fact, many of the functions in R are functions of existing functions. The structure of a function looks like this: myfunction <- function(arg1, arg2, ... ){ statements return(object) } Download from Wow! eBook 110 CHAPTER 5 Advanced data management Objects in the function are local to the function. The object returned can be any data type, from scalar to list. Let’s take a look at an example. Say you’d like to have a function that calculates the central tendency and spread of data objects. The function should give you a choice between parametric (mean and standard deviation) and nonparametric (median and median absolute deviation) statistics. The results should be returned as a named list. Additionally, the user should have the choice of automatically printing the results, or not. Unless otherwise specified, the function’s default behavior should be to calculate parametric statistics and not print the results. One solution is given in the following listing. Listing 5.8 mystats() : a user-written function for summary statistics mystats <- function(x, parametric=TRUE, print=FALSE) { if (parametric) { center <- mean(x); spread <- sd(x) } else { center <- median(x); spread <- mad(x) } if (print & parametric) { cat("Mean=", center, "\n", "SD=", spread, "\n") } else if (print & !parametric) { cat("Median=", center, "\n", "MAD=", spread, "\n") } result <- list(center=center, spread=spread) return(result) } To see your function in action, first generate some data (a random sample of size 500 from a normal distribution): set.seed(1234) x <- rnorm(500) After executing the statement y <- mystats(x) y$center will contain the mean (0.00184) and y$spread will contain the standard deviation (1.03). No output is produced. If you execute the statement y <- mystats(x, parametric=FALSE, print=TRUE) y$center will contain the median (–0.0207) and y$spread will contain the median absolute deviation (1.001). In addition, the following output is produced: Median= -0.0207 MAD= 1 Next, let’s look at a user-written function that uses the switch construct . This function gives the user a choice regarding the format of today’s date. Values that are assigned to parameters in the function declaration are taken as defaults. In the mydate() func- tion , long is the default format for dates if type isn’t specified: Download from Wow! eBook User-written functions 111 mydate <- function(type="long") { switch(type, long = format(Sys.time(), "%A %B %d %Y"), short = format(Sys.time(), "%m-%d-%y"), cat(type, "is not a recognized type\n") ) } Here’s the function in action: > mydate("long") [1] "Thursday December 02 2010" > mydate("short") [1] "12-02-10" > mydate() [1] "Thursday December 02 2010" > mydate("medium") medium is not a recognized type Note that the cat() function is only executed if the entered type doesn’t match "long" or "short". It’s usually a good idea to have an expression that catches user-supplied arguments that have been entered incorrectly. Several functions are available that can help add error trapping and correction to your functions. You can use the function warning() to generate a warning message, message() to generate a diagnostic message, and stop() to stop execution of the current expression and carry out an error action. See each function’s online help for more details. TIP Once you start writing functions of any length and complexity, access to good debugging tools becomes important. R has a number of useful built- in functions for debugging, and user-contributed packages are available that provide additional functionality. An excellent resource on this topic is Duncan Murdoch’s “Debugging in R” (http://www.stats.uwo.ca/faculty/murdoch/ software/debuggingR). After creating your own functions, you may want to make them available in every ses- sion. Appendix B describes how to customize the R environment so that user-written functions are loaded automatically at startup. We’ll look at additional examples of user-written functions in chapters 6 and 8. You can accomplish a great deal using the basic techniques provided in this section. If you’d like to explore the subtleties of function writing, or want to write professional- level code that you can distribute to others, I recommend two excellent books that you’ll find in the References section at the end of this book: Venables & Ripley (2000) and Chambers (2008). Together, they provide a significant level of detail and breadth of examples. Now that we’ve covered user-written functions, we’ll end this chapter with a discussion of data aggregation and reshaping. Download from Wow! eBook 112 CHAPTER 5 Advanced data management 5.6 Aggregation and restructuring R provides a number of powerful methods for aggregating and reshaping data. When you aggregate data, you replace groups of observations with summary statistics based on those observations. When you reshape data, you alter the structure (rows and col- umns) determining how the data is organized. This section describes a variety of meth- ods for accomplishing these tasks. In the next two subsections, we’ll use the mtcars data frame that’s included with the base installation of R. This dataset, extracted from Motor Trend magazine (1974), describes the design and performance characteristics (number of cylinders, displacement, horsepower, mpg, and so on) for 34 automobiles. To learn more about the dataset, see help(mtcars) . 5.6.1 Transpose The transpose (reversing rows and columns) is perhaps the simplest method of reshap- ing a dataset. Use the t() function to transpose a matrix or a data frame. In the latter case, row names become variable (column) names. An example is presented in the next listing. Listing 5.9 Transposing a dataset > cars <- mtcars[1:5,1:4] > cars mpg cyl disp hp Mazda RX4 21.0 6 160 110 Mazda RX4 Wag 21.0 6 160 110 Datsun 710 22.8 4 108 93 Hornet 4 Drive 21.4 6 258 110 Hornet Sportabout 18.7 8 360 175 > t(cars) Mazda RX4 Mazda RX4 Wag Datsun 710 Hornet 4 Drive Hornet Sportabout mpg 21 21 22.8 21.4 18.7 cyl 6 6 4.0 6.0 8.0 disp 160 160 108.0 258.0 360.0 hp 110 110 93.0 110.0 175.0 Listing 5.9 uses a subset of the mtcars dataset in order to conserve space on the page. You’ll see a more flexible way of transposing data when we look at the shape package later in this section. 5.6.2 Aggregating data It’s relatively easy to collapse data in R using one or more by variables and a defined function. The format is aggregate(x, by, FUN) where x is the data object to be collapsed, by is a list of variables that will be crossed to form the new observations, and FUN is the scalar function used to calculate summary statistics that will make up the new observation values. Download from Wow! eBook Aggregation and restructuring 113 As an example, we’ll aggregate the mtcars data by number of cylinders and gears, returning means on each of the numeric variables (see the next listing). Listing 5.10 Aggregating data > options(digits=3) > attach(mtcars) > aggdata <-aggregate(mtcars, by=list(cyl,gear), FUN=mean, na.rm=TRUE) > aggdata Group.1 Group.2 mpg cyl disp hp drat wt qsec vs am gear carb 1 4 3 21.5 4 120 97 3.70 2.46 20.0 1.0 0.00 3 1.00 2 6 3 19.8 6 242 108 2.92 3.34 19.8 1.0 0.00 3 1.00 3 8 3 15.1 8 358 194 3.12 4.10 17.1 0.0 0.00 3 3.08 4 4 4 26.9 4 103 76 4.11 2.38 19.6 1.0 0.75 4 1.50 5 6 4 19.8 6 164 116 3.91 3.09 17.7 0.5 0.50 4 4.00 6 4 5 28.2 4 108 102 4.10 1.83 16.8 0.5 1.00 5 2.00 7 6 5 19.7 6 145 175 3.62 2.77 15.5 0.0 1.00 5 6.00 8 8 5 15.4 8 326 300 3.88 3.37 14.6 0.0 1.00 5 6.00 In these results, Group.1 represents the number of cylinders (4, 6, or 8) and Group.2 represents the number of gears (3, 4, or 5). For example, cars with 4 cylinders and 3 gears have a mean of 21.5 miles per gallon (mpg). When you’re using the aggregate() function , the by variables must be in a list (even if there’s only one). You can declare a custom name for the groups from within the list, for instance, using by=list(Group.cyl=cyl, Group.gears=gear) . The function specified can be any built-in or user-provided function. This gives the aggregate command a great deal of power. But when it comes to power, nothing beats the reshape package. 5.6.3 The reshape package The reshape package is a tremendously versatile approach to both restructuring and aggregating datasets. Because of this versatility, it can be a bit challenging to learn. We’ll go through the process slowly and use a small dataset so that it’s clear what’s hap- pening. Because reshape isn’t included in the standard installation of R, you’ll need to install it one time, using install.packages("reshape") . Basically, you’ll “melt” data so that each row is a unique ID-variable combination. Then you’ll “cast” the melted data into any shape you desire. During the cast, you can aggregate the data with any function you wish. The dataset you’ll be working with is shown in table 5.8. In this dataset, the measurements are the values in the last two columns (5, 6, 3, 5, 6, 1, 2, and 4). Each measurement is uniquely identified by a combination of ID variables (in this case ID, Time, and whether the measurement is on X1 or X2). For example, the measured value 5 in the first row is Table 5.8 The original dataset (mydata) IDTime X1 X2 1 1 5 6 1 2 3 5 2 1 6 1 2 2 2 4 Download from Wow! eBook 114 CHAPTER 5 Advanced data management uniquely identified by knowing that it’s from observation (ID) 1, at Time 1, and on variable X1. MELTING When you melt a dataset, you restructure it into a format where each measured vari- able is in its own row, along with the ID variables needed to uniquely identify it. If you melt the data from table 5.8, using the following code library(reshape) md <- melt(mydata, id=(c("id", "time"))) you end up with the structure shown in table 5.9. Note that you must specify the variables needed to uniquely identify each measurement (ID and Time) and that the variable indicating the measurement variable names (X1 or X2) is created for you automatically. Now that you have your data in a melted form, you can recast it into any shape, using the cast() function. CASTING The cast() function starts with melted data and reshapes it using a formula that you provide and an (optional) function used to aggregate the data. The format is newdata <- cast(md, formula, FUN) where md is the melted data, formula describes the desired end result, and FUN is the (optional) aggregating function. The formula takes the form rowvar1 + rowvar2 + … ~ colvar1 + colvar2 + … In this formula, rowvar1 + rowvar2 + … define the set of crossed variables that de- fine the rows, and colvar1 + colvar2 + … define the set of crossed variables that define the columns. See the examples in figure 5.1. Because the formulas on the right side (d, e, and f) don’t include a function, the data is reshaped. In contrast, the examples on the left side (a, b, and c) specify the mean as an aggregating function. Thus the data are not only reshaped but aggregated as well. For example, (a) gives the means on X1 and X2 averaged over time for each observation. Example (b) gives the mean scores of X1 and X2 at Time 1 and Time 2, averaged over observations. In (c) you have the mean score for each observation at Time 1 and Time 2, averaged over X1 and X2. As you can see, the flexibility provided by the melt() and cast() functions is amazing. There are many times when you’ll have to reshape or aggregate your data prior to analysis. For example, you’ll typically need to place your data in what’s called Table 5.9 The melted dataset IDTime Variable Value 1 1 X1 5 1 2 X1 3 2 1 X1 6 2 2 X1 2 1 1 X2 6 1 2 X2 5 2 1 X2 1 2 2 X2 4 Download from Wow! eBook Aggregation and restructuring 115 I D T i m e X 1 X 2 1 1 5 6 1 2 3 5 2 1 6 1 2 2 2 4 I D T i m e V a r i a b l e V a l u e 1 1 X 1 5 1 2 X 1 3 2 1 X 1 6 2 2 X 1 2 1 1 X 2 6 1 2 X 2 5 2 1 X 2 1 2 2 X 2 4 I D T i m e X 1 X 2 1 1 5 6 1 2 3 5 2 1 6 1 2 2 2 4 I D V a r i a b l e T i m e 1 T i m e 2 1 X 1 5 3 1 X 2 6 5 2 X 1 6 2 2 X 2 1 4 I D X 1 T i m e 1 X 1 T i m e 2 X 2 T i m e 1 X 2 T i m e 2 1 5 3 6 5 2 6 2 1 4 I D X 1 X 2 1 4 5 . 5 2 4 2 . 5 T i m e X 1 X 2 1 5 . 5 3 . 5 2 2 . 5 4 . 5 I D T i m e 1 T i m e 2 1 5 . 5 4 2 3 . 5 3 W i t h A g g r e g a t i o n W i t h o u t A g g r e g a t i o n c a s t ( m d , i d + t i m e ~ v a r i a b l e ) c a s t ( m d , i d + v a r i a b l e ~ t i m e ) c a s t ( m d , i d ~ v a r i a b l e + t i m e ) c a s t ( m d , i d ~ v a r i a b l e , m e a n ) c a s t ( m d , t i m e ~ v a r i a b l e , m e a n ) c a s t ( m d , i d ~ t i m e , m e a n ) m y d a t a m d < - m e l t ( m y d a t a , i d = c ( " i d " , " t i m e " ) ) R e s h a p i n g a D a t a s e t ( c ) ( b ) ( a ) ( d ) ( e ) ( f ) F i g u r e 5 . 1 R e s h a p i n g d a t a w i t h t h e m e l t ( ) a n d c a s t ( ) f u n c t i o n s Download from Wow! eBook 116 CHAPTER 5 Advanced data management “long format ” resembling table 5.9 when analyzing repeated measures data (data where multiple measures are recorded for each observation). See section 9.6 for an example. 5.7 Summary This chapter reviewed dozens of mathematical, statistical, and probability func- tions that are useful for manipulating data. We saw how to apply these functions to a wide range of data objects, including vectors, matrices, and data frames. We learned to use control-flow constructs for looping and branching to execute some statements repetitively and execute other statements only when certain conditions are met. You then had a chance to write your own functions and apply them to data. Finally, we explored ways of collapsing, aggregating, and restructuring your data. Now that you’ve gathered the tools you need to get your data into shape (no pun intended), we’re ready to bid part 1 goodbye and enter the exciting world of data analysis! In upcoming chapters, we’ll begin to explore the many statistical and graphical methods available for turning data into information. Download from Wow! eBook Part 2 Basic methods In part 1, we explored the R environment and discussed how to input data from a wide variety of sources, combine and transform it, and prepare it for further analyses. Once your data has been input and cleaned up, the next step is typically to explore each variable one at a time. This provides you with informa- tion about the distribution of each variable, which is useful in understanding the characteristics of the sample, identifying unexpected or problematic values, and selecting appropriate statistical methods. Next, a subset of variables is typi- cally studied two at a time. This step can help you to uncover basic relationships among variables, and is a useful first step in developing more complex models. Part 2 focuses on graphical and statistical techniques for obtaining basic information about data. Chapter 6 describes methods for visualizing the distribution of individual variables. For categorical variables, this includes bar plots, pie charts, and the newer fan plot. For numeric variables, this includes histograms, density plots, box plots, dot plots, and the less well-known violin plot. Each type of graph is useful for understanding the distribution of a single variable. Chapter 7 describes statistical methods for summarizing individual variables and bivariate relationships. This chapter starts with coverage of descriptive statistics for numerical data based on the dataset as a whole, and on subgroups of interest. Next, the use of frequency tables and cross-tabulations for summarizing categorical data is described. The chapter ends with coverage of basic inferential methods for understanding relationships between two variables at a time, including bivariate correlations, chi-square tests, t-tests, and nonparametric methods. When you have finished part 2, you will be able to use basic graphical and statistical methods available in R to describe your data, explore group differences, and identify significant relationships among variables. Download from Wow! eBook Download from Wow! eBook 6 119 Basic graphs This chapter covers ■ Bar, box, and dot plots ■ Pie and fan charts ■ Histograms and kernel density plots Whenever we analyze data, the first thing that we should do is look at it. For each vari- able, what are the most common values? How much variability is present? Are there any unusual observations? R provides a wealth of functions for visualizing data. In this chapter, we’ll look at graphs that help you understand a single categorical or continuous variable. This topic includes ■ Visualizing the distribution of variable ■ Comparing groups on an outcome variable In both cases, the variable could be continuous (for example, car mileage as miles per gallon) or categorical (for example, treatment outcome as none, some, or marked). In later chapters, we’ll explore graphs that display bivariate and multivari- ate relationships among variables. In the following sections, we’ll explore the use of bar plots, pie charts, fan charts, histograms, kernel density plots, box plots, violin plots, and dot plots. Some of these may be familiar to you, whereas others (such as fan plots or violin plots) may be new Download from Wow! eBook 120 CHAPTER 6 Basic graphs to you. Our goal, as always, is to understand your data better and to communicate this understanding to others. Let’s start with bar plots. 6.1 Bar plots Bar plots display the distribution (frequencies) of a categorical variable through verti- cal or horizontal bars. In its simplest form, the format of the barplot() function is barplot(height) where height is a vector or matrix. In the following examples, we’ll plot the outcome of a study investigating a new treatment for rheumatoid arthritis. The data are contained in the Arthritis data frame distributed with the vcd package . Because the vcd package isn’t included in the default R installation, be sure to download and install it before first use (install. packages("vcd")) . Note that the vcd package isn’t needed to create bar plots. We’re loading it in order to gain access to the Arthritis dataset. But we’ll need the vcd package when creating spinogram, which are described in section 6.1.5. 6.1.1 Simple bar plots If height is a vector, the values determine the heights of the bars in the plot and a ver- tical bar plot is produced. Including the option horiz=TRUE produces a horizontal bar chart instead. You can also add annotating options. The main option adds a plot title, whereas the xlab and ylab options add x-axis and y-axis labels, respectively. In the Arthritis study, the variable Improved records the patient outcomes for individuals receiving a placebo or drug. > library(vcd) > counts <- table(Arthritis$Improved) > counts None Some Marked 42 14 28 Here, we see that 28 patients showed marked improvement, 14 showed some improve- ment, and 42 showed no improvement. We’ll discuss the use of the table() function to obtain cell counts more fully in chapter 7. You can graph the variable counts using a vertical or horizontal bar plot. The code is provided in the following listing and the resulting graphs are displayed in figure 6.1. Listing 6.1 Simple bar plots barplot(counts, main="Simple Bar Plot", xlab="Improvement", ylab="Frequency") barplot(counts, main="Horizontal Bar Plot", xlab="Frequency", ylab="Improvement", horiz=TRUE) Simple bar plot Horizontal bar plot Download from Wow! eBook Bar plots 121 None Some Marked Simple Bar Plot Improvement F r e q u e n c y 010203040 N o n e S o m e M a r k e d Horizontal Bar Plot Frequency I m p r o v e m e n t 0 10 20 30 40 Figure 6.1 Simple vertical and horizontal bar charts TIP If the categorical variable to be plotted is a factor or ordered factor, you can create a vertical bar plot quickly with the plot() function . Because Arthritis$Improved is a factor, the code plot(Arthritis$Improved, main="Simple Bar Plot", xlab="Improved", ylab="Frequency") plot(Arthritis$Improved, horiz=TRUE, main="Horizontal Bar Plot", xlab="Frequency", ylab="Improved") will generate the same bar plots as those in listing 6.1, but without the need to tabulate values with the table() function . What happens if you have long labels? In section 6.1.4, you’ll see how to tweak labels so that they don’t overlap. 6.1.2 Stacked and grouped bar plots If height is a matrix rather than a vector, the resulting graph will be a stacked or grouped bar plot. If beside=FALSE (the default), then each column of the matrix produces a bar in the plot, with the values in the column giving the heights of stacked “sub-bars.” If beside=TRUE, each column of the matrix represents a group, and the values in each column are juxtaposed rather than stacked. Consider the cross-tabulation of treatment type and improvement status: > library(vcd) > counts <- table(Arthritis$Improved, Arthritis$Treatment) > counts Treatment Download from Wow! eBook 122 CHAPTER 6 Basic graphs Improved Placebo Treated None 29 13 Some 7 7 Marked 7 21 You can graph the results as either a stacked or a grouped bar plot (see the next listing). The resulting graphs are displayed in figure 6.2. Listing 6.2 Stacked and grouped bar plotsw barplot(counts, main="Stacked Bar Plot", xlab="Treatment", ylab="Frequency", col=c("red", "yellow","green"), legend=rownames(counts)) barplot(counts, main="Grouped Bar Plot", xlab="Treatment", ylab="Frequency", col=c("red", "yellow", "green"), legend=rownames(counts), beside=TRUE) The first barplot function produces a stacked bar plot, whereas the second produces a grouped bar plot. We’ve also added the col option to add color to the bars plotted. The legend.text parameter provides bar labels for the legend (which are only useful when height is a matrix). In chapter 3, we covered ways to format and place the legend to maximum benefit. See if you can rearrange the legend to avoid overlap with the bars. 6.1.3 Mean bar plots Bar plots needn’t be based on counts or frequencies. You can create bar plots that represent means, medians, standard deviations, and so forth by using the aggregate Stacked bar plot Grouped bar plot Placebo Treated Marked Some None Stacked Bar Plot Treatment F r e q u e n c y 010203040 Placebo Treated None Some Marked Grouped Bar Plot Treatment F r e q u e n c y 05 1 0 1 5 2 0 2 5 Figure 6.2 Stacked and grouped bar plots Download from Wow! eBook Bar plots 123 function and passing the results to the barplot() function . The following listing shows an example, which is displayed in figure 6.3. Listing 6.3 Bar plot for sorted mean values > states <- data.frame(state.region, state.x77) > means <- aggregate(states$Illiteracy, by=list(state.region), FUN=mean) > means Group.1 x 1 Northeast 1.00 2 South 1.74 3 North Central 0.70 4 West 1.02 > means <- means[order(means$x),] > means Group.1 x q 3 North Central 0.70 1 Northeast 1.00 4 West 1.02 2 South 1.74 > barplot(means$x, names.arg=means$Group.1) > title("Mean Illiteracy Rate") w Listing 6.3 sorts the means from small- est to largest q. Also note that use of the title() function w is equivalent to adding the main option in the plot call. means$x is the vector containing the heights of the bars, and the option names.arg=means$Group.1 is added to provide labels. You can take this example further. The bars can be connected with straight line segments using the lines() function . You can also create mean bar plots with superimposed confidence intervals using the barplot2() function in the gplots package . See “barplot2: Enhanced Bar Plots” on the R Graph Gallery website (http://addictedtor.free.fr/graphiques) for an example. 6.1.4 Tweaking bar plots There are several ways to tweak the appearance of a bar plot. For example, with many bars, bar labels may start to overlap. You can decrease the font size using the cex. names option . Specifying values smaller than 1 will shrink the size of the labels. Option- ally, the names.arg argument allows you to specify a character vector of names used to label the bars. You can also use graphical parameters to help text spacing. An example is given in the following listing with the output displayed in figure 6.4. Means sorted smallest to largest Title added North Central Northeast West South 0 . 0 0 . 5 1 . 0 1 . 5 Mean Illiteracy Rate Figure 6.3 Bar plot of mean illiteracy rates for US regions sorted by rate Download from Wow! eBook 124 CHAPTER 6 Basic graphs Listing 6.4 Fitting labels in a bar plot par(mar=c(5,8,4,2)) par(las=2) counts <- table(Arthritis$Improved) barplot(counts, main="Treatment Outcome", horiz=TRUE, cex.names=0.8, names.arg=c("No Improvement", "Some Improvement", "Marked Improvement")) In this example, we’ve rotated the bar labels (with las=2), changed the label text, and both increased the size of the y margin (with mar) and decreased the font size in order to fit the labels comfortably (using cex.names=0.8). The par() function allows you to make extensive modifications to the graphs that R produces by default. See chapter 3 for more details. 6.1.5 Spinograms Before finishing our discussion of bar plots, let’s take a look at a specialized version called a spinogram. In a spinogram, a stacked bar plot is rescaled so that the height of each bar is 1 and the segment heights represent proportions. Spinograms are created through the spine() function of the vcd package . The following code produces a simple spinogram: library(vcd) attach(Arthritis) counts <- table(Treatment, Improved) spine(counts, main="Spinogram Example") detach(Arthritis) No Improvement Some Improvement Marked Improvement Treatment Outcome 0 1 0 2 0 3 0 4 0 Figure 6.4 Horizontal bar plot with tweaked labels Download from Wow! eBook Pie charts 125 Placebo Treated N o n e S o m e M a r k e d 0 0.2 0.4 0.6 0.8 1 Treatment I m p r o v e d Spinogram Example Figure 6.5 Spinogram of arthritis treatment outcome The output is provided in figure 6.5. The larger percentage of patients with marked improvement in the Treated condition is quite evident when compared with the Placebo condition. In addition to bar plots, pie charts are a popular vehicle for displaying the distribution of a categorical variable. We consider them next. 6.2 Pie charts Whereas pie charts are ubiquitous in the business world, they’re denigrated by most statisticians, including the authors of the R documentation. They recommend bar or dot plots over pie charts because people are able to judge length more accurately than volume. Perhaps for this reason, the pie chart options in R are quite limited when compared with other statistical software. Pie charts are created with the function pie(x, labels) where x is a non-negative numeric vector indicating the area of each slice and labels provides a character vector of slice labels. Four examples are given in the next listing; the resulting plots are provided in figure 6.6. Download from Wow! eBook 126 CHAPTER 6 Basic graphs US UK Australia Germany France Simple Pie Chart US 20% UK 24% Australia 8% Germany 32% France 16% Pie Chart with Percentages 3D Pie Chart USUK Australia Germany France Northeast 9 South 16 North Central 12 West 13 Pie Chart from a Table (with sample sizes) Figure 6.6 Pie chart examples Listing 6.5 Pie charts par(mfrow=c(2, 2)) slices <- c(10, 12,4, 16, 8) lbls <- c("US", "UK", "Australia", "Germany", "France") q pie( slices, labels = lbls, main="Simple Pie Chart") pct <- round(slices/sum(slices)*100) lbls2 <- paste(lbls, " ", pct, "%", sep="") pie(slices, labels=lbls2, col=rainbow(length(lbls2)), w main="Pie Chart with Percentages") library(plotrix) pie3D(slices, labels=lbls,explode=0.1, main="3D Pie Chart ") mytable <- table(state.region) lbls3 <- paste(names(mytable), "\n", mytable, sep="") e pie(mytable, labels = lbls3, main="Pie Chart from a Table\n (with sample sizes)") Combine four graphs into one Add percentages to pie chart Create chart from table Download from Wow! eBook Pie charts 127 First you set up the plot so that four graphs are combined into one q. (Combining multiple graphs is covered in chapter 3.) Then you input the data that will be used for the first three graphs. For the second pie chart w, you convert the sample sizes to percentages and add the information to the slice labels. The second pie chart also defines the colors of the slices using the rainbow() function , described in chapter 3. Here rainbow(length(lbls2)) resolves to rainbow(5), providing five colors for the graph. The third pie chart is a 3D chart created using the pie3D() function from the plotrix package . Be sure to download and install this package before using it for the first time. If statisticians dislike pie charts, they positively despise 3D pie charts (although they may secretly find them pretty). This is because the 3D effect adds no additional insight into the data and is considered distracting eye candy. The fourth pie chart demonstrates how to create a chart from a table e. In this case, you count the number of states by US region, and append the information to the labels before producing the plot. Pie charts make it difficult to compare the values of the slices (unless the values are appended to the labels). For example, looking at the simple pie chart, can you tell how the US compares to Germany? (If you can, you’re more perceptive than I am.) In an attempt to improve on this situation, a variation of the pie chart, called a fan plot , has been developed. The fan plot (Lemon & Tyagi, 2009) provides the user with a way to display both relative quantities and differences. In R, it’s implemented through the fan.plot() function in the plotrix package . Consider the following code and the resulting graph (figure 6.7): library(plotrix) slices <- c(10, 12,4, 16, 8) lbls <- c("US", "UK", "Australia", "Germany", "France") fan.plot(slices, labels = lbls, main="Fan Plot") In a fan plot , the slices are rearranged to overlap each other and the radii have been modified so that each slice is visible. Here you can see that Germany is the largest slice Fan Plot Germany UK USFrance Australia Figure 6.7 A fan plot of the country data Download from Wow! eBook 128 CHAPTER 6 Basic graphs and that the US slice is roughly 60 percent as large. France appears to be half as large as Germany and twice as large as Australia. Remember that the width of the slice and not the radius is what’s important here. As you can see, it’s much easier to determine the relative sizes of the slice in a fan plot than in a pie chart. Fan plots haven’t caught on yet, but they’re new. Now that we’ve covered pie and fan charts, let’s move on to histograms. Unlike bar plots and pie charts, histograms describe the distribution of a continuous variable. 6.3 Histograms Histograms display the distribution of a continuous variable by dividing up the range of scores into a specified number of bins on the x-axis and displaying the frequency of scores in each bin on the y-axis. You can create histograms with the function hist(x) where x is a numeric vector of values. The option freq=FALSE creates a plot based on probability densities rather than frequencies. The breaks option controls the number of bins. The default produces equally spaced breaks when defining the cells of the histogram. Listing 6.6 provides the code for four variations of a histogram; the results are plotted in figure 6.8. Listing 6.6 Histograms par(mfrow=c(2,2)) hist(mtcars$mpg) q hist(mtcars$mpg, breaks=12, w col="red", xlab="Miles Per Gallon", main="Colored histogram with 12 bins") hist(mtcars$mpg, freq=FALSE, e breaks=12, col="red", xlab="Miles Per Gallon", main="Histogram, rug plot, density curve") rug(jitter(mtcars$mpg)) lines(density(mtcars$mpg), col="blue", lwd=2) x <- mtcars$mpg r h<-hist(x, breaks=12, col="red", xlab="Miles Per Gallon", main="Histogram with normal curve and box") xfit<-seq(min(x), max(x), length=40) yfit<-dnorm(xfit, mean=mean(x), sd=sd(x)) yfit <- yfit*diff(h$mids[1:2])*length(x) lines(xfit, yfit, col="blue", lwd=2) box() Simple histogram With specified bins and color With rug plot and frame With normal curve Download from Wow! eBook Histograms 129 The first histogram q demonstrates the default plot when no options are specified. In this case, five bins are created, and the default axis labels and titles are printed. For the second histogram w, you’ve specified 12 bins, a red fill for the bars, and more attrac- tive and informative labels and title. The third histogram e maintains the colors, bins, labels, and titles as the previous plot, but adds a density curve and rug plot overlay. The density curve is a kernel density estimate and is described in the next section. It provides a smoother description of the distribution of scores. You use the lines() function to overlay this curve in a blue color and a width that’s twice the default thickness for lines. Finally, a rug plot is a one- dimensional representation of the actual data values. If there are many tied values, you can jitter the data on the rug plot using code like the following: rug(jitter(mtcars$mpag, amount=0.01)) This will add a small random value to each data point (a uniform random variate be- tween ±amount), in order to avoid overlapping points. Histogram of mtcars$mpg mtcars$mpg F r e q u e n c y 10 15 20 25 30 35 02468 1 0 1 2 Colored histogram with 12 bins Miles Per Gallon F r e q u e n c y 10 15 20 25 30 01234567 Histogram, rug plot, density curve Miles Per Gallon D e n s i t y 10 15 20 25 30 0 . 0 0 0 . 0 4 0 . 0 8 Histogram with normal curve and box Miles Per Gallon F r e q u e n c y 10 15 20 25 30 01234567 Figure 6.8 Histograms examples Download from Wow! eBook 130 CHAPTER 6 Basic graphs The fourth histogram r is similar to the second but has a superimposed normal curve and a box around the figure. The code for superimposing the normal curve comes from a suggestion posted to the R-help mailing list by Peter Dalgaard. The surround- ing box is produced by the box() function. 6.4 Kernel density plots In the previous section, you saw a kernel density plot superimposed on a histogram. Technically, kernel density estimation is a nonparametric method for estimating the probability density function of a random variable. Although the mathematics are be- yond the scope of this text, in general kernel density plots can be an effective way to view the distribution of a continuous variable. The format for a density plot (that’s not being superimposed on another graph) is plot(density(x)) where x is a numeric vector. Because the plot() function begins a new graph, use the lines() function (listing 6.6) when superimposing a density curve on an existing graph. Two kernel density examples are given in the next listing, and the results are plotted in figure 6.9. Listing 6.7 Kernel density plots par(mfrow=c(2,1)) d <- density(mtcars$mpg) plot(d) d <- density(mtcars$mpg) plot(d, main="Kernel Density of Miles Per Gallon") polygon(d, col="red", border="blue") rug(mtcars$mpg, col="brown") In the first plot, you see the minimal graph created with all the defaults in place. In the second plot, you add a title, color the curve blue, fill the area under the curve with solid red, and add a brown rug. The polygon() function draws a polygon whose verti- ces are given by x and y (provided by the density() function in this case). Kernel density plots can be used to compare groups. This is a highly underutilized approach, probably due to a general lack of easily accessible software. Fortunately, the sm package fills this gap nicely. The sm.density.compare() function in the sm package allows you to superimpose the kernel density plots of two or more groups. The format is sm.density.compare(x, factor) where x is a numeric vector and factor is a grouping variable. Be sure to install the sm package before first use. An example comparing the mpg of cars with 4, 6, or 8 cylin- ders is provided in listing 6.8. Download from Wow! eBook Kernel density plots 131 10 20 30 40 0 . 0 0 0 . 0 3 0 . 0 6 density.default(x = mtcars$mpg) N = 32 Bandwidth = 2.477 D e n s i t y 10 20 30 40 0 . 0 0 0 . 0 3 0 . 0 6 Kernel Density of Miles Per Gallon N = 32 Bandwidth = 2.477 D e n s i t y Figure 6.9 Kernel density plots Listing 6.8 Comparative kernel density plots par(lwd=2) library(sm) qattach(mtcars) cyl.f <- factor(cyl, levels= c(4,6,8), labels = c("4 cylinder", "6 cylinder", w "8 cylinder")) sm.density.compare(mpg, cyl, xlab="Miles Per Gallon") e title(main="MPG Distribution by Car Cylinders") colfill<-c(2:(1+length(levels(cyl.f)))) legend(locator(1), levels(cyl.f), fill=colfill) r detach(mtcars) The par() function is used to double the width of the plotted lines (lwd=2) so that they’d be more readable in this book q. The sm packages is loaded and the mtcars data frame is attached. Double width of plotted lines Create grouping factor Plot densities Add legend via mouse click Download from Wow! eBook 132 CHAPTER 6 Basic graphs In the mtcars data frame w, the variable cyl is a numeric variable coded 4, 6, or 8. cyl is transformed into a factor, named cyl.f, in order to provide value labels for the plot. The sm.density.compare() function creates the plot e and a title() statement adds a main title. Finally, you add a legend to improve interpretability r. (Legends are covered in chapter 3.) First, a vector of colors is created. Here colfill is c(2, 3, 4). Then a legend is added to the plot via the legend() function . The locator(1) option indicates that you’ll place the legend interactively by clicking on the graph where you want the legend to appear. The second option provides a character vector of the labels. The third option assigns a color from the vector colfill to each level of cyl.f. The results are displayed in figure 6.10. As you can see, overlapping kernel density plots can be a powerful way to compare groups of observations on an outcome variable. Here you can see both the shapes of the distribution of scores for each group and the amount of overlap between groups. (The moral of the story is that my next car will have four cylinders—or a battery.) Box plots are also a wonderful (and more commonly used) graphical approach to visualizing distributions and differences among groups. We’ll discuss them next. 5 10 15 20 25 30 35 40 0 . 0 0 0 . 0 5 0 . 1 0 0 . 1 5 0 . 2 0 Miles Per Gallon D e n s i t y MPG Distribution by Car Cylinders 4 cylinder 6 cylinder 8 cylinder Figure 6.10 Kernel density plots of mpg by number of cylinders Download from Wow! eBook Box plots 133 6.5 Box plots A “box-and-whiskers” plot describes the distribution of a continuous variable by plot- ting its five-number summary: the minimum, lower quartile (25th percentile), median (50th percentile), upper quartile (75th percentile), and maximum. It can also display observations that may be outliers (values outside the range of ± 1.5*IQR, where IQR is the interquartile range defined as the upper quartile minus the lower quartile). For example: boxplot(mtcars$mpg, main="Box plot", ylab="Miles per Gallon") produces the plot shown in figure 6.11. I added annotations by hand to illustrate the components. By default, each whisker extends to the most extreme data point, which is no more than the 1.5 times the interquartile range for the box. Values outside this range are depicted as dots (not shown here). For example, in our sample of cars the median mpg is 19.2, 50 percent of the scores fall between 15.3 and 22.8, the smallest value is 10.4, and the largest value is 33.9. How did I read this so precisely from the graph? Issuing boxplot.stats(mtcars$mpg) 10 15 20 25 30 Box plot Upper hinge Upper quartile Lower quartile Lower hinge Whisker Median Whisker M i l e s P e r G a l l o n Figure 6.11 Box plot with annotations added by hand Download from Wow! eBook 134 CHAPTER 6 Basic graphs prints the statistics used to build the graph (in other words, I cheated). There doesn’t appear to be any outliers, and there is a mild positive skew (the upper whisker is longer than the lower whisker). 6.5.1 Using parallel box plots to compare groups Box plots can be created for individual variables or for variables by group. The format is boxplot(formula, data=dataframe) where formula is a formula and dataframe denotes the data frame (or list) provid- ing the data. An example of a formula is y ~ A, where a separate box plot for numeric variable y is generated for each value of categorical variable A. The formula y ~ A*B would produce a box plot of numeric variable y, for each combination of levels in categorical variables A and B. Adding the option varwidth=TRUE will make the box plot widths proportional to the square root of their sample sizes. Add horizontal=TRUE to reverse the axis orientation. In the following code, we revisit the impact of four, six, and eight cylinders on auto mpg with parallel box plots. The plot is provided in figure 6.12. boxplot(mpg ~ cyl, data=mtcars, main="Car Mileage Data", xlab="Number of Cylinders", ylab="Miles Per Gallon") You can see in figure 6.12 that there’s a good separation of groups based on gas mile- age. You can also see that the distribution of mpg for six-cylinder cars is more sym- metrical than for the other two car types. Cars with four cylinders show the greatest spread (and positive skew) of mpg scores, when compared with six- and eight-cylinder cars. There’s also an outlier in the eight-cylinder group. Box plots are very versatile. By adding notch=TRUE, you get notched box plots . If two boxes’ notches don’t overlap, there’s strong evidence that their medians differ (Chambers et al., 1983, p. 62). The following code will create notched box plots for our mpg example: boxplot(mpg ~ cyl, data=mtcars, notch=TRUE, varwidth=TRUE, col="red", main="Car Mileage Data", xlab="Number of Cylinders", ylab="Miles Per Gallon") The col option fills the box plots with a red color, and varwidth=TRUE produces box plots with widths that are proportional to their sample sizes. You can see in figure 6.13 that the median car mileage for four-, six-, and eight- cylinder cars differ. Mileage clearly decreases with number of cylinders. Download from Wow! eBook Box plots 135 Figure 6.12 Box plots of car mileage versus number of cylinders 4 6 8 1 0 1 5 2 0 2 5 3 0 Car Milage Data Number of Cylinders M i l e s P e r G a l l o n 4 6 8 1 0 1 5 2 0 2 5 3 0 Car Mileage Data Number of Cylinders M i l e s P e r G a l l o n Figure 6.13 Notched box plots for car mileage versus number of cylinders Download from Wow! eBook 136 CHAPTER 6 Basic graphs Finally, you can produce box plots for more than one grouping factor. Listing 6.9 provides box plots for mpg versus the number of cylinders and transmission type in an automobile. Again, you use the col option to fill the box plots with color. Note that colors recycle. In this case, there are six box plots and only two specified colors, so the colors repeat three times. Listing 6.9 Box plots for two crossed factors mtcars$cyl.f <- factor(mtcars$cyl, levels=c(4,6,8), labels=c("4","6","8")) mtcars$am.f <- factor(mtcars$am, levels=c(0,1), labels=c("auto", "standard")) boxplot(mpg ~ am.f *cyl.f, data=mtcars, varwidth=TRUE, col=c("gold","darkgreen"), main="MPG Distribution by Auto Type", xlab="Auto Type") The plot is provided in figure 6.14. From figure 6.14 it’s again clear that median mileage decreases with cylinder number. For four- and six-cylinder cars, mileage is higher for standard transmissions. But for eight-cylinder cars there doesn’t appear to be a difference. You can also see Create factor for # of cylinders Create factor for transmission type Generate box plot auto.4 standard.4 auto.6 standard.6 auto.8 standard.8 1 0 1 5 2 0 2 5 3 0 MPG Distribution by Auto Type Auto Type Figure 6.14 Box plots for car mileage versus transmission type and number of cylinders Download from Wow! eBook Box plots 137 from the widths of the box plots that standard four-cylinder and automatic eight- cylinder cars are the most common in this dataset. 6.5.2 Violin plots Before we end our discussion of box plots, it’s worth examining a variation called a violin plot. A violin plot is a combination of a box plot and a kernel density plot. You can create one using the vioplot() function from the vioplot package . Be sure to install the vioplot package before first use. The format for the vioplot() function is vioplot(x1, x2, … , names=, col=) where x1, x2, … represent one or more numeric vectors to be plotted (one violin plot will be produced for each vector). The names parameter provides a character vector of labels for the violin plots, and col is a vector specifying the colors for each violin plot. An example is given in the following listing. Listing 6.10 Violin plots library(vioplot) x1 <- mtcars$mpg[mtcars$cyl==4] x2 <- mtcars$mpg[mtcars$cyl==6] x3 <- mtcars$mpg[mtcars$cyl==8] vioplot(x1, x2, x3, names=c("4 cyl", "6 cyl", "8 cyl"), col="gold") title("Violin Plots of Miles Per Gallon") Note that the vioplot() function requires you to separate the groups to be plotted into separate variables. The results are displayed in figure 6.15. 1 0 1 5 2 0 2 5 3 0 4 cyl 6 cyl 8 cyl Violin Plots of Miles Per Gallon Figure 6.15 Violin plots of mpg versus number of cylinders Download from Wow! eBook 138 CHAPTER 6 Basic graphs Violin plots are basically kernel density plots superimposed in a mirror image fashion over box plots. Here, the white dot is the median, the black boxes range from the lower to the upper quartile, and the thin black lines represent the whiskers. The outer shape provides the kernel density plots. Violin plots haven’t really caught on yet. Again, this may be due to a lack of easily accessible software. Time will tell. We’ll end this chapter with a look at dot plots. Unlike the graphs you’ve seen previously, dot plots plot every value for a variable. 6.6 Dot plots Dot plots provide a method of plotting a large number of labeled values on a simple horizontal scale. You create them with the dotchart() function , using the format dotchart(x, labels=) where x is a numeric vector and labels specifies a vector that labels each point. You can add a groups option to designate a factor specifying how the elements of x are grouped. If so, the option gcolor controls the color of the groups label and cex con- trols the size of the labels. Here’s an example with the mtcars dataset: dotchart(mtcars$mpg, labels=row.names(mtcars), cex=.7, main="Gas Mileage for Car Models", xlab="Miles Per Gallon") The resulting plot is given in figure 6.16. Mazda RX4 Mazda RX4 Wag Datsun 710 Hornet 4 Drive Hornet Sportabout Valiant Duster 360 Merc 240D Merc 230 Merc 280 Merc 280C Merc 450SE Merc 450SL Merc 450SLC Cadillac Fleetwood Lincoln Continental Chrysler Imperial Fiat 128 Honda Civic Toyota Corolla Toyota Corona Dodge Challenger AMC Javelin Camaro Z28 Pontiac Firebird Fiat X1−9 Porsche 914−2 Lotus Europa Ford Pantera L Ferrari Dino Maserati Bora Volvo 142E 10 15 20 25 30 Gas Milage for Car Models Miles Per Gallon Figure 6.16 Dot plot of mpg for each car model Download from Wow! eBook Dot plots 139 The graph in figure 6.16 allows you to see the mpg for each make of car on the same horizontal axis. Dot plots typically become most interesting when they’re sorted and grouping factors are distinguished by symbol and color. An example is given in the following listing. Listing 6.11 Dot plot grouped, sorted, and colored x <- mtcars[order(mtcars$mpg),] x$cyl <- factor(x$cyl) x$color[x$cyl==4] <- "red" x$color[x$cyl==6] <- "blue" x$color[x$cyl==8] <- "darkgreen" dotchart(x$mpg, labels = row.names(x), cex=.7, groups = x$cyl, gcolor = "black", color = x$color, pch=19, main = "Gas Mileage for Car Models\ngrouped by cylinder", xlab = "Miles Per Gallon") In this example, the data frame mtcars is sorted by mpg (lowest to highest) and saved as data frame x. The numeric vector cyl is transformed into a factor. A character vec- tor (color) is added to data frame x and contains the values "red", "blue", or "dark- green" depending on the value of cyl. In addition, the labels for the data points are taken from the row names of the data frame (car makes). Data points are grouped by number of cylinders. The numbers 4, 6, and 8 are printed in black. The color of the points and labels are derived from the color vector , and points are represented by filled circles. The code produces the graph in figure 6.17. In figure 6.17, a number of features become evident for the first time. Again, you see an increase in gas mileage as the number of cylinders decrease. But you also see exceptions. For example, the Pontiac Firebird, with eight cylinders, gets higher gas mileage than the Mercury 280C and the Valiant, each with six cylinders. The Hornet 4 Drive, with six cylinders, gets the same miles per gallon as the Volvo 142E, which has four cylinders. It’s also clear that the Toyota Corolla gets the best gas mileage by far, whereas the Lincoln Continental and Cadillac Fleetwood are outliers on the low end. You can gain significant insight from a dot plot in this example because each point is labeled, the value of each point is inherently meaningful, and the points are arranged in a manner that promotes comparisons. But as the number of data points increase, the utility of the dot plot decreases. NOTE There are many variations of the dot plot. Jacoby (2006) provides a very informative discussion of the dot plot and provides R code for innovative applications. Additionally, the Hmisc package offers a dot plot function (aptly named dotchart2) with a number of additional features. Download from Wow! eBook 140 CHAPTER 6 Basic graphs Cadillac Fleetwood Lincoln Continental Camaro Z28 Duster 360 Chrysler Imperial Maserati Bora Merc 450SLC AMC Javelin Dodge Challenger Ford Pantera L Merc 450SE Merc 450SL Hornet Sportabout Pontiac Firebird Merc 280C Valiant Merc 280 Ferrari Dino Mazda RX4 Mazda RX4 Wag Hornet 4 Drive Volvo 142E Toyota Corona Datsun 710 Merc 230 Merc 240D Porsche 914−2 Fiat X1−9 Honda Civic Lotus Europa Fiat 128 Toyota Corolla 4 6 8 10 15 20 25 30 Gas Milage for Car Models grouped by cylinder Miles Per Gallon Figure 6.17 Dot plot of mpg for car models grouped by number of cylinders 6.7 Summary In this chapter, we learned how to describe continuous and categorical variables. We saw how bar plots and (to a lesser extent) pie charts can be used to gain insight into the distribution of a categorical variable, and how stacked and grouped bar charts can help us understand how groups differ on a categorical outcome. We also explored how histograms, kernel density plots, box plots, rug plots, and dot plots can help us visualize the distribution of continuous variables. Finally, we explored how overlapping kernel density plots, parallel box plots, and grouped dot plots can help you visualize group differences on a continuous outcome variable. In later chapters, we’ll extend this univariate focus to include bivariate and multivariate graphical methods. You’ll see how to visually depict relationships among many variables at once, using such methods as scatter plots, multigroup line plots, mosaic plots, correlograms, lattice graphs, and more. In the next chapter, we’ll look at basic statistical methods for describing distributions and bivariate relationships numerically, as well as inferential methods for evaluating whether relationships among variables exist or are due to sampling error. Download from Wow! eBook 7 141 Basic statistics This chapter covers Descriptive statistics■ ■ Frequency and contingency tables ■ Correlations and covariances t-tests ■ Nonparametric statistics■ In previous chapters, you learned how to import data into R and use a variety of functions to organize and transform the data into a useful format. We then reviewed basic methods for visualizing data. Once your data is properly organized and you’ve begun to explore the data visually, the next step will typically be to describe the distribution of each variable numerically, followed by an exploration of the relationships among selected variables two at a time. The goal is to answer questions like these: ■ What kind of mileage are cars getting these days? Specifically, what’s the dis- tribution of miles per gallon (mean, standard deviation, median, range, etc.) in a survey of automobile makes? ■ After a new drug trial, what’s the outcome (no improvement, some improve- ment, marked improvement) for drug versus placebo groups? Does the gen- der of the participants have an impact on the outcome? Download from Wow! eBook 142 CHAPTER 7 Basic statistics ■ What’s the correlation between income and life expectancy? Is it significantly different from zero? ■ Are you more likely to receive imprisonment for a crime in different regions of the United States? Are the differences between regions statistically significant? In this chapter we’ll review R functions for generating basic descriptive and inferential statistics. First we’ll look at measures of location and scale for quantitative variables. Then we’ll learn how to generate frequency and contingency tables (and associated chi-square tests) for categorical variables. Next, we’ll examine the various forms of correlation coefficients available for continuous and ordinal variables. Finally, we’ll turn to the study of group differences through parametric (t-tests) and nonparametric (Mann–Whitney U test, Kruskal–Wallis test) methods. Although our focus is on numer- ical results, we’ll refer to graphical methods for visualizing these results throughout. The statistical methods covered in this chapter are typically taught in a first-year undergraduate statistics course. If these methodologies are unfamiliar to you, two excellent references are McCall (2000) and Snedecor & Cochran (1989). Alternatively, there are many informative online resources available (such as Wikipedia) for each of the topics covered. 7.1 Descriptive statistics In this section, we’ll look at measures of central tendency, variability, and distribution shape for continuous variables. For illustrative purposes, we’ll use several of the vari- ables from the Motor Trend Car Road Tests (mtcars) dataset you first saw in chapter 1. Our focus will be on miles per gallon (mpg), horsepower (hp), and weight (wt). > vars <- c("mpg", "hp", "wt") > head(mtcars[vars]) mpg hp wt Mazda RX4 21.0 110 2.62 Mazda RX4 Wag 21.0 110 2.88 Datsun 710 22.8 93 2.32 Hornet 4 Drive 21.4 110 3.21 Hornet Sportabout 18.7 175 3.44 Valiant 18.1 105 3.46 First we’ll look at descriptive statistics for all 32 cars. Then we’ll examine descriptive statistics by transmission type (am) and number of cylinders (cyl). Transmission type is a dichotomous variable coded 0=automatic, 1=manual, and the number of cylinders can be 4, 5, or 6. 7.1.1 A menagerie of methods When it comes to calculating descriptive statistics, R has an embarrassment of riches. Let’s start with functions that are included in the base installation. Then we’ll look at extensions that are available through the use of user-contributed packages. In the base installation, you can use the summary() function to obtain descriptive statistics. An example is presented in the following listing. Download from Wow! eBook Descriptive statistics 143 Listing 7.1 Descriptive statistics via summary() > summary(mtcars[vars]) mpg hp wt Min. :10.4 Min. : 52.0 Min. :1.51 1st Qu.:15.4 1st Qu.: 96.5 1st Qu.:2.58 Median :19.2 Median :123.0 Median :3.33 Mean :20.1 Mean :146.7 Mean :3.22 3rd Qu.:22.8 3rd Qu.:180.0 3rd Qu.:3.61 Max. :33.9 Max. :335.0 Max. :5.42 The summary() function provides the minimum, maximum, quartiles, and the mean for numerical variables and frequencies for factors and logical vectors. You can use the apply() or sapply() function from chapter 5 to provide any descriptive statistics you choose. For the sapply() function, the format is sapply(x, FUN, options) where x is your data frame (or matrix) and FUN is an arbitrary function. If options are present, they’re passed to FUN. Typical functions that you can plug in here are mean, sd, var, min, max, median, length, range, and quantile. The function fivenum() returns Tukey’s five-number summary (minimum, lower-hinge, median, upper-hinge, and maximum). Surprisingly, the base installation doesn’t provide functions for skew and kurtosis, but you can add your own. The example in the next listing provides several descriptive statistics, including skew and kurtosis. Listing 7.2 Descriptive statistics via sapply() > mystats <- function(x, na.omit=FALSE){ if (na.omit) x <- x[!is.na(x)] m <- mean(x) n <- length(x) s <- sd(x) skew <- sum((x-m)^3/s^3)/n kurt <- sum((x-m)^4/s^4)/n - 3 return(c(n=n, mean=m, stdev=s, skew=skew, kurtosis=kurt)) } > sapply(mtcars[vars], mystats) mpg hp wt n 32.000 32.000 32.0000 mean 20.091 146.688 3.2172 stdev 6.027 68.563 0.9785 skew 0.611 0.726 0.4231 kurtosis -0.373 -0.136 -0.0227 For cars in this sample, the mean mpg is 20.1, with a standard deviation of 6.0. The distribution is skewed to the right (+0.61) and somewhat flatter than a normal dis- tribution (–0.37). This will be most evident if you graph the data. Note that if Download from Wow! eBook 144 CHAPTER 7 Basic statistics you’d wanted to omit missing values, you would have used sapply(mtcars[vars], mystats, na.omit=TRUE). EXTENSIONS Several user-contributed packages offer functions for descriptive statistics, including Hmisc, pastecs, and psych. Because these packages aren’t included in the base dis- tribution, you’ll need to install them on first use (see chapter 1, section 1.4). The describe() function in the Hmisc package returns the number of variables and observations, the number of missing and unique values, the mean, quantiles, and the five highest and lowest values. An example is provided in the following listing. Listing 7.3 Descriptive statistics via describe() in the Hmisc package() > library(Hmisc) > describe(mtcars[vars]) 3 Variables 32 Observations --------------------------------------------------------------------------- mpg n missing unique Mean .05 .10 .25 .50 .75 .90 .95 32 0 25 20.09 12.00 14.34 15.43 19.20 22.80 30.09 31.30 lowest : 10.4 13.3 14.3 14.7 15.0, highest: 26.0 27.3 30.4 32.4 33.9 --------------------------------------------------------------------------- hp n missing unique Mean .05 .10 .2 .50 .75 .90 .95 32 0 22 146.7 63.65 66.00 96.50 123.00 180.00 243.50 253.55 lowest : 52 62 65 66 91, highest: 215 230 245 264 335 --------------------------------------------------------------------------- wt n missing unique Mean .05 .10 .25 .50 .75 .90 .95 32 0 29 3.217 1.736 1.956 2.581 3.325 3.610 4.048 5.293 lowest : 1.513 1.615 1.835 1.935 2.140, highest: 3.845 4.070 5.250 5.345 5.424 --------------------------------------------------------------------------- The pastecs package includes a function named stat.desc() that provides a wide range of descriptive statistics. The format is stat.desc(x, basic=TRUE, desc=TRUE, norm=FALSE, p=0.95) where x is a data frame or time series. If basic=TRUE (the default), the number of val- ues, null values, missing values, minimum, maximum, range, and sum are provided. If desc=TRUE (also the default), the median, mean, standard error of the mean, 95 per- cent confidence interval for the mean, variance, standard deviation, and coefficient of variation are also provided. Finally, if norm=TRUE (not the default), normal distribu- tion statistics are returned, including skewness and kurtosis (and their statistical signifi- cance), and the Shapiro–Wilk test of normality. A p-value option is used to calculate the confidence interval for the mean (.95 by default). Listing 7.4 gives an example. Download from Wow! eBook Descriptive statistics 145 Listing 7.4 Descriptive statistics via stat.desc() in the pastecs package > library(pastecs) > stat.desc(mtcars[vars]) mpg hp wt nbr.val 32.00 32.000 32.000 nbr.null 0.00 0.000 0.000 nbr.na 0.00 0.000 0.000 min 10.40 52.000 1.513 max 33.90 335.000 5.424 range 23.50 283.000 3.911 sum 642.90 4694.000 102.952 median 19.20 123.000 3.325 mean 20.09 146.688 3.217 SE.mean 1.07 12.120 0.173 CI.mean.0.95 2.17 24.720 0.353 var 36.32 4700.867 0.957 std.dev 6.03 68.563 0.978 coef.var 0.30 0.467 0.304 As if this isn’t enough, the psych package also has a function called describe() that provides the number of nonmissing observations, mean, standard deviation, median, trimmed mean, median absolute deviation, minimum, maximum, range, skew, kurto- sis, and standard error of the mean. You can see an example in the following listing. Listing 7.5 Descriptive statistics via describe() in the psych package > library(psych) Attaching package: 'psych' The following object(s) are masked from package:Hmisc : describe > describe(mtcars[vars]) var n mean sd median trimmed mad min max mpg 1 32 20.09 6.03 19.20 19.70 5.41 10.40 33.90 hp 2 32 146.69 68.56 123.00 141.19 77.10 52.00 335.00 wt 3 32 3.22 0.98 3.33 3.15 0.77 1.51 5.42 range skew kurtosis se mpg 23.50 0.61 -0.37 1.07 hp 283.00 0.73 -0.14 12.12 wt 3.91 0.42 -0.02 0.17 I told you that it was an embarrassment of riches! NOTE In the previous examples, the packages psych and Hmisc both provided functions named describe(). How does R know which one to use? Simply put, the package last loaded takes precedence, as seen in listing 7.5. Here, psych is loaded after Hmisc, and a message is printed indicating that the describe() function in Hmisc is masked by the function in psych. When you type in the describe() function and R searches for it, R comes to the psych package first and executes it. If you want the Hmisc version instead, you can type Hmisc::describe(mt). The function is still there. Download from Wow! eBook 146 CHAPTER 7 Basic statistics You have to give R more information to find it. Now that you know how to generate descriptive statistics for the data as a whole, let’s review how to obtain statistics for subgroups of the data. 7.1.2 Descriptive statistics by group When comparing groups of individuals or observations, the focus is usually on the de- scriptive statistics of each group, rather than the total sample. Again, there are several ways to accomplish this in R. We’ll start by getting descriptive statistics for each level of transmission type. In chapter 5, we discussed methods of aggregating data. You can use the aggregate() function (section 5.6.2) to obtain descriptive statistics by group, as shown in the following listing. Listing 7.6 Descriptive statistics by group using aggregate() > aggregate(mtcars[vars], by=list(am=mtcars$am), mean) am mpg hp wt 1 0 17.1 160 3.77 2 1 24.4 127 2.41 > aggregate(mtcars[vars], by=list(am=mtcars$am), sd) am mpg hp wt 1 0 3.83 53.9 0.777 2 1 6.17 84.1 0.617 Note the use of list(am=mtca rs$am). If you had used list(mtcars$am), the am col- umn would have been labeled Group.1 rather than am. You use the assignment to pro- vide a more useful column label. If you have more than one grouping variable, you can use code like by=list(name1=groupvar1, name2=groupvar2, … , groupvarN). Unfortunately, aggregate() only allows you to use single value functions such as mean, standard deviation, and the like in each call. It won’t return several statistics at once. For that task, you can use the by() function. The format is by(data, INDICES, FUN) where data is a data frame or matrix, INDICES is a factor or list of factors that define the groups, and FUN is an arbitrary function. This next listing provides an example. Listing 7.7 Descriptive statistics by group using by() > dstats <- function(x)(c(mean=mean(x), sd=sd(x))) > by(mtcars[vars], mtcars$am, dstats) mtcars$am: 0 mean.mpg mean.hp mean.wt sd.mpg sd.hp sd.wt 17.147 160.263 3.769 3.834 53.908 0.777 ------------------------------------------------ mtcars$am: 1 mean.mpg mean.hp mean.wt sd.mpg sd.hp sd.wt 24.392 126.846 2.411 6.167 84.062 0.617 Download from Wow! eBook Descriptive statistics 147 EXTENSIONS The doBy package and the psych package also provide functions for descriptive sta- tistics by group. Again, they aren’t distributed in the base installation and must be in- stalled before first use. The summaryBy() function in the doBy package has the format summaryBy(formula, data=dataframe, FUN=function) where the formula takes the form var1 + var2 + var3 + ... + varN ~ groupvar1 + groupvar2 + … + groupvarN Variables on the left of the ~ are the numeric variables to be analyzed and variables on the right are categorical grouping variables. The function can be any built-in or user- created R function. An example using the mystats() function you created in section 7.2.1 is shown in the following listing. Listing 7.8 Summary statistics by group using summaryBy() in the doBy package > library(doBy) > summaryBy(mpg+hp+wt~am, data=mtcars, FUN=mystats) am mpg.n mpg.mean mpg.stdev mpg.skew mpg.kurtosis hp.n hp.mean hp.stdev 1 0 19 17.1 3.83 0.0140 -0.803 19 160 53.9 2 1 13 24.4 6.17 0.0526 -1.455 13 127 84.1 hp.skew hp.kurtosis wt.n wt.mean wt.stdev wt.skew wt.kurtosis 1 -0.0142 -1.210 19 3.77 0.777 0.976 0.142 2 1.3599 0.563 13 2.41 0.617 0.210 -1.174 The describe.by() function contained in the psych package provides the same de- scriptive statistics as describe, stratified by one or more grouping variables, as you can see in the following listing. Listing 7.9 Summary statistics by group using describe.by() in the psych package > library(psych) > describe.by(mtcars[vars], mtcars$am) group: 0 var n mean sd median trimmed mad min max mpg 1 19 17.15 3.83 17.30 17.12 3.11 10.40 24.40 hp 2 19 160.26 53.91 175.00 161.06 77.10 62.00 245.00 wt 3 19 3.77 0.78 3.52 3.75 0.45 2.46 5.42 range skew kurtosis se mpg 14.00 0.01 -0.80 0.88 hp 183.00 -0.01 -1.21 12.37 wt 2.96 0.98 0.14 0.18 ------------------------------------------------ group: 1 var n mean sd median trimmed mad min max mpg 1 13 24.39 6.17 22.80 24.38 6.67 15.00 33.90 hp 2 13 126.85 84.06 109.00 114.73 63.75 52.00 335.00 wt 3 13 2.41 0.62 2.32 2.39 0.68 1.51 3.57 range skew kurtosis se Download from Wow! eBook 148 CHAPTER 7 Basic statistics mpg 18.90 0.05 -1.46 1.71 hp 283.00 1.36 0.56 23.31 wt 2.06 0.21 -1.17 0.17 Unlike the previous example, the describe.by() function doesn’t allow you to specify an arbitrary function, so it’s less generally applicable. If there’s more than one group- ing variable, you can write them as list(groupvar1, groupvar2, … , groupvarN). But this will only work if there are no empty cells when the grouping variables are crossed. Finally, you can use the reshape package described in section 5.6.3 to derive descriptive statistics by group in a flexible way. (If you haven’t read that section, I suggest you review it before continuing.) First, you melt the data frame using dfm <- melt(dataframe, measure.vars=y, id.vars=g) where dataframe contains the data, y is a vector indicating the numeric variables to be summarized (the default is to use all), and g is a vector of one or more grouping variables. You then cast the data using cast(dfm, groupvar1 + groupvar2 + … + variable ~ ., FUN) where the grouping variables are separated by + signs, the word variable is entered exactly as is, and FUN is an arbitrary function. In the final example of this section, we’ll apply the reshape approach to obtaining descriptive statistics for each subgroup formed by transmission type and number of cylinders. For descriptive statistics, we’ll get the sample size, mean, and standard deviation. The code and results are shown in the following listing. Listing 7.10 Summary statistics by group via the reshape package > library(reshape) > dstats <- function(x)(c(n=length(x), mean=mean(x), sd=sd(x))) > dfm <- melt(mtcars, measure.vars=c("mpg", "hp", "wt"), id.vars=c("am", "cyl")) > cast(dfm, am + cyl + variable ~ ., dstats) am cyl variable n mean sd 1 0 4 mpg 3 22.90 1.453 2 0 4 hp 3 84.67 19.655 3 0 4 wt 3 2.94 0.408 4 0 6 mpg 4 19.12 1.632 5 0 6 hp 4 115.25 9.179 6 0 6 wt 4 3.39 0.116 7 0 8 mpg 12 15.05 2.774 8 0 8 hp 12 194.17 33.360 9 0 8 wt 12 4.10 0.768 10 1 4 mpg 8 28.07 4.484 11 1 4 hp 8 81.88 22.655 12 1 4 wt 8 2.04 0.409 Download from Wow! eBook Frequency and contingency tables 149 13 1 6 mpg 3 20.57 0.751 14 1 6 hp 3 131.67 37.528 15 1 6 wt 3 2.75 0.128 16 1 8 mpg 2 15.40 0.566 17 1 8 hp 2 299.50 50.205 18 1 8 wt 2 3.37 0.283 Personally, I find this approach the most compact and appealing. Data analysts have their own preferences for which descriptive statistics to display and how they like to see them formatted. This is probably why there are many variations available. Choose the one that works best for you, or create your own! 7.1.3 Visualizing results Numerical summaries of a distribution’s characteristics are important, but they’re no substitute for a visual representation. For quantitative variables you have histograms (section 6.3), density plots (section 6.4), box plots (section 6.5), and dot plots (sec- tion 6.6). They can provide insights that are easily missed by reliance on a small set of descriptive statistics. The functions considered so far provide summaries of quantitative variables. The functions in the next section allow you to examine the distributions of categorical variables. 7.2 Frequency and contingency tables In this section, we’ll look at frequency and contingency tables from categorical vari- ables, along with tests of independence, measures of association, and methods for graphically displaying results. We’ll be using functions in the basic installation, along with functions from the vcd and gmodels package. In the following examples, assume that A, B, and C represent categorical variables. The data for this section come from the Arthritis dataset included with the vcd package. The data are from Kock & Edward (1988) and represent a double-blind clinical trial of new treatments for rheumatoid arthritis. Here are the first few observations: > library(vcd) > head(Arthritis) ID Treatment Sex Age Improved 1 57 Treated Male 27 Some 2 46 Treated Male 29 None 3 77 Treated Male 30 None 4 17 Treated Male 32 Marked 5 36 Treated Male 46 Marked 6 23 Treated Male 58 Marked Treatment (Placebo, Treated), Sex (Male, Female), and Improved (None, Some, Marked) are all categorical factors. In the next section, we’ll create frequency and contingency tables (cross-classifications) from the data. Download from Wow! eBook 150 CHAPTER 7 Basic statistics 7.2.1 Generating frequency tables R provides several methods for creating frequency and contingency tables. The most important functions are listed in table 7.1. Table 7.1 Functions for creating and manipulating contingency tables Function Description table(var1, var2, …, varN)Creates an N-way contingency table from N categorical variables (factors) xtabs(formula, data)Creates an N-way contingency table based on a formula and a matrix or data frame prop.table(table, margins)Expresses table entries as fractions of the marginal table defined by the margins margin.table(table, margins)Computes the sum of table entries for a marginal table defined by the margins addmargins(table, margins)Puts summary margins (sums by default) on a table ftable(table)Creates a compact "flat" contingency table In the following sections, we’ll use each of these functions to explore categorical vari- ables. We’ll begin with simple frequencies, followed by two-way contingency tables, and end with multiway contingency tables. The first step is to create a table using either the table() or the xtabs() function, then manipulate it using the other functions. ONE-WAY TABLES You can generate simple frequency counts using the table() function. Here’s an example: > mytable <- with(Arthritis, table(Improved)) > mytable Improved None Some Marked 42 14 28 You can turn these frequencies into proportions with prop.table(): > prop.table(mytable) Improved None Some Marked 0.500 0.167 0.333 or into percentages, using prop.table()*100: > prop.table(mytable)*100 Improved None Some Marked 50.0 16.7 33.3 Download from Wow! eBook Frequency and contingency tables 151 Here you can see that 50 percent of study participants had some or marked improve- ment (16.7 + 33.3). TWO-WAY TABLES For two-way tables, the format for the table() function is mytable <- table(A, B) where A is the row variable, and B is the column variable. Alternatively, the xtabs() function allows you to create a contingency table using formula style input. The for- mat is mytable <- xtabs(~ A + B, data=mydata) where mydata is a matrix or data frame. In general, the variables to be cross-classified appear on the right of the formula (that is, to the right of the ~) separated by + signs. If a variable is included on the left side of the formula, it’s assumed to be a vector of frequencies (useful if the data have already been tabulated). For the Arthritis data, you have > mytable <- xtabs(~ Treatment+Improved, data=Arthritis) > mytable Improved Treatment None Some Marked Placebo 29 7 7 Treated 13 7 21 You can generate marginal frequencies and proportions using the margin.table() and prop.table() functions, respectively. For row sums and row proportions, you have > margin.table(mytable, 1) Treatment Placebo Treated 43 41 > prop.table(mytable, 1) Improved Treatment None Some Marked Placebo 0.674 0.163 0.163 Treated 0.317 0.171 0.512 The index (1) refers to the first variable in the table() statement. Looking at the table, you can see that 51 percent of treated individuals had marked improvement, compared to 16 percent of those receiving a placebo. For column sums and column proportions, you have > margin.table(mytable, 2) Improved None Some Marked 42 14 28 > prop.table(mytable, 2) Improved Treatment None Some Marked Download from Wow! eBook 152 CHAPTER 7 Basic statistics Placebo 0.690 0.500 0.250 Treated 0.310 0.500 0.750 Here, the index (2) refers to the second variable in the table() statement. Cell proportions are obtained with this statement: > prop.table(mytable) Improved Treatment None Some Marked Placebo 0.3452 0.0833 0.0833 Treated 0.1548 0.0833 0.2500 You can use the addmargins() function to add marginal sums to these tables. For example, the following code adds a sum row and column: > addmargins(mytable) Improved Treatment None Some Marked Sum Placebo 29 7 7 43 Treated 13 7 21 41 Sum 42 14 28 84 > addmargins(prop.table(mytable)) Improved Treatment None Some Marked Sum Placebo 0.3452 0.0833 0.0833 0.5119 Treated 0.1548 0.0833 0.2500 0.4881 Sum 0.5000 0.1667 0.3333 1.0000 When using addmargins(), the default is to create sum margins for all variables in a table. In contrast: > addmargins(prop.table(mytable, 1), 2) Improved Treatment None Some Marked Sum Placebo 0.674 0.163 0.163 1.000 Treated 0.317 0.171 0.512 1.000 adds a sum column alone. Similarly, > addmargins(prop.table(mytable, 2), 1) Improved Treatment None Some Marked Placebo 0.690 0.500 0.250 Treated 0.310 0.500 0.750 Sum 1.000 1.000 1.000 adds a sum row. In the table, you see that 25 percent of those patients with marked improvement received a placebo. NOTE The table() function ignores missing values (NAs) by default. To include NA as a valid category in the frequency counts, include the table option useNA="ifany". A third method for creating two-way tables is the CrossTable() function in the gmod- els package. The CrossTable() function produces two-way tables modeled after PROC FREQ in SAS or CROSSTABS in SPSS. See listing 7.11 for an example. Download from Wow! eBook Frequency and contingency tables 153 Listing 7.11 Two-way table using CrossTable > library(gmodels) > CrossTable(Arthritis$Treatment, Arthritis$Improved) Cell Contents |-------------------------| | N | | Chi-square contribution | | N / Row Total | | N / Col Total | | N / Table Total | |-------------------------| Total Observations in Table: 84 | Arthritis$Improved Arthritis$Treatment | None | Some | Marked | Row Total | --------------------|-----------|-----------|-----------|-----------| Placebo | 29 | 7 | 7 | 43 | | 2.616 | 0.004 | 3.752 | | | 0.674 | 0.163 | 0.163 | 0.512 | | 0.690 | 0.500 | 0.250 | | | 0.345 | 0.083 | 0.083 | | --------------------|-----------|-----------|-----------|-----------| Treated | 13 | 7 | 21 | 41 | | 2.744 | 0.004 | 3.935 | | | 0.317 | 0.171 | 0.512 | 0.488 | | 0.310 | 0.500 | 0.750 | | | 0.155 | 0.083 | 0.250 | | --------------------|-----------|-----------|-----------|-----------| Column Total | 42 | 14 | 28 | 84 | | 0.500 | 0.167 | 0.333 | | --------------------|-----------|-----------|-----------|-----------| The CrossTable() function has options to report percentages (row, column, cell); specify decimal places; produce chi-square, Fisher, and McNemar tests of indepen- dence; report expected and residual values (Pearson, standardized, adjusted standard- ized); include missing values as valid; annotate with row and column titles; and format as SAS or SPSS style output. See help(CrossTable) for details. If you have more than two categorical variables, you’re dealing with multidimensional tables. We’ll consider these next. MULTIDIMENSIONAL TABLES Both table() and xtabs() can be used to generate multidimensional tables based on three or more categorical variables. The margin.table(), prop.table(), and addmargins() functions extend naturally to more than two dimensions. Additionally, the ftable() function can be used to print multidimensional tables in a compact and attractive manner. An example is given in listing 7.12. Download from Wow! eBook 154 CHAPTER 7 Basic statistics Listing 7.12 Three-way contingency table > mytable <- xtabs(~ Treatment+Sex+Improved, data=Arthritis) > mytable , , Improved = None q Sex Treatment Female Male Placebo 19 10 Treated 6 7 , , Improved = Some Sex Treatment Female Male Placebo 7 0 Treated 5 2 , , Improved = Marked Sex Treatment Female Male Placebo 6 1 Treated 16 5 > ftable(mytable) Sex Female Male Treatment Improved Placebo None 19 10 Some 7 0 Marked 6 1 Treated None 6 7 Some 5 2 Marked 16 5 > margin.table(mytable, 1) Treatment Placebo Treated w 43 41 > margin.table(mytable, 2) Sex Female Male 59 25 > margin.table(mytable, 3) Improved None Some Marked 42 14 28 > margin.table(mytable, c(1, 3)) Improved Treatment None Some Marked e Placebo 29 7 7 Treated 13 7 21 > ftable(prop.table(mytable, c(1, 2))) Improved None Some Marked Treatment Sex r Cell frequencies Marginal frequencies Treatment x Improved marginal frequencies Improve proportions for Treatment x Sex Download from Wow! eBook Frequency and contingency tables 155 Placebo Female 0.594 0.219 0.188 Male 0.909 0.000 0.091 Treated Female 0.222 0.185 0.593 Male 0.500 0.143 0.357 > ftable(addmargins(prop.table(mytable, c(1, 2)), 3)) Improved None Some Marked Sum Treatment Sex Placebo Female 0.594 0.219 0.188 1.000 Male 0.909 0.000 0.091 1.000 Treated Female 0.222 0.185 0.593 1.000 Male 0.500 0.143 0.357 1.000 The code in q produces cell frequencies for the three-way classification. The code also demonstrates how the ftable() function can be used to print a more compact and attractive version of the table. The code in w produces the marginal frequencies for Treatment, Sex, and Improved. Because you created the table with the formula ~Treatement+Sex+Improve, Treatment is referred to by index 1, Sex is referred to by index 2, and Improve is referred to by index 3. The code in e produces the marginal frequencies for the Treatment x Improved classification, summed over Sex. The proportion of patients with None, Some, and Marked improvement for each Treatment x Sex combination is provided in r. Here you see that 36 percent of treated males had marked improvement, compared to 59 percent of treated females. In general, the proportions will add to one over the indices not included in the prop.table() call (the third index, or Improve in this case). You can see this in the last example, where you add a sum margin over the third index. If you want percentages instead of proportions, you could multiply the resulting table by 100. For example: ftable(addmargins(prop.table(mytable, c(1, 2)), 3)) * 100 would produce this table: Sex Female Male Sum Treatment Improved Placebo None 65.5 34.5 100.0 Some 100.0 0.0 100.0 Marked 85.7 14.3 100.0 Treated None 46.2 53.8 100.0 Some 71.4 28.6 100.0 Marked 76.2 23.8 100.0 While contingency tables tell you the frequency or proportions of cases for each com- bination of the variables that comprise the table, you’re probably also interested in whether the variables in the table are related or independent. Tests of independence are covered in the next section. Download from Wow! eBook 156 CHAPTER 7 Basic statistics 7.2.2 Tests of independence R provides several methods of testing the independence of the categorical variables. The three tests described in this section are the chi-square test of independence, the Fisher exact test, and the Cochran-Mantel–Haenszel test. CHI-SQUARE TEST OF INDEPENDENCE You can apply the function chisq.test() to a two-way table in order to produce a chi-square test of independence of the row and column variables. See this next listing for an example. Listing 7.13 Chi-square test of independence > library(vcd) > mytable <- xtabs(~Treatment+Improved, data=Arthritis) > chisq.test(mytable) Pearson’s Chi-squared test data: mytable q X-squared = 13.1, df = 2, p-value = 0.001463 > mytable <- xtabs(~Improved+Sex, data=Arthritis) > chisq.test(mytable) Pearson’s Chi-squared test w data: mytable X-squared = 4.84, df = 2, p-value = 0.0889 Warning message: In chisq.test(mytable) : Chi-squared approximation may be incorrect From the results q, there appears to be a relationship between treatment received and level of improvement (p < .01). But there doesn’t appear to be a relationship w between patient sex and improvement (p > .05). The p-values are the probability of ob- taining the sampled results assuming independence of the row and column variables in the population. Because the probability is small for q, you reject the hypothesis that treatment type and outcome are independent. Because the probability for w isn’t small, it’s not unreasonable to assume that outcome and gender are independent. The warning message in listing 7.13 is produced because one of the six cells in the table (male-some improvement) has an expected value less than five, which may invalidate the chi-square approximation. FISHER’S EXACT TEST You can produce a Fisher’s exact test via the fisher.test() function. Fisher’s exact test evaluates the null hypothesis of independence of rows and columns in a contingen- cy table with fixed marginals. The format is fisher.test(mytable), where mytable is a two-way table. Here’s an example: > mytable <- xtabs(~Treatment+Improved, data=Arthritis) > fisher.test(mytable) Treatment and Improved not independent Gender and Improved independent Download from Wow! eBook Frequency and contingency tables 157 Fisher’s Exact Test for Count Data data: mytable p-value = 0.001393 alternative hypothesis: two.sided In contrast to many statistical packages, the fisher.test() function can be applied to any two-way table with two or more rows and columns, not a 2x2 table. COCHRAN–MANTEL–HAENSZEL TEST The mantelhaen.test() function provides a Cochran–Mantel–Haenszel chi-square test of the null hypothesis that two nominal variables are conditionally independent in each stratum of a third variable. The following code tests the hypothesis that Treat- ment and Improved variables are independent within each level Sex. The test assumes that there’s no three-way (Treatment x Improved x Sex) interaction. > mytable <- xtabs(~Treatment+Improved+Sex, data=Arthritis) > mantelhaen.test(mytable) Cochran-Mantel-Haenszel test data: mytable Cochran-Mantel-Haenszel M^2 = 14.6, df = 2, p-value = 0.0006647 The results suggest that the treatment received and the improvement reported aren’t independent within each level of sex (that is, treated individuals improved more than those receiving placebos when controlling for sex). 7.2.3 Measures of association The significance tests in the previous section evaluated whether or not sufficient evi- dence existed to reject a null hypothesis of independence between variables. If you can reject the null hypothesis, your interest turns naturally to measures of association in or- der to gauge the strength of the relationships present. The assocstats() function in the vcd package can be used to calculate the phi coefficient, contingency coefficient, and Cramer’s V for a two-way table. An example is given in the following listing. Listing 7.14 Measures of association for a two-way table > library(vcd) > mytable <- xtabs(~Treatment+Improved, data=Arthritis) > assocstats(mytable) X^2 df P(> X^2) Likelihood Ratio 13.530 2 0.0011536 Pearson 13.055 2 0.0014626 Phi-Coefficient : 0.394 Contingency Coeff.: 0.367 Cramer’s V : 0.394 In general, larger magnitudes indicated stronger associations. The vcd package also provides a kappa() function that can calculate Cohen’s kappa and weighted kappa for Download from Wow! eBook 158 CHAPTER 7 Basic statistics a confusion matrix (for example, the degree of agreement between two judges classify- ing a set of objects into categories). 7.2.4 Visualizing results R has mechanisms for visually exploring the relationships among categorical variables that go well beyond those found in most other statistical platforms. You typically use bar charts to visualize frequencies in one dimension (see chapter 6, section 6.1). The vcd package has excellent functions for visualizing relationships among categorical variables in multidimensional datasets using mosaic and association plots (see chapter 11, section 11.4). Finally, correspondence analysis functions in the ca package allow you to visually explore relationships between rows and columns in contingency tables using various geometric representations (Nenadic and Greenacre, 2007). 7.2.5 Converting tables to flat files We’ll end this section with a topic that’s rarely covered in books on R but that can be very useful. What happens if you have a table but need the original raw data? For ex- ample, say you have the following: Sex Female Male Treatment Improved Placebo None 19 10 Some 7 0 Marked 6 1 Treated None 6 7 Some 5 2 Marked 16 5 but you need this: ID Treatment Sex Age Improved 1 57 Treated Male 27 Some 2 46 Treated Male 29 None 3 77 Treated Male 30 None 4 17 Treated Male 32 Marked 5 36 Treated Male 46 Marked 6 23 Treated Male 58 Marked [78 more rows go here] There are many statistical functions in R that expect the latter format rather than the former. You can use the function provided in the following listing to convert an R table back into a flat data file. Listing 7.15 Converting a table into a flat file via table2flat table2flat <- function(mytable) { df <- as.data.frame(mytable) rows <- dim(df)[1] cols <- dim(df)[2] x <- NULL for (i in 1:rows){ for (j in 1:df$Freq[i]){ Download from Wow! eBook Correlations 159 row <- df[i,c(1:(cols-1))] x <- rbind(x,row) } } row.names(x)<-c(1:dim(x)[1]) return(x) } This function takes an R table (with any number of rows and columns) and returns a data frame in flat file format. You can also use this function to input tables from pub- lished studies. For example, let’s say that you came across table 7.2 in a journal and wanted to save it into R as a flat file. Table 7.2 Contingency table for treatment versus improvement from the Arthritis dataset Treatment Improved None Some Marked Placebo 29 7 7 Treated 13 17 21 This next listing describes a method that would do the trick. Listing 7.16 Using the table2flat() function with published data > treatment <- rep(c("Placebo", "Treated"), times=3) > improved <- rep(c("None", "Some", "Marked"), each=2) > Freq <- c(29,13,7,17,7,21) > mytable <- as.data.frame(cbind(treatment, improved, Freq)) > mydata <- table2flat(mytable) > head(mydata) treatment improved 1 Placebo None 2 Placebo None 3 Placebo None 4 Treated None 5 Placebo Some 6 Placebo Some [12 more rows go here] This ends the discussion of contingency tables, until we take up more advanced topics in chapters 11 and 15. Next, let’s look at various types of correlation coefficients. 7.3 Correlations Correlation coefficients are used to describe relationships among quantitative vari- ables. The sign ± indicates the direction of the relationship (positive or inverse) and the magnitude indicates the strength of the relationship (ranging from 0 for no rela- tionship to 1 for a perfectly predictable relationship). In this section, we’ll look at a variety of correlation coefficients, as well as tests of significance. We’ll use the state.x77 dataset available in the base R installation. It Download from Wow! eBook 160 CHAPTER 7 Basic statistics provides data on the population, income, illiteracy rate, life expectancy, murder rate, and high school graduation rate for the 50 US states in 1977. There are also temperature and land area measures, but we’ll drop them to save space. Use help(state.x77) to learn more about the file. In addition to the base installation, we’ll be using the psych and ggm packages. 7.3.1 Types of correlations R can produce a variety of correlation coefficients, including Pearson, Spearman, Ken- dall, partial, polychoric, and polyserial. Let’s look at each in turn. PEARSON, SPEARMAN, AND KENDALL CORRELATIONS The Pearson product moment correlation assesses the degree of linear relationship between two quantitative variables. Spearman’s Rank Order correlation coefficient as- sesses the degree of relationship between two rank-ordered variables. Kendall’s Tau is also a nonparametric measure of rank correlation. The cor() function produces all three correlation coefficients, whereas the cov() function provides covariances. There are many options, but a simplified format for producing correlations is cor(x, use= , method= ) The options are described in table 7.3. Table 7.3 cor/cov options Option Description x Matrix or data frame. use Specifies the handling of missing data. The options are all.obs (assumes no missing data—missing data will produce an error), everything (any correlation involving a case with missing values will be set to missing), complete.obs (listwise deletion), and pairwise.complete.obs (pairwise deletion). method Specifies the type of correlation. The options are pearson, spearman, or kendall. The default options are use="everything" and method="pearson". You can see an example in the following listing. Listing 7.17 Covariances and correlations > states<- state.x77[,1:6] > cov(states) Population Income Illiteracy Life Exp Murder HS Grad Population 19931684 571230 292.868 -407.842 5663.52 -3551.51 Income 571230 377573 -163.702 280.663 -521.89 3076.77 Illiteracy 293 -164 0.372 -0.482 1.58 -3.24 Life Exp -408 281 -0.482 1.802 -3.87 6.31 Murder 5664 -522 1.582 -3.869 13.63 -14.55 HS Grad -3552 3077 -3.235 6.313 -14.55 65.24 Download from Wow! eBook Correlations 161 > cor(states) Population Income Illiteracy Life Exp Murder HS Grad Population 1.0000 0.208 0.108 -0.068 0.344 -0.0985 Income 0.2082 1.000 -0.437 0.340 -0.230 0.6199 Illiteracy 0.1076 -0.437 1.000 -0.588 0.703 -0.6572 Life Exp -0.0681 0.340 -0.588 1.000 -0.781 0.5822 Murder 0.3436 -0.230 0.703 -0.781 1.000 -0.4880 HS Grad -0.0985 0.620 -0.657 0.582 -0.488 1.0000 > cor(states, method="spearman") Population Income Illiteracy Life Exp Murder HS Grad Population 1.000 0.125 0.313 -0.104 0.346 -0.383 Income 0.125 1.000 -0.315 0.324 -0.217 0.510 Illiteracy 0.313 -0.315 1.000 -0.555 0.672 -0.655 Life Exp -0.104 0.324 -0.555 1.000 -0.780 0.524 Murder 0.346 -0.217 0.672 -0.780 1.000 -0.437 HS Grad -0.383 0.510 -0.655 0.524 -0.437 1.000 The first call produces the variances and covariances. The second provides Pearson Product Moment correlation coefficients, whereas the third produces Spearman Rank Order correlation coefficients. You can see, for example, that a strong positive correla- tion exists between income and high school graduation rate and that a strong negative correlation exists between illiteracy rates and life expectancy. Notice that you get square matrices by default (all variables crossed with all other variables). You can also produce nonsquare matrices; see the following example: > x <- states[,c("Population", "Income", "Illiteracy", "HS Grad")] > y <- states[,c("Life Exp", "Murder")] > cor(x,y) Life Exp Murder Population -0.068 0.344 Income 0.340 -0.230 Illiteracy -0.588 0.703 HS Grad 0.582 -0.488 This version of the function is particularly useful when you’re interested in the rela- tionships between one set of variables and another. Notice that the results don’t tell you if the correlations differ significantly from 0 (that is, whether there’s sufficient evidence based on the sample data to conclude that the population correlations differ from 0). For that, you need tests of significance (described in section 7.3.2). PARTIAL CORRELATIONS A partial correlation is a correlation between two quantitative variables, controlling for one or more other quantitative variables. You can use the pcor() function in the ggm package to provide partial correlation coefficients. The ggm package isn’t installed by default, so be sure to install it on first use. The format is pcor(u, S) where u is a vector of numbers, with the first two numbers the indices of the variables to be correlated, and the remaining numbers the indices of the conditioning variables Download from Wow! eBook 162 CHAPTER 7 Basic statistics (that is, the variables being partialed out). S is the covariance matrix among the vari- ables. An example will help clarify this: > library(ggm) > # partial correlation of population and murder rate, controlling > # for income, illiteracy rate, and HS graduation rate > pcor(c(1,5,2,3,6), cov(states)) [1] 0.346 In this case, 0.346 is the correlation between population and murder rate, controlling for the influence of income, illiteracy rate, and HS graduation rate. The use of partial correlations is common in the social sciences. OTHER TYPES OF CORRELATIONS The hetcor() function in the polycor package can compute a heterogeneous cor- relation matrix containing Pearson product-moment correlations between numeric variables, polyserial correlations between numeric and ordinal variables, polychoric correlations between ordinal variables, and tetrachoric correlations between two di- chotomous variables. Polyserial, polychoric, and tetrachoric correlations assume that the ordinal or dichotomous variables are derived from underlying normal distribu- tions. See the documentation that accompanies this package for more information. 7.3.2 Testing correlations for significance Once you’ve generated correlation coefficients, how do you test them for statistical sig- nificance? The typical null hypothesis is no relationship (that is, the correlation in the population is 0). You can use the cor.test() function to test an individual Pearson, Spearman, and Kendall correlation coefficient. A simplified format is cor.test(x, y, alternative = , method = ) where x and y are the variables to be correlated, alternative specifies a two-tailed or one- tailed test ("two.side", "less", or "greater") and method specifies the type of corre- lation ("pearson", "kendall", or "spearman") to compute. Use alternative="less" when the research hypothesis is that the population correlation is less than 0. Use alternative="greater" when the research hypothesis is that the population correla- tion is greater than 0. By default, alternative="two.side" (population correlation isn’t equal to 0) is assumed. See the following listing for an example. Listing 7.18 Testing a correlation coefficient for significance > cor.test(states[,3], states[,5]) Pearson’s product-moment correlation data: states[, 3] and states[, 5] t = 6.85, df = 48, p-value = 1.258e-08 alternative hypothesis: true correlation is not equal to 0 95 percent confidence interval: 0.528 0.821 sample estimates: cor 0.703 Download from Wow! eBook Correlations 163 This code tests the null hypothesis that the Pearson correlation between life expec- tancy and murder rate is 0. Assuming that the population correlation is 0, you’d expect to see a sample correlation as large as 0.703 less than 1 time out of 10 million (that is, p = 1.258e-08). Given how unlikely this is, you reject the null hypothesis in favor of the research hypothesis, that the population correlation between life expectancy and murder rate is not 0. Unfortunately, you can test only one correlation at a time using cor.test. Luckily, the corr.test() function provided in the psych package allows you to go further. The corr.test() function produces correlations and significance levels for matrices of Pearson, Spearman, or Kendall correlations. An example is given in the following listing. Listing 7.19 Correlation matrix and tests of significance via corr.test > library(psych) > corr.test(states, use="complete") Call:corr.test(x = states, use = "complete") Correlation matrix Population Income Illiteracy Life Exp Murder HS Grad Population 1.00 0.21 0.11 -0.07 0.34 -0.10 Income 0.21 1.00 -0.44 0.34 -0.23 0.62 Illiteracy 0.11 -0.44 1.00 -0.59 0.70 -0.66 Life Exp -0.07 0.34 -0.59 1.00 -0.78 0.58 Murder 0.34 -0.23 0.70 -0.78 1.00 -0.49 HS Grad -0.10 0.62 -0.66 0.58 -0.49 1.00 Sample Size [1] 50 Probability value Population Income Illiteracy Life Exp Murder HS Grad Population 0.00 0.15 0.46 0.64 0.01 0.5 Income 0.15 0.00 0.00 0.02 0.11 0.0 Illiteracy 0.46 0.00 0.00 0.00 0.00 0.0 Life Exp 0.64 0.02 0.00 0.00 0.00 0.0 Murder 0.01 0.11 0.00 0.00 0.00 0.0 HS Grad 0.50 0.00 0.00 0.00 0.00 0.0 The use= options can be "pairwise" or "complete" (for pairwise or listwise dele- tion of missing values, respectively). The method= option is "pearson" (the default), "spearman", or "kendall". Here you see that the correlation between population size and high school graduation rate (–0.10) is not significantly different from 0 (p = 0.5). OTHER TESTS OF SIGNIFICANCE In section 7.4.1, we looked at partial correlations. The pcor.test() function in the psych package can be used to test the conditional independence of two variables con- trolling for one or more additional variables, assuming multivariate normality. The format is pcor.test(r, q, n) where r is the partial correlation produced by the pcor() function, q is the number of variables being controlled, and n is the sample size. Download from Wow! eBook 164 CHAPTER 7 Basic statistics Before leaving this topic, it should be mentioned that the r.test() function in the psych package also provides a number of useful significance tests. The function can be used to test the following: ■ The significance of a correlation coefficient ■ The difference between two independent correlations ■ The difference between two dependent correlations sharing one single variable ■ The difference between two dependent correlations based on completely differ- ent variables See help(r.test) for details. 7.3.3 Visualizing correlations The bivariate relationships underlying correlations can be visualized through scatter plots and scatter plot matrices, whereas correlograms provide a unique and powerful method for comparing a large numbers of correlation coefficients in a meaningful way. Each is covered in chapter 11. 7.4 t-tests The most common activity in research is the comparison of two groups. Do patients receiving a new drug show greater improvement than patients using an existing medication? Does one manufacturing process produce fewer defects than another? Which of two teaching methods is most cost-effective? If your outcome variable is categorical, you can use the methods described in section 7.3. Here, we’ll focus on group comparisons, where the outcome variable is continuous and assumed to be distributed normally. For this illustration, we’ll use the UScrime dataset distributed with the MASS package. It contains information on the effect of punishment regimes on crime rates in 47 US states in 1960. The outcome variables of interest will be Prob (the probability of imprisonment), U1 (the unemployment rate for urban males ages 14– 24) and U2 (the unemployment rate for urban males ages 35–39). The categorical variable So (an indicator variable for Southern states) will serve as the grouping variable. The data have been rescaled by the original authors. (Note: I considered naming this section “Crime and Punishment in the Old South," but cooler heads prevailed.) 7.4.1 Independent t-test Are you more likely to be imprisoned if you commit a crime in the South? The com- parison of interest is Southern versus non-Southern states and the dependent variable is the probability of incarceration. A two-group independent t-test can be used to test the hypothesis that the two population means are equal. Here, you assume that the two groups are independent and that the data are sampled from normal populations. The format is either Download from Wow! eBook t-tests 165 t.test(y ~ x, data) where y is numeric and x is a dichotomous variable, or t.test(y1, y2) where y1 and y2 are numeric vectors (the outcome variable for each group). The optional data argument refers to a matrix or data frame containing the variables. In contrast to most statistical packages, the default test assumes unequal variance and applies the Welsh degrees of freedom modification. You can add a var.equal=TRUE option to specify equal variances and a pooled variance estimate. By default, a two- tailed alternative is assumed (that is, the means differ but the direction isn’t specified). You can add the option alternative="less" or alternative="greater" to specify a directional test. In the following code, you compare Southern (group 1) and non-Southern (group 0) states on the probability of imprisonment using a two-tailed test without the assumption of equal variances: > library(MASS) > t.test(Prob ~ So, data=UScrime) Welch Two Sample t-test data: Prob by So t = -3.8954, df = 24.925, p-value = 0.0006506 alternative hypothesis: true difference in means is not equal to 0 95 percent confidence interval: -0.03852569 -0.01187439 sample estimates: mean in group 0 mean in group 1 0.03851265 0.06371269 You can reject the hypothesis that Southern states and non-Southern states have equal probabilities of imprisonment (p < .001). NOTE Because the outcome variable is a proportion, you might try to transform it to normality before carrying out the t-test. In the current case, all reasonable transformations of the outcome variable (Y/1-Y, log(Y/1-Y), arcsin(Y), arcsin(sqrt(Y)) would’ve led to the same conclusions. Transformations are covered in detail in chapter 8. 7.4.2 Dependent t-test As a second example, you might ask if unemployment rate for younger males (14–24) is greater than for older males (35–39). In this case, the two groups aren’t indepen- dent. You wouldn’t expect the unemployment rate for younger and older males in Alabama to be unrelated. When observations in the two groups are related, you have a dependent groups design. Pre-post or repeated measures designs also produce de- pendent groups. A dependent t-test assumes that the difference between groups is normally distributed. In this case, the format is Download from Wow! eBook 166 CHAPTER 7 Basic statistics t.test(y1, y2, paired=TRUE) where y1 and y2 are the numeric vectors for the two dependent groups. The results are as follows: > library(MASS) > sapply(UScrime[c("U1","U2")], function(x)(c(mean=mean(x),sd=sd(x)))) U1 U2 mean 95.5 33.98 sd 18.0 8.45 > with(UScrime, t.test(U1, U2, paired=TRUE)) Paired t-test data: U1 and U2 t = 32.4066, df = 46, p-value < 2.2e-16 alternative hypothesis: true difference in means is not equal to 0 95 percent confidence interval: 57.67003 65.30870 sample estimates: mean of the differences 61.48936 The mean difference (61.5) is large enough to warrant rejection of the hypothesis that the mean unemployment rate for older and younger males is the same. Younger males have a higher rate. In fact, the probability of obtaining a sample difference this large if the population means are equal is less than 0.00000000000000022 (that is, 2.2e–16). 7.4.3 When there are more than two groups What do you do if you want to compare more than two groups? If you can assume that the data are independently sampled from normal populations, you can use analysis of variance (ANOVA). ANOVA is a comprehensive methodology that covers many experi- mental and quasi-experimental designs. As such, it has earned its own chapter. Feel free to abandon this section and jump to chapter 9 at any time. 7.5 Nonparametric tests of group differences If you’re unable to meet the parametric assumptions of a t-test or ANOVA, you can turn to nonparametric approaches. For example, if the outcome variables are severely skewed or ordinal in nature, you may wish to use the techniques in this section. 7.5.1 Comparing two groups If the two groups are independent, you can use the Wilcoxon rank sum test (more popularly known as the Mann–Whitney U test) to assess whether the observations are sampled from the same probability distribution (that is, whether the probability of obtaining higher scores is greater in one population than the other). The format is either wilcox.test(y ~ x, data) Download from Wow! eBook Nonparametric tests of group differences 167 where y is numeric and x is a dichotomous variable, or wilcox.test(y1, y2) where y1 and y2 are the outcome variables for each group. The optional data argu- ment refers to a matrix or data frame containing the variables. The default is a two-tailed test. You can add the option exact to produce an exact test, and alternative="less" or alternative="greater" to specify a directional test. If you apply the Mann–Whitney U test to the question of incarceration rates from the previous section, you’ll get these results: > with(UScrime, by(Prob, So, median)) So: 0 [1] 0.0382 -------------------- So: 1 [1] 0.0556 > wilcox.test(Prob ~ So, data=UScrime) Wilcoxon rank sum test data: Prob by So W = 81, p-value = 8.488e-05 alternative hypothesis: true location shift is not equal to 0 Again, you can reject the hypothesis that incarceration rates are the same in Southern and non-Southern states (p < .001). The Wilcoxon signed rank test provides a nonparametric alternative to the dependent sample t-test. It’s appropriate in situations where the groups are paired and the assumption of normality is unwarranted. The format is identical to the Mann–Whitney U test, but you add the paired=TRUE option. Let’s apply it to the unemployment question from the previous section: > sapply(UScrime[c("U1","U2")], median) U1 U2 92 34 > with(UScrime, wilcox.test(U1, U2, paired=TRUE)) Wilcoxon signed rank test with continuity correction data: U1 and U2 V = 1128, p-value = 2.464e-09 alternative hypothesis: true location shift is not equal to 0 Again, you’d reach the same conclusion reached with the paired t-test. In this case, the parametric t-tests and their nonparametric equivalents reach the same conclusions. When the assumptions for the t-tests are reasonable, the Download from Wow! eBook 168 CHAPTER 7 Basic statistics parametric tests will be more powerful (more likely to find a difference if it exists). The nonparametric tests are more appropriate when the assumptions are grossly unreasonable (for example, rank ordered data). 7.5.2 Comparing more than two groups When there are more than two groups to be compared, you must turn to other methods. Consider the state.x77 dataset from section 7.4. It contains population, income, illiteracy rate, life expectancy, murder rate, and high school graduation rate data for US states. What if you want to compare the illiteracy rates in four regions of the country (Northeast, South, North Central, and West)? This is called a one-way design, and there are both parametric and nonparametric approaches available to address the question. If you can’t meet the assumptions of ANOVA designs, you can use nonparametric methods to evaluate group differences. If the groups are independent, a Kruskal– Wallis test will provide you with a useful approach. If the groups are dependent (for example, repeated measures or randomized block design), the Friedman test is more appropriate. The format for the Kruskal–Wallis test is kruskal.test(y ~ A, data) where y is a numeric outcome variable and A is a grouping variable with two or more levels (if there are two levels, it’s equivalent to the Mann–Whitney U test). For the Friedman test, the format is friedman.test(y ~ A | B, data) where y is the numeric outcome variable, A is a grouping variable, and B is a blocking variable that identifies matched observations. In both cases, data is an option argu- ment specifying a matrix or data frame containing the variables. Let’s apply the Kruskal–Wallis test to the illiteracy question. First, you’ll have to add the region designations to the dataset. These are contained in the dataset state. region distributed with the base installation of R. states <- as.data.frame(cbind(state.region, state.x77)) Now you can apply the test: > kruskal.test(Illiteracy ~ state.region, data=states) Kruskal-Wallis rank sum test data: states$Illiteracy by states$state.region Kruskal-Wallis chi-squared = 22.7, df = 3, p-value = 4.726e-05 The significance test suggests that the illiteracy rate isn’t the same in each of the four regions of the country (p <.001). Although you can reject the null hypothesis of no difference, the test doesn’t tell you which regions differ significantly from each other. To answer this question, you Download from Wow! eBook Nonparametric tests of group differences 169 could compare groups two at a time using the Mann–Whitney U test. A more elegant approach is to apply a simultaneous multiple comparisons procedure that makes all pairwise comparisons, while controlling the type I error rate (the probability of finding a difference that isn’t there). The npmc package provides the nonparametric multiple comparisons you need. To be honest, I’m stretching the definition of basic in the chapter title quite a bit, but because it fits well here, I hope you’ll bear with me. First, be sure to install the npmc package. The npmc() function in this package expects input to be a two-column data frame with a column named var (the dependent variable) and class (the grouping variable). The following listing contains the code you can use to accomplish this. Listing 7.20 Nonparametric multiple comparisons > class <- state.region > var <- state.x77[,c("Illiteracy")] > mydata <- as.data.frame(cbind(class, var)) > rm(class, var) > library(npmc) > summary(npmc(mydata), type="BF")$'Data-structure' group.index class.level nobs Northeast 1 Northeast 9 South 2 South 16 North Central 3 North Central 12 West 4 West 13 $'Results of the multiple Behrens-Fisher-Test' cmp effect lower.cl upper.cl p.value.1s p.value.2s 1 1-2 0.8750 0.66149 1.0885 0.000665 0.00135 q 2 1-3 0.1898 -0.13797 0.5176 0.999999 0.06547 3 1-4 0.3974 -0.00554 0.8004 0.998030 0.92004 4 2-3 0.0104 -0.02060 0.0414 1.000000 0.00000 5 2-4 0.1875 -0.07923 0.4542 1.000000 0.02113 6 3-4 0.5641 0.18740 0.9408 0.797198 0.98430 > aggregate(mydata, by=list(mydata$class), median) Group.1 class var 1 1 1 1.10 w 2 2 2 1.75 3 3 3 0.70 4 4 4 0.60 The npmc call generates six statistical comparisons (Northeast versus South, Northeast versus North Central, Northeast versus West, South versus North Central, South ver- sus West, and North Central versus West) q. You can see from the two-sided p-values (p.value.2s) that the South differs significantly from the other three regions, and that the other three regions don’t differ from each other. In w you see that the South has a higher median illiteracy rate. Note that npmc uses randomized values for integral calculations, so results differ slightly from call to call. Pairwise group comparisons Median illiteracy by class Download from Wow! eBook 170 CHAPTER 7 Basic statistics 7.6 Visualizing group differences In sections 7.4 and 7.5, we looked at statistical methods for comparing groups. Exam- ining group differences visually is also a crucial part of a comprehensive data analysis strategy. It allows you to assess the magnitude of the differences, identify any distribu- tional characteristics that influence the results (such as skew, bimodality, or outliers), and evaluate the appropriateness of the test assumptions. R provides a wide range of graphical methods for comparing groups, including box plots (simple, notched, and violin), covered in section 6.5; overlapping kernel density plots, covered in section 6.4.1; and graphical methods of assessing test assumptions, discussed in chapter 9. 7.7 Summary In this chapter, we reviewed the functions in R that provide basic statistical summaries and tests. We looked at sample statistics and frequency tables, tests of independence and measures of association for categorical variables, correlations between quantita- tive variables (and their associated significance tests), and comparisons of two or more groups on a quantitative outcome variable. In the next chapter, we’ll explore simple and multiple regression, where the focus is on understanding relationships between one (simple) or more than one (multiple) predictor variables and a predicted or criterion variable. Graphical methods will help you diagnose potential problems, evaluate and improve the fit of your models, and uncover unexpected gems of information in your data. Download from Wow! eBook Part 3 Intermediate methods While part 2 covered basic graphical and statistical methods, section 3 offers coverage of intermediate methods. We move from describing the relation- ship between two variables, to modeling the relationship between a numerical outcome variable and a set of numeric and/or categorical predictor variables. Chapter 8 introduces regression methods for modeling the relationship between a numeric outcome variable and a set of one or more predictor variables. Modeling data is typically a complex, multistep, interactive process. Chapter 8 provides step-by-step coverage of the methods available for fitting linear models, evaluating their appropriateness, and interpreting their meaning. Chapter 9 considers the analysis of basic experimental and quasi-experimental designs through the analysis of variance and its variants. Here we’re interested in how treatment combinations or conditions affect a numerical outcome variable. The chapter introduces the functions in R that are used to perform an analysis of variance, analysis of covariance, repeated measures analysis of variance, multi- factor analysis of variance, and multivariate analysis of variance. Methods for assessing the appropriateness of these analyses, and visualizing the results are also discussed. In designing experimental and quasi-experimental studies, it’s important to determine if the sample size is adequate for detecting the effects of interest (power analysis). Otherwise, why conduct the study? A detailed treatment of power analysis is provided in chapter 10. Starting with a discussion of hypothesis testing, the presentation focuses on how to use R functions 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 studies that are likely to yield useful results. Download from Wow! eBook Chapter 11 expands on the material in chapter 5 by covering the creation of graphs that help you to visualize relationships among two or more variables. This includes the various types of two- and three-dimensional scatter plots, scatter plot matrices, line plots, and bubble plots. It also introduces the useful, but less well-known, correlograms and mosaic plots. The linear models described in chapters 8 and 9 assume that the outcome or response variable is not only numeric, but also randomly sampled from a normal distribution. There are situations where this distributional assumption is untenable. 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 mathematically intractable. They include both resampling and bootstrapping approaches—computer intensive methods that are powerfully implemented in R. The methods described in this chapter will allow you to devise hypothesis tests for data that do not fit traditional parametric assumptions. After completing part 3, you’ll have the tools to analyze most common data analytic problems encountered in practice. And you will be able to create some gorgeous graphs! Download from Wow! eBook 8 173 Regression This chapter covers .n Fitting and interpreting linear models .n Evaluating model assumptions .n Selecting among competing models In many ways, regression analysis lives at the heart of statistics. It’s a broad term for a set of methodologies used to predict a response variable (also called a dependent, criterion, or outcome variable) from one or more predictor variables (also called independent or explanatory variables). In general, regression analysis can be used to identify the explanatory variables that are related to a response variable, to describe the form of the relationships involved, and to provide an equation for predicting the response variable from the explanatory variables. For example, an exercise physiologist might use regression analysis to develop an equation for predicting the expected number of calories a person will burn while exercising on a treadmill. The response variable is the number of calories burned (calculated from the amount of oxygen consumed), and the predictor variables might include duration of exercise (minutes), percentage of time spent at their target heart rate, average speed (mph), age (years), gender, and body mass index (BMI). Download from Wow! eBook 74 Chapter 8 Regression From a theoretical point of view, the analysis will help answer such questions as these: .n What’s the relationship between exercise duration and calories burned? Is it lin- ear or curvilinear? For example, does exercise have less impact on the number of calories burned after a certain point? .n How does effort (the percentage of time at the target heart rate, the average walking speed) factor in? .n Are these relationships the same for young and old, male and female, heavy and slim? From a practical point of view, the analysis will help answer such questions as the following: .n How many calories can a 30-year-old man with a BMI of 28.7 expect to burn if he walks for 45 minutes at an average speed of 4 miles per hour and stays within his target heart rate 80 percent of the time? .n What’s the minimum number of variables you need to collect in order to accu- rately predict the number of calories a person will burn when walking? .n How accurate will your prediction tend to be? Because regression analysis plays such a central role in modern statistics, we'll cover it in some depth in this chapter. First, we’ll look at how to fit and interpret regression models. Next, we’ll review a set of techniques for identifying potential problems with these models and how to deal with them. Third, we’ll explore the issue of variable selection. Of all the potential predictor variables available, how do you decide which ones to include in your final model? Fourth, we’ll address the question of generaliz- ability. How well will your model work when you apply it in the real world? Finally, we’ll look at the issue of relative importance. Of all the predictors in your model, which one is the most important, the second most important, and the least important? As you can see, we’re covering a lot of ground. Effective regression analysis is an interactive, holistic process with many steps, and it involves more than a little skill. Rather than break it up into multiple chapters, I’ve opted to present this topic in a single chapter in order to capture this flavor. As a result, this will be the longest and most involved chapter in the book. Stick with it to the end and you’ll have all the tools you need to tackle a wide variety of research questions. Promise! 8.1 The many faces of regression The term regression can be confusing because there are so many specialized varieties (see table 8.1). In addition, R has powerful and comprehensive features for fitting regression models, and the abundance of options can be confusing as well. For ex- ample, in 2005, Vito Ricci created a list of over 205 functions in R that are used to generate regression analyses (http://cran.r-project.org/doc/contrib/Ricci-refcard- regression.pdf). Download from Wow! eBook he many faces of regression 175 Table 8.1 Varieties of regression analysis Type of regression Typical use Simple linear Predicting a quantitative response variable from a quantitative explanatory variable Polynomial Predicting a quantitative response variable from a quantitative explanatory variable, where the relationship is modeled as an nth order polynomial Multiple linear Predicting a quantitative response variable from two or more explanatory variables Multivariate Predicting more than one response variable from one or more explanatory variables Logistic Predicting a categorical response variable from one or more explanatory variables Poisson Predicting a response variable representing counts from one or more explanatory variables Cox proportional hazards Predicting time to an event (death, failure, relapse) from one or more explanatory variables Time-series Modeling time-series data with correlated errors Nonlinear Predicting a quantitative response variable from one or more explanatory variables, where the form of the model is nonlinear Nonparametric Predicting a quantitative response variable from one or more explanatory variables, where the form of the model is derived from the data and not specified a priori Robust Predicting a quantitative response variable from one or more explanatory variables using an approach that’s resistant to the effect of influential observations In this chapter, we’ll focus on regression methods that fall under the rubric of ordinary least squares (OLS) regression, including simple linear regression, polynomial regres- sion, and multiple linear regression. OLS regression is the most common variety of sta- tistical analysis today. Other types of regression models (including logistic regression and Poisson regression) will be covered in chapter 13. 8.1.1 Scenarios for using OLS regression In OLS regression, a quantitative dependent variable is predicted from a weighted sum of predictor variables, where the weights are parameters estimated from the data. Let’s take a look at a concrete example (no pun intended), loosely adapted from Fwa (2006). An engineer wants to identify the most important factors related to bridge deterioration (such as age, traffic volume, bridge design, construction materials and methods, construction quality, and weather conditions) and determine the Download from Wow! eBook 76 Chapter 8 Regression mathematical form of these relationships. She collects data on each of these variables from a representative sample of bridges and models the data using OLS regression. The approach is highly interactive. She fits a series of models, checks their compliance with underlying statistical assumptions, explores any unexpected or aberrant findings, and finally chooses the “best” model from among many possible models. If successful, the results will help her to .n Focus on important variables, by determining which of the many collected variables are useful in predicting bridge deterioration, along with their relative importance. .n Look for bridges that are likely to be in trouble, by providing an equation that can be used to predict bridge deterioration for new cases (where the values of the predictor variables are known, but the degree of bridge deterioration isn’t). .n Take advantage of serendipity, by identifying unusual bridges. If she finds that some bridges deteriorate much faster or slower than predicted by the model, a study of these “outliers” may yield important findings that could help her to understand the mechanisms involved in bridge deterioration. Bridges may hold no interest for you. I’m a clinical psychologist and statistician, and I know next to nothing about civil engineering. But the general principles ap- ply to an amazingly wide selection of problems in the physical, biological, and so- cial sciences. Each of the following questions could also be addressed using an OLS approach: .n What’s the relationship between surface stream salinity and paved road surface area (Montgomery, 2007)? .n What aspects of a user’s experience contribute to the overuse of massively multi- player online role playing games (MMORPGs) (Hsu, Wen, & Wu, 2009)? .n Which qualities of an educational environment are most strongly related to higher student achievement scores? .n What’s the form of the relationship between blood pressure, salt intake, and age? Is it the same for men and women? .n What’s the impact of stadiums and professional sports on metropolitan area de- velopment (Baade & Dye, 1990)? .n What factors account for interstate differences in the price of beer (Culbertson & Bradford, 1991)? (That one got your attention!) Our primary limitation is our ability to formulate an interesting question, devise a use- ful response variable to measure, and gather appropriate data. 8.1.2 What you need to know For the remainder of this chapter I’ll describe how to use R functions to fit OLS regres- sion models, evaluate the fit, test assumptions, and select among competing models. It’s assumed that the reader has had exposure to least squares regression as typical- ly taught in a second semester undergraduate statistics course. However, I’ve made Download from Wow! eBook LS regression 177 efforts to keep the mathematical notation to a minimum and focus on practical rather than theoretical issues. A number of excellent texts are available that cover the statis- tical material outlined in this chapter. My favorites are John Fox’s Applied Regression Analysis and Generalized Linear Models (for theory) and An R and S-Plus Companion to Applied Regression (for application). They both served as major sources for this chapter. A good nontechnical overview is provided by Licht (1995). 8.2 OLS regression For most of this chapter, we’ll be predicting the response variable from a set of pre- dictor variables (also called “regressing” the response variable on the predictor vari- ables—hence the name) using OLS. OLS regression fits models of the form Yˆi = bˆ 0 + bˆ 1 X1i + …+ bˆ k Xki i = 1…n where n is the number of observations and k is the number of predictor variables. (Al- though I’ve tried to keep equations out of our discussions, this is one of the few places where it simplifies things.) In this equation: Yi is the predicted value of the dependent variable for observation i (specifically, it’s the estimated mean of the Y distribution, conditional on the set of predictor values) Xji is the jth predictor value for the ith observation b 0 is the intercept (the predicted value of Y when all the predictor variables equal zero) b j is the regression coefficient for the jth predictor (slope representing the change in Y for a unit change in Xj) Our goal is to select model parameters (intercept and slopes) that minimize the dif- ference between actual response values and those predicted by the model. Specifically, model parameters are selected to minimize the sum of squared residuals To properly interpret the coefficients of the OLS model, you must satisfy a number of statistical assumptions: .n Normality —For fixed values of the independent variables, the dependent variable is normally distributed. .n Independence —The Yi values are independent of each other. .n Linearity —The dependent variable is linearly related to the independent variables. .n Homoscedasticity —The variance of the dependent variable doesn’t vary with the levels of the independent variables. We could call this constant variance, but saying homoscedasticity makes me feel smarter. Download from Wow! eBook 78 Chapter 8 Regression If you violate these assumptions, your statistical significance tests and confidence inter- vals may not be accurate. Note that OLS regression also assumes that the independent variables are fixed and measured without error, but this assumption is typically relaxed in practice. 8.2.1 Fitting regression models with lm() In R, the basic function for fitting a linear model is lm(). The format is myfit <- lm(formula, data) where formula describes the model to be fit and data is the data frame containing the data to be used in fitting the model. The resulting object (myfit in this case) is a list that contains extensive information about the fitted model. The formula is typically written as Y ~ X1 + X2 + … + Xk where the ~ separates the response variable on the left from the predictor variables on the right, and the predictor variables are separated by + signs. Other symbols can be used to modify the formula in various ways (see table 8.2). Table 8.2 Symbols commonly used in R formulas Symbol Usage ~ Separates response variables on the left from the explanatory variables on the right. For example, a prediction of y from x, z, and w would be coded y ~ x + z + w. + Separates predictor variables. :Denotes an interaction between predictor variables. A prediction of y from x, z, and the interaction between x and z would be coded y ~ x + z + x:z. *A shortcut for denoting all possible interactions. The code y ~ x * z * w expands to y ~ x + z + w + x:z + x:w + z:w + x:z:w. ^ Denotes interactions up to a specified degree. The code y ~ (x + z + w)^2 expands to y ~ x + z + w + x:z + x:w + z:w. .A place holder for all other variables in the data frame except the dependent variable. For example, if a data frame contained the variables x, y, z, and w, then the code y ~ . would expand to y ~ x + z + w. -A minus sign removes a variable from the equation. For example, y ~ (x + z + w)^2 – x:w expands to y ~ x + z + w + x:z + z:w. -1 Suppresses the intercept. For example, the formula y ~ x -1 fits a regression of y on x, and forces the line through the origin at x=0. I() Elements within the parentheses are interpreted arithmetically. For example, y ~ x + (z + w)^2 would expand to y ~ x + z + w + z:w. In contrast, the code y ~ x + I((z + w)^2) would expand to y ~ x + h, where h is a new variable created by squaring the sum of z and w. function Mathematical functions can be used in formulas. For example, log(y) ~ x + z + w would predict log(y) from x, z, and w. Download from Wow! eBook LS regression 179 In addition to lm(), table 8.3 lists several functions that are useful when generating a simple or multiple regression analysis. Each of these functions is applied to the object returned by lm() in order to generate additional information based on that fitted model. Table 8.3 Other functions that are useful when fitting linear models Function Action summary()Displays detailed results for the fitted model coefficients()Lists the model parameters (intercept and slopes) for the fitted model confint()Provides confidence intervals for the model parameters (95 percent by default) fitted()Lists the predicted values in a fitted model residuals()Lists the residual values in a fitted model anova()Generates an ANOVA table for a fitted model, or an ANOVA table comparing two or more fitted models vcov()Lists the covariance matrix for model parameters AIC()Prints Akaike’s Information Criterion plot()Generates diagnostic plots for evaluating the fit of a model predict()Uses a fitted model to predict response values for a new dataset When the regression model contains one dependent variable and one independent variable, we call the approach simple linear regression. When there’s one predictor variable but powers of the variable are included (for example, X, X2, X3), we call it polynomial regression. When there’s more than one predictor variable, you call it mul- tiple linear regression. We’ll start with an example of a simple linear regression, then progress to examples of polynomial and multiple linear regression, and end with an example of multiple regression that includes an interaction among the predictors. 8.2.2 Simple linear regression Let’s take a look at the functions in table 8.3 through a simple regression example. The dataset women in the base installation provides the height and weight for a set of 15 women ages 30 to 39. We want to predict weight from height. Having an equation for predicting weight from height can help us to identify overweight or underweight individuals. The analysis is provided in the following listing, and the resulting graph is shown in figure 8.1. Listing 8.1 Simple linear regression > fit <- lm(weight ~ height, data=women) > summary(fit) Download from Wow! eBook 80 Chapter 8 Regression Call: lm(formula=weight ~ height, data=women) Residuals: Min 1Q Median 3Q Max -1.733 -1.133 -0.383 0.742 3.117 Coefficients: Estimate Std. Error t value Pr(>|t|) (Intercept) -87.5167 5.9369 -14.7 1.7e-09 *** height 3.4500 0.0911 37.9 1.1e-14 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 '' 1 Residual standard error: 1.53 on 13 degrees of freedom Multiple R-squared: 0.991, Adjusted R-squared: 0.99 F-statistic: 1.43e+03 on 1 and 13 DF, p-value: 1.09e-14 > women$weight [1] 115 117 120 123 126 129 132 135 139 142 146 150 154 159 164 > fitted(fit) 1 2 3 4 5 6 7 8 9 112.58 116.03 119.48 122.93 126.38 129.83 133.28 136.73 140.18 10 11 12 13 14 15 143.63 147.08 150.53 153.98 157.43 160.88 > residuals(fit) 1 2 3 4 5 6 7 8 9 10 11 2.42 0.97 0.52 0.07 -0.38 -0.83 -1.28 -1.73 -1.18 -1.63 -1.08 12 13 14 15 -0.53 0.02 1.57 3.12 > plot(women$height,women$weight, xlab="Height (in inches)", ylab="Weight (in pounds)") > abline(fit) From the output, you see that the prediction equation is Weight .. ×= − +87 52 3 45 Height Because a height of 0 is impossible, you wouldn’t try to give a physical interpretation to the intercept. It merely becomes an adjustment constant. From the Pr(>|t|) col- umn, you see that the regression coefficient (3.45) is significantly different from zero (p < 0.001) and indicates that there’s an expected increase of 3.45 pounds of weight for every 1 inch increase in height. The multiple R-squared (0.991) indicates that the model accounts for 99.1 percent of the variance in weights. The multiple R-squared is also the correlation between the actual and predicted value (that is, R rYY 2 =  ). The residual standard error (1.53 lbs.) can be thought of as the average error in Download from Wow! eBook LS regression 181 predicting weight from height using this model. The F statistic tests whether the pre- dictor variables taken together, predict the response variable above chance levels. Be- cause there’s only one predictor variable in simple regression, in this example the F test is equivalent to the t-test for the regression coefficient for height. For demonstration purposes, we’ve printed out the actual, predicted, and residual values. Evidently, the largest residuals occur for low and high heights, which can also be seen in the plot (figure 8.1). The plot suggests that you might be able to improve on the prediction by using a line with one bend. For example, a model of the form Y = + +β β β0 1 2 2XX may provide a better fit to the data. Polynomial regression allows you to predict a response variable from an explanatory variable, where the form of the relationship is an nth degree polynomial. 8.2.3 Polynomial regression The plot in figure 8.1 suggests that you might be able to improve your prediction using a regression with a quadratic term (that is, X 2). You can fit a quadratic equation using the statement fit2 <- lm(weight ~ height + I(height^2), data=women) The new term I(height^2) requires explanation. height^2 adds a height-squared term to the prediction equation. The I function treats the contents within the paren- theses as an R regular expression. You need this because the ^ operator has a special meaning in formulas that you don’t want to invoke here (see table 8.2). Listing 8.2 shows the results of fitting the quadratic equation. 58 60 62 64 66 68 70 72 1 2 0 1 3 0 1 4 0 1 5 0 1 6 0 Height (in inches) W e i g h t ( i n p o u n d s ) Figure 8.1 Scatter plot with regression line for weight predicted from height Download from Wow! eBook 82 Chapter 8 Regression Listing 8.2 Polynomial regression > fit2 <- lm(weight ~ height + I(height^2), data=women) > summary(fit2) Call: lm(formula=weight ~ height + I(height^2), data=women) Residuals: Min 1Q Median 3Q Max -0.5094 -0.2961 -0.0094 0.2862 0.5971 Coefficients: Estimate Std. Error t value Pr(>|t|) (Intercept) 261.87818 25.19677 10.39 2.4e-07 *** height -7.34832 0.77769 -9.45 6.6e-07 *** I(height^2) 0.08306 0.00598 13.89 9.3e-09 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Residual standard error: 0.384 on 12 degrees of freedom Multiple R-squared: 0.999, Adjusted R-squared: 0.999 F-statistic: 1.14e+04 on 2 and 12 DF, p-value: <2e-16 > plot(women$height,women$weight, xlab="Height (in inches)", ylab="Weight (in lbs)") > lines(women$height,fitted(fit2)) From this new analysis, the prediction equation is and both regression coefficients are significant at the p < 0.0001 level. The amount of variance accounted for has increased to 99.9 percent. The significance of the squared term (t = 13.89, p < .001) suggests that inclusion of the quadratic term improves the model fit. If you look at the plot of fit2 (figure 8.2) you can see that the curve does indeed provides a better fit. 58 60 62 64 66 68 70 72 1 2 0 1 3 0 1 4 0 1 5 0 1 6 0 Height (in inches) W e i g h t ( i n l b s ) Figure 8.2 Quadratic regression for weight predicted by height Download from Wow! eBook LS regression 183 In general, an nth degree polynomial produces a curve with n-1 bends. To fit a cubic polynomial, you’d use fit3 <- lm(weight ~ height + I(height^2) +I(height^3), data=women) Although higher polynomials are possible, I’ve rarely found that terms higher than cubic are necessary. Before we move on, I should mention that the scatterplot() function in the car package provides a simple and convenient method of plotting a bivariate relationship. The code library(car) scatterplot(weight ~ height, data=women, spread=FALSE, lty.smooth=2, pch=19, main="Women Age 30-39", xlab="Height (inches)", ylab="Weight (lbs.)") produces the graph in figure 8.3. This enhanced plot provides the scatter plot of weight with height, box plots for each variable in their respective margins, the linear line of best fit, and a smoothed (loess) fit line. The spread=FALSE options suppress spread and asymmetry information. The lty.smooth=2 option specifies that the loess fit be rendered as a dashed line. The Linear versus nonlinear models Note that this polynomial equation still fits under the rubric of linear regression. It’s linear because the equation involves a weighted sum of predictor variables (height and height-squared in this case). Even a model such as would be considered a linear model (linear in terms of the parameters) and fit with the formula Y ~ log(X1) + sin(X2) In contrast, here’s an example of a truly nonlinear model: Nonlinear models of this form can be fit with the nls() function. 58 60 62 64 66 68 70 72 1 2 0 1 3 0 1 4 0 1 5 0 1 6 0 Wo men Age 30−39 Height (inches) W e i g h t ( l b s . ) Figure 8.3 Scatter plot of height by weight, with linear and smoothed fits, and marginal box plots Download from Wow! eBook 84 Chapter 8 Regression pch=19 options display points as filled circles (the default is open circles). You can tell at a glance that the two variables are roughly symmetrical and that a curved line will fit the data points better than a straight line. 8.2.4 Multiple linear regression When there’s more than one predictor variable, simple linear regression becomes mul- tiple linear regression, and the analysis grows more involved. Technically, polynomial regression is a special case of multiple regression. Quadratic regression has two predic- tors (X and X 2), and cubic regression has three predictors (X, X 2, and X 3). Let’s look at a more general example. We’ll use the state.x77 dataset in the base package for this example. We want to explore the relationship between a state’s murder rate and other characteristics of the state, including population, illiteracy rate, average income, and frost levels (mean number of days below freezing). Because the lm() function requires a data frame (and the state.x77 dataset is contained in a matrix), you can simplify your life with the following code: states <- as.data.frame(state.x77[,c("Murder", "Population", "Illiteracy", "Income", "Frost")]) This code creates a data frame called states, containing the variables we’re interested in. We’ll use this new data frame for the remainder of the chapter. A good first step in multiple regression is to examine the relationships among the variables two at a time. The bivariate correlations are provided by the cor() function, and scatter plots are generated from the scatterplotMatrix() function in the car package (see the following listing and figure 8.4). Listing 8.3 Examining bivariate relationships > cor(states) Murder Population Illiteracy Income Frost Murder 1.00 0.34 0.70 -0.23 -0.54 Population 0.34 1.00 0.11 0.21 -0.33 Illiteracy 0.70 0.11 1.00 -0.44 -0.67 Income -0.23 0.21 -0.44 1.00 0.23 Frost -0.54 -0.33 -0.67 0.23 1.00 > library(car) > scatterplotMatrix(states, spread=FALSE, lty.smooth=2, main="Scatter Plot Matrix") By default, the scatterplotMatrix() function provides scatter plots of the variables with each other in the off-diagonals and superimposes smoothed (loess) and linear fit lines on these plots. The principal diagonal contains density and rug plots for each variable. You can see that murder rate may be bimodal and that each of the predictor variables is skewed to some extent. Murder rates rise with population and illiteracy, and fall with higher income levels and frost. At the same time, colder states have lower illiteracy rates and population and higher incomes. Download from Wow! eBook LS regression 185 Murder 0 10000 20000 3000 4500 6000 26 1 0 1 4 0 1 0 0 0 0 2 0 0 0 0 P opulation Illiteracy 0 . 5 1 . 5 2 . 5 3 0 0 0 4 5 0 0 6 0 0 0 Income 2 6 10 14 0.5 1.5 2.5 0 5 0 100 05 0 1 0 0 Frost Scatterplot Matrix Figure 8.4 Scatter plot matrix of dependent and independent variables for the states data, including linear and smoothed fits, and marginal distributions (kernel density plots and rug plots) Now let’s fit the multiple regression model with the lm() function (see the following listing). Listing 8.4 Multiple linear regression > fit <- lm(Murder ~ Population + Illiteracy + Income + Frost, data=states) > summary(fit) Call: lm(formula=Murder ~ Population + Illiteracy + Income + Frost, data=states) Download from Wow! eBook 86 Chapter 8 Regression Residuals: Min 1Q Median 3Q Max -4.7960 -1.6495 -0.0811 1.4815 7.6210 Coefficients: Estimate Std. Error t value Pr(>|t|) (Intercept) 1.23e+00 3.87e+00 0.32 0.751 Population 2.24e-04 9.05e-05 2.47 0.017 * Illiteracy 4.14e+00 8.74e-01 4.74 2.2e-05 *** Income 6.44e-05 6.84e-04 0.09 0.925 Frost 5.81e-04 1.01e-02 0.06 0.954 --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.v 0.1 'v' 1 Residual standard error: 2.5 on 45 degrees of freedom Multiple R-squared: 0.567, Adjusted R-squared: 0.528 F-statistic: 14.7 on 4 and 45 DF, p-value: 9.13e-08 When there’s more than one predictor variable, the regression coefficients indicate the increase in the dependent variable for a unit change in a predictor variable, hold- ing all other predictor variables constant. For example, the regression coefficient for Illiteracy is 4.14, suggesting that an increase of 1 percent in illiteracy is associated with a 4.14 percent increase in the murder rate, controlling for population, income, and temperature. The coefficient is significantly different from zero at the p < .0001 level. On the other hand, the coefficient for Frost isn’t significantly different from zero (p = 0.954) suggesting that Frost and Murder aren’t linearly related when controlling for the other predictor variables. Taken together, the predictor variables account for 57 percent of the variance in murder rates across states. Up to this point, we’ve assumed that the predictor variables don’t interact. In the next section, we’ll consider a case in which they do. 8.2.5 Multiple linear regression with interactions Some of the most interesting research findings are those involving interactions among predictor variables. Consider the automobile data in the mtcars data frame. Let’s say that you’re interested in the impact of automobile weight and horse power on mileage. You could fit a regression model that includes both predictors, along with their interac- tion, as shown in the next listing. Listing 8.5 Multiple linear regression with a significant interaction term > fit <- lm(mpg ~ hp + wt + hp:wt, data=mtcars) > summary(fit) Call: lm(formula=mpg ~ hp + wt + hp:wt, data=mtcars) Residuals: Min 1Q Median 3Q Max -3.063 -1.649 -0.736 1.421 4.551 Download from Wow! eBook LS regression 187 Coefficients: Estimate Std. Error t value Pr(>|t|) (Intercept) 49.80842 3.60516 13.82 5.0e-14 *** hp -0.12010 0.02470 -4.86 4.0e-05 *** wt -8.21662 1.26971 -6.47 5.2e-07 *** hp:wt 0.02785 0.00742 3.75 0.00081 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ‘ 1 Residual standard error: 2.1 on 28 degrees of freedom Multiple R-squared: 0.885, Adjusted R-squared: 0.872 F-statistic: 71.7 on 3 and 28 DF, p-value: 2.98e-13 You can see from the Pr(>|t|) column that the interaction between horse power and car weight is significant. What does this mean? A significant interaction between two predictor variables tells you that the relationship between one predictor and the response variable depends on the level of the other predictor. Here it means that the relationship between miles per gallon and horse power varies by car weight. Our model for predicting mpg is mpg = 49.81 – 0.12 × hp – 8.22 × wt + 0.03 × hp × wt. To interpret the interaction, you can plug in various values of wt and simplify the equation. For example, you can try the mean of wt (3.2) and one standard deviation below and above the mean (2.2 and 4.2, respectively). For wt=2.2, the equation simplifies to mpg = 49.81 – 0.12 × hp – 8.22 × (2.2) + 0.03 × hp ×(2.2) = 31.41 – 0.06 × hp. For wt=3.2, this becomes mpg = 23.37 – 0.03 × hp. Finally, for wt=4.2 the equation becomes mpg = 15.33 – 0.003 × hp. You see that as weight increases (2.2, 3.2, 4.2), the expected change in mpg from a unit increase in hp decreases (0.06, 0.03, 0.003). You can visualize interactions using the effect() function in the effects package. The format is plot(effect(term, mod, xlevels), multiline=TRUE) where term is the quoted model term to plot, mod is the fitted model returned by lm(), and xlevels is a list specifying the variables to be set to constant values and the values to employ. The multiline=TRUE op- tion superimposes the lines being plotted. For the previous model, this becomes library(effects) plot(effect("hp:wt", fit, list(wt=c(2.2,3.2,4.2))), multiline=TRUE) The resulting graph is displayed in figure 8.5. hp*wt effect plot hp m p g 15 20 25 50 100 150 200 250 300 wt 2.2 3.2 4.2 Figure 8.5 Interaction plot for hp*wt. This plot displays the relationship between mpg and hp at 3 values of wt. Download from Wow! eBook 88 Chapter 8 Regression You can see from this graph that as the weight of the car increases, the relationship between horse power and miles per gallon weakens. For wt=4.2, the line is almost horizontal, indicating that as hp increases, mpg doesn’t change. Unfortunately, fitting the model is only the first step in the analysis. Once you fit a regression model, you need to evaluate whether you’ve met the statistical assumptions underlying your approach before you can have confidence in the inferences you draw. This is the topic of the next section. 8.3 Regression diagnostics In the previous section, you used the lm() function to fit an OLS regression model and the summary() function to obtain the model parameters and summary statistics. Unfortunately, there’s nothing in this printout that tells you if the model you have fit is appropriate. Your confidence in inferences about regression parameters depends on the degree to which you’ve met the statistical assumptions of the OLS model. Although the summary() function in listing 8.4 describes the model, it provides no information concerning the degree to which you’ve satisfied the statistical assumptions underlying the model. Why is this important? Irregularities in the data or misspecifications of the relationships between the predictors and the response variable can lead you to settle on a model that’s wildly inaccurate. On the one hand, you may conclude that a predictor and response variable are unrelated when, in fact, they are. On the other hand, you may conclude that a predictor and response variable are related when, in fact, they aren’t! You may also end up with a model that makes poor predictions when applied in real-world settings, with significant and unnecessary error. Let’s look at the output from the confint() function applied to the states multiple regression problem in section 8.2.4. > fit <- lm(Murder ~ Population + Illiteracy + Income + Frost, data=states) > confint(fit) 2.5 % 97.5 % (Intercept) -6.55e+00 9.021318 Population 4.14e-05 0.000406 Illiteracy 2.38e+00 5.903874 Income -1.31e-03 0.001441 Frost -1.97e-02 0.020830 The results suggest that you can be 95 percent confident that the interval [2.38, 5.90] contains the true change in murder rate for a 1 percent change in illiteracy rate. Ad- ditionally, because the confidence interval for Frost contains 0, you can conclude that a change in temperature is unrelated to murder rate, holding the other variables con- stant. But your faith in these results is only as strong as the evidence that you have that your data satisfies the statistical assumptions underlying the model. A set of techniques called regression diagnostics provides you with the necessary tools for evaluating the appropriateness of the regression model and can help you to uncover and correct problems. First, we’ll start with a standard approach that uses Download from Wow! eBook egression diagnostics 189 functions that come with R’s base installation. Then we’ll look at newer, improved methods available through the car package. 8.3.1 A typical approach R’s base installation provides numerous methods for evaluating the statistical assump- tions in a regression analysis. The most common approach is to apply the plot() function to the object returned by the lm(). Doing so produces four graphs that are useful for evaluating the model fit. Applying this approach to the simple linear regres- sion example fit <- lm(weight ~ height, data=women) par(mfrow=c(2,2)) plot(fit) produces the graphs shown in figure 8.6. The par(mfrow=c(2,2)) statement is used to combine the four plots produced by the plot() function into one large 2x2 graph. The par() function is described in chapter 3. 4 6 81 0 1 2 1 4 − 5 05 Fitted va lues R e s i d u a l s Residuals vs Fitted Ne v ada Rhode Island Massachusetts −2 −1 0 1 2 − 2 − 1 0123 Theoretical Quantile s S t a n d a r d i z e d r e s i d u a l s Nor mal Q−Q Ne v ada Rhode Island Alaska 4 6 81 0 1 2 1 4 0 0 0 . . 5 1 . 01 . 5 Fitted va lues S t a n d a r d i z e d r e s i d u a l s Scale−Location Ne v ada Rhode Island Alaska 0. 0 0 .1 0. 2 0 .3 0. 4 − 2 − 1 012 3 Le ve rage S t a n d a r d i z e d r e s i d u a l s Cook’s distance 1 0.5 0.5 1 Residuals vs Le ve rage Alaska Ne v ada Ha w aii Figure 8.6 Diagnostic plots for the regression of weight on height Download from Wow! eBook 90 Chapter 8 Regression To understand these graphs, consider the assumptions of OLS regression: .n Normality —If the dependent variable is normally distributed for a fixed set of predictor values, then the residual values should be normally distributed with a mean of 0. The Normal Q-Q plot (upper right) is a probability plot of the stan- dardized residuals against the values that would be expected under normality. If you’ve met the normality assumption, the points on this graph should fall on the straight 45-degree line. Because they don’t, you’ve clearly violated the normality assumption. .n Independence —You can’t tell if the dependent variable values are independent from these plots. You have to use your understanding of how the data were col- lected. There’s no a priori reason to believe that one woman’s weight influences another woman’s weight. If you found out that the data were sampled from fami- lies, you may have to adjust your assumption of independence. .n Linearity —If the dependent variable is linearly related to the independent vari- ables, there should be no systematic relationship between the residuals and the predicted (that is, fitted) values. In other words, the model should capture all the systematic variance present in the data, leaving nothing but random noise. In the Residuals versus Fitted graph (upper left), you see clear evidence of a curved relationship, which suggests that you may want to add a quadratic term to the regression. .n Homoscedasticity —If you’ve met the constant variance assumption, the points in the Scale-Location graph (bottom left) should be a random band around a hori- zontal line. You seem to meet this assumption. Finally, the Residual versus Leverage graph (bottom right) provides information on individual observations that you may wish to attend to. The graph identifies outliers, high-leverage points, and influential observations. Specifically: .n An outlier is an observation that isn’t predicted well by the fitted regression model (that is, has a large positive or negative residual). .n An observation with a high leverage value has an unusual combination of predic- tor values. That is, it’s an outlier in the predictor space. The dependent variable value isn’t used to calculate an observation’s leverage. .n An influential observation is an observation that has a disproportionate impact on the determination of the model parameters. Influential observations are identi- fied using a statistic called Cook’s distance, or Cook’s D. To be honest, I find the Residual versus Leverage plot difficult to read and not useful. You’ll see better representations of this information in later sections. To complete this section, let’s look at the diagnostic plots for the quadratic fit. The necessary code is fit2 <- lm(weight ~ height + I(height^2), data=women) par(mfrow=c(2,2)) plot(fit2) and the resulting graph is provided in figure 8.7. Download from Wow! eBook egression diagnostics 191 120 130 140 150 160 − 0 . 6 − 0 . 20 . 2 0 . 6 Fitted va lues R e s i d u a l s Residuals vs Fitted 15 13 2 −1 0 1 − 1 01 2 Theoretical Quantile s S t a n d a r d i z e d r e s i d u a l s Nor mal Q−Q 15 13 2 120 130 140 150 160 0 0 0 . . 5 1 . 01 . 5 Fitted va lues S t a n d a r d i z e d r e s i d u a l s Scale−Location 15 13 2 0. 0 0 .1 0. 2 0 .3 0. 4 − 1 012 Le ve rage S t a n d a r d i z e d r e s i d u a l s Cook’s distance 1 0.5 0.5 1 Residuals vs Le ve rage 15 2 13 Figure 8.7 Diagnostic plots for the regression of weight on height and height-squared This second set of plots suggests that the polynomial regression provides a better fit with regard to the linearity assumption, normality of residuals (except for observation 13), and homoscedasticity (constant residual variance). Observation 15 appears to be influential (based on a large Cook’s D value), and deleting it has an impact on the parameter estimates. In fact, dropping both observation 13 and 15 produces a better model fit. To see this, try newfit <- lm(weight~ height + I(height^2), data=women[-c(13,15),]) for yourself. But you need to be careful when deleting data. Your models should fit your data, not the other way around! Finally, let’s apply the basic approach to the states multiple regression problem: fit <- lm(Murder ~ Population + Illiteracy + Income + Frost, data=states) par(mfrow=c(2,2)) plot(fit) Download from Wow! eBook 92 Chapter 8 Regression The results are displayed in figure 8.8. As you can see from the graph, the model assumptions appear to be well satisfied, with the exception that Nevada is an outlier. Although these standard diagnostic plots are helpful, better tools are now available in R and I recommend their use over the plot(fit) approach. 8.3.2 An enhanced approach The car package provides a number of functions that significantly enhance your ability to fit and evaluate regression models (see table 8.4). 4 6 8 1 0 1 2 1 4 − 5 05 Fitted va lues R e s i d u a l s Residuals vs Fitted Ne v ada Rhode Island Massachusetts −2 −1 0 1 2 − 2 − 1 0123 Theoretical Quantile s S t a n d a r d i z e d r e s i d u a l s Nor mal Q−Q Ne v ada Rhode Island Alaska 4 6 8 1 0 1 2 1 4 0 0 0 . . 5 1 . 01 . 5 Fitted va lues S t a n d a r d i z e d r e s i d u a l s Scale−Location Ne v ada Rhode Island Alaska 0. 0 0 .1 0. 2 0 .3 0. 4 − 2 − 1 012 3 Le ve rage S t a n d a r d i z e d r e s i d u a l s Cook’s distance 1 0.5 0.5 1 Residuals vs Le ve rage Alaska Ne v ada Ha w aii Figure 8.8 Diagnostic plots for the regression of murder rate on state characteristics Download from Wow! eBook egression diagnostics 193 Table 8.4 Useful functions for regression diagnostics (car package) Function Purpose qqPlot()Quantile comparisons plot durbinWatsonTest()Durbin–Watson test for autocorrelated errors crPlots()Component plus residual plots ncvTest()Score test for nonconstant error variance spreadLevelPlot()Spread-level plot outlierTest()Bonferroni outlier test avPlots()Added variable plots influencePlot()Regression influence plot scatterplot()Enhanced scatter plot scatterplotMatrix()Enhanced scatter plot matrix vif()Variance inflation factors It’s important to note that there are many changes between version 1.x and version 2.x of the car package, including changes in function names and behavior. This chapter is based on version 2. In addition, the gvlma package provides a global test for linear model assumptions. Let’s look at each in turn, by applying them to our multiple regression example. NORMALITY The qqPlot() function provides a more accurate method of assessing the normality assumption than provided by the plot() function in the base package. It plots the studentized residuals (also called studentized deleted residuals or jackknifed residuals) against a t distribution with n-p-1 degrees of freedom, where n is the sample size and p is the number of regression parameters (including the intercept). The code follows: library(car) fit <- lm(Murder ~ Population + Illiteracy + Income + Frost, data=states) qqPlot(fit, labels=row.names(states), id.method="identify", simulate=TRUE, main="Q-Q Plot") The qqPlot() function generates the probability plot displayed in figure 8.9. The option id.method="identify" makes the plot interactive—after the graph is drawn, mouse clicks on points within the graph will label them with values specified in the labels option of the function. Hitting the Esc key, selecting Stop from the graph’s drop-down menu, or right-clicking on the graph will turn off this interactive mode. Here, I identified Nevada. When simulate=TRUE, a 95 percent confidence envelope is produced using a parametric bootstrap. (Bootstrap methods are considered in chapter 12.) Download from Wow! eBook 94 Chapter 8 Regression 2 1 0 1 2 2 1 0123 QQ Plot t Quantiles S t u d e n t i z e d R e s i d u a l s ( f i t ) Nevada Figure 8.9 Q-Q plot for studentized residuals With the exception of Nevada, all the points fall close to the line and are within the con- fidence envelope, suggesting that you’ve met the normality assumption fairly well. But you should definitely look at Nevada. It has a large positive residual (actual-predicted), indicating that the model underestimates the murder rate in this state. Specifically: > states["Nevada",] Murder Population Illiteracy Income Frost Nevada 11.5 590 0.5 5149 188 > fitted(fit)["Nevada"] Nevada 3.878958 > residuals(fit)["Nevada"] Nevada 7.621042 > rstudent(fit)["Nevada"] Nevada 3.542929 Here you see that the murder rate is 11.5 percent, but the model predicts a 3.9 percent murder rate. The question that you need to ask is, “Why does Nevada have a higher murder rate than predicted from population, income, illiteracy, and temperature?” Anyone (who hasn’t see Goodfellas) want to guess? Download from Wow! eBook egression diagnostics 195 For completeness, here’s another way of visualizing errors. Take a look at the code in the next listing. The residplot() function generates a histogram of the studen- tized residuals and superimposes a normal curve, kernel density curve, and rug plot. It doesn’t require the car package. Listing 8.6 Function for plotting studentized residuals residplot <- function(fit, nbreaks=10) { z <- rstudent(fit) hist(z, breaks=nbreaks, freq=FALSE, xlab="Studentized Residual", main="Distribution of Errors") rug(jitter(z), col="brown") curve(dnorm(x, mean=mean(z), sd=sd(z)), add=TRUE, col="blue", lwd=2) lines(density(z)$x, density(z)$y, col="red", lwd=2, lty=2) legend("topright", legend = c( "Normal Curve", "Kernel Density Curve"), lty=1:2, col=c("blue","red"), cex=.7) } residplot(fit) The results are displayed in figure 8.10. Distrib ution of Err or s Studentiz ed Residual D e n s i t y −2 −1 0 1 2 3 4 0 . 0 0 . 1 0 . 2 0 . 3 0 . 4 No rm al Cur ve Ke r nel Density Cur ve Figure 8.10 Distribution of studentized residuals using the residplot() function Download from Wow! eBook 96 Chapter 8 Regression As you can see, the errors follow a normal distribution quite well, with the exception of a large outlier. Although the Q-Q plot is probably more informative, I’ve always found it easier to gauge the skew of a distribution from a histogram or density plot than from a probability plot. Why not use both? INDEPENDENCE OF ERRORS As indicated earlier, the best way to assess whether the dependent variable values (and thus the residuals) are independent is from your knowledge of how the data were col- lected. For example, time series data will often display autocorrelation—observations collected closer in time will be more correlated with each other than with observations distant in time. The car package provides a function for the Durbin–Watson test to detect such serially correlated errors. You can apply the Durbin–Watson test to the multiple regression problem with the following code: > durbinWatsonTest(fit) lag Autocorrelation D-W Statistic p-value 1 -0.201 2.32 0.282 Alternative hypothesis: rho != 0 The nonsignificant p-value (p=0.282) suggests a lack of autocorrelation, and conversely an independence of errors. The lag value (1 in this case) indicates that each observa- tion is being compared with the one next to it in the dataset. Although appropriate for time-dependent data, the test is less applicable for data that isn’t clustered in this fashion. Note that the durbinWatsonTest() function uses bootstrapping (see chapter 12) to derive p-values. Unless you add the option simulate=FALSE, you’ll get a slightly different value each time you run the test. LINEARITY You can look for evidence of nonlinearity in the relationship between the dependent variable and the independent variables by using component plus residual plots (also known as partial residual plots). The plot is produced by crPlots() function in the car package. You’re looking for any systematic departure from the linear model that you’ve specified. To create a component plus residual plot for variable Xj , you plot the points ε , where the residuals ε are based on the full model, and i =1…n. The straight line in each graph is given by . Loess fit lines are described in chapter 11. The code to produce these plots is as follows: > library(car) > crPlots(fit) The resulting plots are provided in figure 8.11. Nonlinearity in any of these plots sug- gests that you may not have adequately modeled the functional form of that predictor in the regression. If so, you may need to add curvilinear components such as polyno- mial terms, transform one or more variables (for example, use log(X) instead of X), or abandon linear regression in favor of some other regression variant. Transformations are discussed later in this chapter. Download from Wow! eBook egression diagnostics 197 0 5000 10000 15000 20000 − 6 − 4 − 2 0246 P opulatio n C o m p o n e n t + R e s i d u a l ( M u r d e r ) 0. 5 1 .0 1. 5 2 .0 2. 5 − 4 − 2 02468 Illiteracy C o m p o n e n t + R e s i d u a l ( M u r d e r ) 3000 4000 5000 6000 − 4 − 2 0246 8 Income C o m p o n e n t + R e s i d u a l ( M u r d e r ) 0 5 0 100 150 − 4 − 2 02468 Frost C o m p o n e n t + R e s i d u a l ( M u r d e r ) Component + Residual Plots Figure 8.11 Component plus residual plots for the regression of murder rate on state characteristics The component plus residual plots confirm that you’ve met the linearity assumption. The form of the linear model seems to be appropriate for this dataset. HOMOSCEDASTICITY The car package also provides two useful functions for identifying non-constant error variance. The ncvTest() function produces a score test of the hypothesis of constant error variance against the alternative that the error variance changes with the level of the fitted values. A significant result suggests heteroscedasticity (nonconstant error variance). The spreadLevelPlot() function creates a scatter plot of the absolute standardized residuals versus the fitted values, and superimposes a line of best fit. Both functions are demonstrated in listing 8.7. Download from Wow! eBook 98 Chapter 8 Regression Listing 8.7 Assessing homoscedasticity > library(car) > ncvTest(fit) Non-constant Variance Score Test Variance formula: ~ fitted.values Chisquare=1.7 Df=1 p=0.19 > spreadLevelPlot(fit) Suggested power transformation: 1.2 The score test is nonsignificant (p = 0.19), suggesting that you’ve met the constant variance assumption. You can also see this in the spread-level plot (figure 8.12). The points form a random horizontal band around a horizontal line of best fit. If you’d vio- lated the assumption, you’d expect to see a nonhorizontal line. The suggested power transformation in listing 8.7 is the suggested power p (Y p) that would stabilize the nonconstant error variance. For example, if the plot showed a nonhorizontal trend and the suggested power transformation was 0.5, then using Y rather than Y in the regression equation might lead to a model that satisfies homoscedasticity. If the sug- gested power was 0, you’d use a log transformation. In the current example, there’s no evidence of heteroscedasticity and the suggested power is close to 1 (no transforma- tion required). 4 6 8 1 0 1 2 1 4 0 . 0 5 0 . 1 0 0 . 2 0 0 . 5 0 1 . 0 0 2 . 0 0 Spread−Le vel Plot f or fit Fitted V alues A b s o l u t e S t u d e n t i z e d R e s i d u a l s Figure 8.12 Spread-level plot for assessing constant error variance Download from Wow! eBook egression diagnostics 199 8.3.3 Global validation of linear model assumption Finally, let’s examine the gvlma() function in the gvlma package. Written by Pena and Slate (2006), the gvlma() function performs a global validation of linear model assumptions as well as separate evaluations of skewness, kurtosis, and heteroscedastic- ity. In other words, it provides a single omnibus (go/no go) test of model assumptions. The following listing applies the test to the states data. Listing 8.8 Global test of linear model assumptions > library(gvlma) > gvmodel <- gvlma(fit) > summary(gvmodel) ASSESSMENT OF THE LINEAR MODEL ASSUMPTIONS USING THE GLOBAL TEST ON 4 DEGREES-OF-FREEDOM: Level of Significance= 0.05 Call: gvlma(x=fit) Value p-value Decision Global Stat 2.773 0.597 Assumptions acceptable. Skewness 1.537 0.215 Assumptions acceptable. Kurtosis 0.638 0.425 Assumptions acceptable. Link Function 0.115 0.734 Assumptions acceptable. Heteroscedasticity 0.482 0.487 Assumptions acceptable. You can see from the printout (the Global Stat line) that the data meet all the statistical assumptions that go with the OLS regression model (p = 0.597). If the decision line had indicated that the assumptions were violated (say, p < 0.05), you’d have had to explore the data using the previous methods discussed in this section to determine which as- sumptions were the culprit. 8.3.4 Multicollinearity Before leaving this section on regression diagnostics, let’s focus on a problem that’s not directly related to statistical assumptions but is important in allowing you to inter- pret multiple regression results. Imagine you’re conducting a study of grip strength. Your independent variables include date of birth (DOB) and age. You regress grip strength on DOB and age and find a significant overall F test at p < .001. But when you look at the individual regression coefficients for DOB and age, you find that they’re both nonsignificant (that is, there’s no evidence that either is related to grip strength). What happened? The problem is that DOB and age are perfectly correlated within rounding error. A regression coefficient measures the impact of one predictor variable on the response variable, holding all other predictor variables constant. This amounts to looking at the relationship of grip strength and age, holding age constant. The problem is called multicollinearity. It leads to large confidence intervals for your model parameters and makes the interpretation of individual coefficients difficult. Download from Wow! eBook 00 Chapter 8 Regression Multicollinearity can be detected using a statistic called the variance inflation factor (VIF). For any predictor variable, the square root of the VIF indicates the degree to which the confidence interval for that variable’s regression parameter is expanded relative to a model with uncorrelated predictors (hence the name). VIF values are provided by the vif() function in the car package. As a general rule, vif > 2 indicates a multicollinearity problem. The code is provided in the following listing. The results indicate that multicollinearity isn’t a problem with our predictor variables. Listing 8.9 Evaluating multicollinearity >library(car) > vif(fit) Population Illiteracy Income Frost 1.2 2.2 1.3 2.1 > sqrt(vif(fit)) > 2 # problem? Population Illiteracy Income Frost FALSE FALSE FALSE FALSE 8.4 Unusual observations A comprehensive regression analysis will also include a screening for unusual observations—namely outliers, high-leverage observations, and influential observa- tions. These are data points that warrant further investigation, either because they’re different than other observations in some way, or because they exert a disproportion- ate amount of influence on the results. Let’s look at each in turn. 8.4.1 Outliers Outliers are observations that aren’t predicted well by the model. They have either unusually large positive or negative residuals (YYi i–  ). Positive residuals indicate that the model is underestimating the response value, while negative residuals indicate an overestimation. You’ve already seen one way to identify outliers. Points in the Q-Q plot of figure 8.9 that lie outside the confidence band are considered outliers. A rough rule of thumb is that standardized residuals that are larger than 2 or less than –2 are worth attention. The car package also provides a statistical test for outliers. The outlierTest() function reports the Bonferroni adjusted p-value for the largest absolute studentized residual: > library(car) > outlierTest(fit) rstudent unadjusted p-value Bonferonni p Nevada 3.5 0.00095 0.048 Here, you see that Nevada is identified as an outlier (p = 0.048). Note that this function tests the single largest (positive or negative) residual for significance as an outlier. If it Download from Wow! eBook nusual observations 201 isn’t significant, there are no outliers in the dataset. If it is significant, you must delete it and rerun the test to see if others are present. 8.4.2 High leverage points Observations that have high leverage are outliers with regard to the other predictors. In other words, they have an unusual combination of predictor values. The response value isn’t involved in determining leverage. Observations with high leverage are identified through the hat statistic. For a given dataset, the average hat value is p/n, where p is the number of parameters estimated in the model (including the intercept) and n is the sample size. Roughly speaking, an observation with a hat value greater than 2 or 3 times the average hat value should be examined. The code that follows plots the hat values: hat.plot <- function(fit) { p <- length(coefficients(fit)) n <- length(fitted(fit)) plot(hatvalues(fit), main="Index Plot of Hat Values") abline(h=c(2,3)*p/n, col="red", lty=2) identify(1:n, hatvalues(fit), names(hatvalues(fit))) } hat.plot(fit) The resulting graph is shown in figure 8.13. 0 1 0 2 0 3 0 4 0 50 0 . 1 0 . 2 0 . 3 0 . 4 Inde x Plot of Hat V alues Inde x h a t v a l u e s ( f i t ) Alaska Calif or nia Ha w aii Ne w Yo rk W ashington Figure 8.13 Index plot of hat values for assessing observations with high leverage Download from Wow! eBook 02 Chapter 8 Regression Horizontal lines are drawn at 2 and 3 times the average hat value. The locator function places the graph in interactive mode. Clicking on points of interest labels them until the user presses Esc, selects Stop from the graph drop-down menu, or right-clicks on the graph. Here you see that Alaska and California are particularly unusual when it comes to their predictor values. Alaska has a much higher income than other states, while having a lower population and temperature. California has a much higher popu- lation than other states, while having a higher income and higher temperature. These states are atypical compared with the other 48 observations. High leverage observations may or may not be influential observations. That will depend on whether they’re also outliers. 8.4.3 Influential observations Influential observations are observations that have a disproportionate impact on the values of the model parameters. Imagine finding that your model changes dramatical- ly with the removal of a single observation. It’s this concern that leads you to examine your data for influential points. There are two methods for identifying influential observations: Cook’s distance, or D statistic and added variable plots. Roughly speaking, Cook’s D values greater than 4/(n-k-1), where n is the sample size and k is the number of predictor variables, indicate influential observations. You can create a Cook’s D plot (figure 8.14) with the following code: cutoff <- 4/(nrow(states)-length(fit$coefficients)-2) plot(fit, which=4, cook.levels=cutoff) abline(h=cutoff, lty=2, col="red") The graph identifies Alaska, Hawaii, and Nevada as influential observations. Deleting these states will have a notable impact on the values of the intercept and slopes in the 0 1 0 2 0 3 0 4 0 50 0 . 0 0 . 1 0 . 2 0 . 3 0 . 4 0 . 5 Obs . number C o o k ’ s d i s t a n c e lm(Murder ~ P opulation + Illiteracy + Income + Frost) Cook’s distance Alaska Ne v ada Ha wa ii Figure 8.14 Cook’s D plot for identifying influential observations Download from Wow! eBook nusual observations 203 regression model. Note that although it’s useful to cast a wide net when searching for influential observations, I tend to find a cutoff of 1 more generally useful than 4/ (n-k-1). Given a criterion of D=1, none of the observations in the dataset would appear to be influential. Cook’s D plots can help identify influential observations, but they don’t provide information on how these observations affect the model. Added-variable plots can help in this regard. For one response variable and k predictor variables, you’d create k added-variable plots as follows. For each predictor Xk , plot the residuals from regressing the response variable on the other k-1 predictors versus the residuals from regressing Xk on the other k-1 predictors. Added-variable plots can be created using the avPlots() function in the car package: library(car) avPlots(fit, ask=FALSE, onepage=TRUE, id.method="identify") The resulting graphs are provided in figure 8.15. The graphs are produced one at a time, and users can click on points to identify them. Press Esc, choose Stop from the graph’s menu, or right-click to move on to the next plot. Here, I’ve identified Alaska in the bottom-left plot. −5000 0 5000 10000 − 4 − 2 0246 P opulation | other s M u r d e r | o t h e r s −1.0 −0. 5 0 .0 0. 5 1 .0 − 4 − 2 02468 Illiteracy | other s M u r d e r | o t h e r s −500 0 500 1500 − 4 − 2 0246 8 Income | other s M u r d e r | o t h e r s Alask a −100 −50 0 50 − 4 − 2 0246 8 Frost | other s M u r d e r | o t h e r s Added−V ar iab le Plots Figure 8.15 Added-variable plots for assessing the impact of influential observations Download from Wow! eBook 04 Chapter 8 Regression The straight line in each plot is the actual regression coefficient for that predictor variable. You can see the impact of influential observations by imagining how the line would change if the point representing that observation was deleted. For example, look at the graph of Murder | others versus Income | others in the lower-left corner. You can see that eliminating the point labeled Alaska would move the line in a negative direction. In fact, deleting Alaska changes the regression coefficient for Income from positive (.00006) to negative (–.00085). You can combine the information from outlier, leverage, and influence plots into one highly informative plot using the influencePlot() function from the car package: library(car) influencePlot(fit, id.method="identify", main="Influence Plot", sub="Circle size is proportional to Cook’s distance") The resulting plot (figure 8.16) shows that Nevada and Rhode Island are outliers; New York, California, Hawaii, and Washington have high leverage; and Nevada, Alaska, and Hawaii are influential observations. 0.1 0.2 0.3 0.4 − 2 − 1 0123 Influence Plot Circle size is proportial to Cook’s Distance Hat−Values S t u d e n t i z e d R e s i d u a l s Alaska California Hawaii Nevada New York Rhode Island Washington Figure 8.16 Influence plot. States above +2 or below –2 on the vertical axis are considered outliers. States above 0.2 or 0.3 on the horizontal axis have high leverage (unusual combinations of predictor values). Circle size is proportional to influence. Observations depicted by large circles may have disproportionate influence on the parameters estimates of the model. Download from Wow! eBook orrective measures 205 8.5 Corrective measures Having spent the last 20 pages learning about regression diagnostics, you may ask, “What do you do if you identify problems?” There are four approaches to dealing with violations of regression assumptions: .n Deleting observations .n Transforming variables .n Adding or deleting variables .n Using another regression approach Let’s look at each in turn. 8.5.1 Deleting observations Deleting outliers can often improve a dataset’s fit to the normality assumption. Influ- ential observations are often deleted as well, because they have an inordinate impact on the results. The largest outlier or influential observation is deleted, and the model is refit. If there are still outliers or influential observations, the process is repeated until an acceptable fit is obtained. Again, I urge caution when considering the deletion of observations. Sometimes, you can determine that the observation is an outlier because of data errors in recording, or because a protocol wasn’t followed, or because a test subject misunderstood instructions. In these cases, deleting the offending observation seems perfectly reasonable. In other cases, the unusual observation may be the most interesting thing about the data you’ve collected. Uncovering why an observation differs from the rest can contribute great insight to the topic at hand, and to other topics you might not have thought of. Some of our greatest advances have come from the serendipity of noticing that something doesn’t fit our preconceptions (pardon the hyperbole). 8.5.2 Transforming variables When models don’t meet the normality, linearity, or homoscedasticity assumptions, transforming one or more variables can often improve or correct the situation. Trans- formations typically involve replacing a variable Y with Y l. Common values of l and their interpretations are given in table 8.5. If Y is a proportion, a logit transformation [ln (Y/1-Y)] is often used. Table 8.5 Common transformations –2 –1 –0.5 0 0.5 1 2 Transformation 1/Y 2 1/Y 1/Y log(Y)YNone Y 2 Download from Wow! eBook 06 Chapter 8 Regression When the model violates the normality assumption, you typically attempt a transforma- tion of the response variable. You can use the powerTransform() function in the car package to generate a maximum-likelihood estimation of the power l most likely to normalize the variable X l. In the next listing, this is applied to the states data. Listing 8.10 Box–Cox transformation to normality > library(car) > summary(powerTransform(states$Murder)) bcPower Transformation to Normality Est.Power Std.Err. Wald Lower Bound Wald Upper Bound states$Murder 0.6 0.26 0.088 1.1 Likelihood ratio tests about transformation parameters LRT df pval LR test, lambda=(0) 5.7 1 0.017 LR test, lambda=(1) 2.1 1 0.145 The results suggest that you can normalize the variable Murder by replacing it with Murder0.6. Because 0.6 is close to 0.5, you could try a square root transformation to improve the model’s fit to normality. But in this case the hypothesis that l=1 can’t be rejected (p = 0.145), so there’s no strong evidence that a transformation is actually needed in this case. This is consistent with the results of the Q-Q plot in figure 8.9. When the assumption of linearity is violated, a transformation of the predictor variables can often help. The boxTidwell() function in the car package can be used to generate maximum-likelihood estimates of predictor powers that can improve linearity. An example of applying the Box–Tidwell transformations to a model that predicts state murder rates from their population and illiteracy rates follows: > library(car) > boxTidwell(Murder~Population+Illiteracy,data=states) Score Statistic p-value MLE of lambda Population -0.32 0.75 0.87 Illiteracy 0.62 0.54 1.36 The results suggest trying the transformations Population.87 and Population1.36 to achieve greater linearity. But the score tests for Population (p = .75) and Illiteracy (p = .54) suggest that neither variable needs to be transformed. Again, these results are consistent with the component plus residual plots in figure 8.11. Finally, transformations of the response variable can help in situations of heteroscedasticity (nonconstant error variance). You saw in listing 8.7 that the spreadLevelPlot() function in the car package offers a power transformation for improving homoscedasticity. Again, in the case of the states example, the constant error variance assumption is met and no transformation is necessary. Download from Wow! eBook electing the “best” regression model 207 8.5.3 Adding or deleting variables Changing the variables in a model will impact the fit of a model. Sometimes, adding an important variable will correct many of the problems that we’ve discussed. Deleting a troublesome variable can do the same thing. Deleting variables is a particularly important approach for dealing with multicollinearity. If your only goal is to make predictions, then multicollinearity isn’t a problem. But if you want to make interpretations about individual predictor variables, then you must deal with it. The most common approach is to delete one of the variables involved in the multicollinearity (that is, one of the variables with a vif > 2). An alternative is to use ridge regression, a variant of multiple regression designed to deal with multicollinearity situations. 8.5.4 Trying a different approach As you’ve just seen, one approach to dealing with multicollinearity is to fit a different type of model (ridge regression in this case). If there are outliers and/or influential observations, you could fit a robust regression model rather than an OLS regression. If you’ve violated the normality assumption, you can fit a nonparametric regression model. If there’s significant nonlinearity, you can try a nonlinear regression model. If you’ve violated the assumptions of independence of errors, you can fit a model that specifically takes the error structure into account, such as time-series models or multi- level regression models. Finally, you can turn to generalized linear models to fit a wide range of models in situations where the assumptions of OLS regression don’t hold. We’ll discuss some of these alternative approaches in chapter 13. The decision regarding when to try to improve the fit of an OLS regression model and when to try a different approach, is a complex one. It’s typically based on knowledge of the subject matter and an assessment of which approach will provide the best result. Speaking of best results, let’s turn now to the problem of deciding which predictor variables to include in our regression model. 8.6 Selecting the “best” regression model When developing a regression equation, you’re implicitly faced with a selection of many possible models. Should you include all the variables under study, or drop ones A caution concerning transformations There’s an old joke in statistics: If you can’t prove A, prove B and pretend it was A. (For statisticians, that’s pretty funny.) The relevance here is that if you transform your variables, your interpretations must be based on the transformed variables, not the original variables. If the transformation makes sense, such as the log of income or the inverse of distance, the interpretation is easier. But how do you interpret the relationship between the frequency of suicidal ideation and the cube root of depression? If a transformation doesn’t make sense, you should avoid it. Download from Wow! eBook 08 Chapter 8 Regression that don’t make a significant contribution to prediction? Should you add polynomial and/or interaction terms to improve the fit? The selection of a final regression model always involves a compromise between predictive accuracy (a model that fits the data as well as possible) and parsimony (a simple and replicable model). All things being equal, if you have two models with approximately equal predictive accuracy, you fa- vor the simpler one. This section describes methods for choosing among competing models. The word “best” is in quotation marks, because there’s no single criterion you can use to make the decision. The final decision requires judgment on the part of the investigator. (Think of it as job security.) 8.6.1 Comparing models You can compare the fit of two nested models using the anova() function in the base installation. A nested model is one whose terms are completely included in the other model. In our states multiple regression model, we found that the regression coeffi- cients for Income and Frost were nonsignificant. You can test whether a model without these two variables predicts as well as one that includes them (see the following listing). Listing 8.11 Comparing nested models using the anova() function > fit1 <- lm(Murder ~ Population + Illiteracy + Income + Frost, data=states) > fit2 <- lm(Murder ~ Population + Illiteracy, data=states) > anova(fit2, fit1) Analysis of Variance Table Model 1: Murder ~ Population + Illiteracy Model 2: Murder ~ Population + Illiteracy + Income + Frost Res.Df RSS Df Sum of Sq F Pr(>F) 1 47 289.246 2 45 289.167 2 0.079 0.0061 0.994 Here, model 1 is nested within model 2. The anova() function provides a simultane- ous test that Income and Frost add to linear prediction above and beyond Population and Illiteracy. Because the test is nonsignificant (p = .994), we conclude that they don’t add to the linear prediction and we’re justified in dropping them from our model. The Akaike Information Criterion (AIC) provides another method for comparing models. The index takes into account a model’s statistical fit and the number of parameters needed to achieve this fit. Models with smaller AIC values—indicating adequate fit with fewer parameters—are preferred. The criterion is provided by the AIC() function (see the following listing). Listing 8.12 Comparing models with the AIC > fit1 <- lm(Murder ~ Population + Illiteracy + Income + Frost, data=states) > fit2 <- lm(Murder ~ Population + Illiteracy, data=states) Download from Wow! eBook electing the “best” regression model 209 > AIC(fit1,fit2) df AIC fit1 6 241.6429 fit2 4 237.6565 The AIC values suggest that the model without Income and Frost is the better model. Note that although the ANOVA approach requires nested models, the AIC approach doesn’t. Comparing two models is relatively straightforward, but what do you do when there are four, or ten, or a hundred possible models to consider? That’s the topic of the next section. 8.6.2 Variable selection Two popular approaches to selecting a final set of predictor variables from a larger pool of candidate variables are stepwise methods and all-subsets regression. STEPWISE REGRESSION In stepwise selection, variables are added to or deleted from a model one at a time, until some stopping criterion is reached. For example, in forward stepwise regression you add predictor variables to the model one at a time, stopping when the addition of variables would no longer improve the model. In backward stepwise regression, you start with a model that includes all predictor variables, and then delete them one at a time until removing variables would degrade the quality of the model. In stepwise stepwise regression (usually called stepwise to avoid sounding silly), you combine the forward and backward stepwise approaches. Variables are entered one at a time, but at each step, the variables in the model are reevaluated, and those that don’t contribute to the model are deleted. A predictor variable may be added to, and deleted from, a model several times before a final solution is reached. The implementation of stepwise regression methods vary by the criteria used to enter or remove variables. The stepAIC() function in the MASS package performs stepwise model selection (forward, backward, stepwise) using an exact AIC criterion. In the next listing, we apply backward stepwise regression to the multiple regression problem. Listing 8.13 Backward stepwise selection > library(MASS) > fit1 <- lm(Murder ~ Population + Illiteracy + Income + Frost, data=states) > stepAIC(fit, direction="backward") Start: AIC=97.75 Murder ~ Population + Illiteracy + Income + Frost Df Sum of Sq RSS AIC - Frost 1 0.02 289.19 95.75 - Income 1 0.06 289.22 95.76 Download from Wow! eBook 10 Chapter 8 Regression 289.17 97.75 - Population 1 39.24 328.41 102.11 - Illiteracy 1 144.26 433.43 115.99 Step: AIC=95.75 Murder ~ Population + Illiteracy + Income Df Sum of Sq RSS AIC - Income 1 0.06 289.25 93.76 289.19 95.75 - Population 1 43.66 332.85 100.78 - Illiteracy 1 236.20 525.38 123.61 Step: AIC=93.76 Murder ~ Population + Illiteracy Df Sum of Sq RSS AIC 289.25 93.76 - Population 1 48.52 337.76 99.52 - Illiteracy 1 299.65 588.89 127.31 Call: lm(formula=Murder ~ Population + Illiteracy, data=states) Coefficients: (Intercept) Population Illiteracy 1.6515497 0.0002242 4.0807366 You start with all four predictors in the model. For each step, the AIC column provides the model AIC resulting from the deletion of the variable listed in that row. The AIC value for is the model AIC if no variables are removed. In the first step, Frost is removed, decreasing the AIC from 97.75 to 95.75. In the second step, Income is re- moved, decreasing the AIC to 93.76. Deleting any more variables would increase the AIC, so the process stops. Stepwise regression is controversial. Although it may find a good model, there’s no guarantee that it will find the best model. This is because not every possible model is evaluated. An approach that attempts to overcome this limitation is all subsets regression. ALL SUBSETS REGRESSION In all subsets regression, every possible model is inspected. The analyst can choose to have all possible results displayed, or ask for the nbest models of each subset size (one predictor, two predictors, etc.). For example, if nbest=2, the two best one-predictor models are displayed, followed by the two best two-predictor models, followed by the two best three-predictor models, up to a model with all predictors. All subsets regression is performed using the regsubsets() function from the leaps package. You can choose R-squared, Adjusted R-squared, or Mallows Cp statistic as your criterion for reporting “best” models. As you’ve seen, R-squared is the amount of variance accounted for in the response variable by the predictors variables. Adjusted R-squared is similar, but takes into account the number of parameters in the model. R-squared always increases with the addition Download from Wow! eBook electing the “best” regression model 211 of predictors. When the number of predictors is large compared to the sample size, this can lead to significant overfitting. The Adjusted R-squared is an attempt to provide a more honest estimate of the population R-squared—one that’s less likely to take advantage of chance variation in the data. The Mallows Cp statistic is also used as a stopping rule in stepwise regression. It has been widely suggested that a good model is one in which the Cp statistic is close to the number of model parameters (including the intercept). In listing 8.14, we’ll apply all subsets regression to the states data. The results can be plotted with either the plot() function in the leaps package or the subsets() function in the car package. An example of the former is provided in figure 8.17, and an example of the latter is given in figure 8.18. Listing 8.14 All subsets regression library(leaps) leaps <-regsubsets(Murder ~ Population + Illiteracy + Income + Frost, data=states, nbest=4) plot(leaps, scale="adjr2") library(car) subsets(leaps, statistic="cp", main="Cp Plot for All Subsets Regression") abline(1,1,lty=2,col="red") a d j r 2 ( I n t e r c e p t ) P o p u l a t i o n I l l i t e r a c y I n c o m e F r o s t 0.033 0.1 0.28 0.29 0.31 0.48 0.48 0.48 0.48 0.53 0.54 0.54 0.55 Figure 8.17 Best four models for each subset size based on Adjusted R-square Download from Wow! eBook 12 Chapter 8 Regression Figure 8.17 can be confusing to read. Looking at the first row (starting at the bottom), you can see that a model with the intercept and Income has an adjusted R-square of 0.33. A model with the intercept and Population has an adjusted R-square of 0.1. Jump- ing to the 12th row, you see that a model with the intercept, Population, Illiteracy, and Income has an adjusted R-square of 0.54, whereas one with the intercept, Population, and Illiteracy alone has an adjusted R-square of 0.55. Here you see that a model with fewer predictors has a larger adjusted R-square (something that can’t happen with an unadjusted R-square). The graph suggests that the two-predictor model (Population and Illiteracy) is the best. In figure 8.18, you see the best four models for each subset size based on the Mallows Cp statistic. Better models will fall close to a line with intercept 1 and slope 1. The plot suggests that you consider a two-predictor model with Population and Illiteracy; a three-predictor model with Population, Illiteracy, and Frost, or Population, Illiteracy and Income (they overlap on the graph and are hard to read); or a four- predictor model with Population, Illiteracy, Income, and Frost. You can reject the other possible models. In most instances, all subsets regression is preferable to stepwise regression, because more models are considered. However, when the number of predictors is large, the 1.0 1.5 2.0 2.5 3.0 3.5 4.0 0 1 0 20 30 4 0 50 Cp Plot for All Subsets Regression Subset Size S t a t i s t i c : c p Il F P In P−Il Il−−−FIl In P−F PPP−−−Il−−−InIl F Il−In−F P−In−F P−Il−In−F P: Population Il: Illiteracy In: Income F: Frost Figure 8.18 Best four models for each subset size based on the Mallows Cp statistic Download from Wow! eBook aking the analysis further 213 procedure can require significant computing time. In general, automated variable se- lection methods should be seen as an aid rather than a directing force in model selec- tion. A well-fitting model that doesn’t make sense doesn’t help you. Ultimately, it’s your knowledge of the subject matter that should guide you. 8.7 Taking the analysis further We’ll end our discussion of regression by considering methods for assessing model generalizability and predictor relative importance. 8.7.1 Cross-validation In the previous section, we examined methods for selecting the variables to include in a regression equation. When description is your primary goal, the selection and interpretation of a regression model signals the end of your labor. But when your goal is prediction, you can justifiably ask, “How well will this equation perform in the real world?” By definition, regression techniques obtain model parameters that are optimal for a given set of data. In OLS regression, the model parameters are selected to minimize the sum of squared errors of prediction (residuals), and conversely, maximize the amount of variance accounted for in the response variable (R-squared). Because the equation has been optimized for the given set of data, it won’t perform as well with a new set of data. We began this chapter with an example involving a research physiologist who wanted to predict the number of calories an individual will burn from the duration and intensity of their exercise, age, gender, and BMI. If you fit an OLS regression equation to this data, you’ll obtain model parameters that uniquely maximize the R-squared for this particular set of observations. But our researcher wants to use this equation to predict the calories burned by individuals in general, not only those in the original study. You know that the equation won’t perform as well with a new sample of observations, but how much will you lose? Cross-validation is a useful method for evaluating the generalizability of a regression equation. In cross-validation, a portion of the data is selected as the training sample and a portion is selected as the hold-out sample. A regression equation is developed on the training sample, and then applied to the hold-out sample. Because the hold-out sample wasn’t involved in the selection of the model parameters, the performance on this sample is a more accurate estimate of the operating characteristics of the model with new data. In k-fold cross-validation, the sample is divided into k subsamples. Each of the k subsamples serves as a hold-out group and the combined observations from the remaining k-1 subsamples serves as the training group. The performance for the k prediction equations applied to the k hold-out samples are recorded and then averaged. (When k equals n, the total number of observations, this approach is called jackknifing.) Download from Wow! eBook 14 Chapter 8 Regression You can perform k-fold cross-validation using the crossval() function in the bootstrap package. The following listing provides a function (called shrinkage()) for cross-validating a model’s R-square statistic using k-fold cross-validation. Listing 8.15 Function for k-fold cross-validated R-square shrinkage <- function(fit, k=10){ require(bootstrap) theta.fit <- function(x,y){lsfit(x,y)} theta.predict <- function(fit,x){cbind(1,x)%*%fit$coef} x <- fit$model[,2:ncol(fit$model)] y <- fit$model[,1] results <- crossval(x, y, theta.fit, theta.predict, ngroup=k) r2 <- cor(y, fit$fitted.values)^2 r2cv <- cor(y, results$cv.fit)^2 cat("Original R-square =", r2, "\n") cat(k, "Fold Cross-Validated R-square =", r2cv, "\n") cat("Change =", r2-r2cv, "\n") } Using this listing you define your functions, create a matrix of predictor and predicted values, get the raw R-squared, and get the cross-validated R-squared. (Chapter 12 cov- ers bootstrapping in detail.) The shrinkage() function is then used to perform a 10-fold cross-validation with the states data, using a model with all four predictor variables: > fit <- lm(Murder ~ Population + Income + Illiteracy + Frost, data=states) > shrinkage(fit) Original R-square=0.567 10 Fold Cross-Validated R-square=0.4481 Change=0.1188 You can see that the R-square based on our sample (0.567) is overly optimistic. A bet- ter estimate of the amount of variance in murder rates our model will account for with new data is the cross-validated R-square (0.448). (Note that observations are assigned to the k groups randomly, so you will get a slightly different result each time you ex- ecute the shrinkage() function.) You could use cross-validation in variable selection by choosing a model that demonstrates better generalizability. For example, a model with two predictors (Population and Illiteracy) shows less R-square shrinkage (.03 versus .12) than the full model: > fit2 <- lm(Murder~Population+Illiteracy,data=states) > shrinkage(fit2) Original R-square=0.5668327 10 Fold Cross-Validated R-square=0.5346871 Change=0.03214554 Download from Wow! eBook aking the analysis further 215 This may make the two-predictor model a more attractive alternative. All other things being equal, a regression equation that’s based on a larger training sample and one that’s more representative of the population of interest will cross- validate better. You’ll get less R-squared shrinkage and make more accurate predictions. 8.7.2 Relative importance Up to this point in the chapter, we’ve been asking, “Which variables are useful for pre- dicting the outcome?” But often your real interest is in the question, “Which variables are most important in predicting the outcome?” You implicitly want to rank-order the predictors in terms of relative importance. There may be practical grounds for asking the second question. For example, if you could rank-order leadership practices by their relative importance for organizational success, you could help managers focus on the behaviors they most need to develop. If predictor variables were uncorrelated, this would be a simple task. You would rank-order the predictor variables by their correlation with the response variable. In most cases, though, the predictors are correlated with each other, and this complicates the task significantly. There have been many attempts to develop a means for assessing the relative importance of predictors. The simplest has been to compare standardized regression coefficients. Standardized regression coefficients describe the expected change in the response variable (expressed in standard deviation units) for a standard deviation change in a predictor variable, holding the other predictor variables constant. You can obtain the standardized regression coefficients in R by standardizing each of the variables in your dataset to a mean of 0 and standard deviation of 1 using the scale() function, before submitting the dataset to a regression analysis. (Note that because the scale() function returns a matrix and the lm() function requires a data frame, you convert between the two in an intermediate step.) The code and results for our multiple regression problem are shown here: > zstates <- as.data.frame(scale(states)) > zfit <- lm(Murder~Population + Income + Illiteracy + Frost, data=zstates) > coef(zfit) (Intercept) Population Income Illiteracy Frost -9.406e-17 2.705e-01 1.072e-02 6.840e-01 8.185e-03 Here you see that a one standard deviation increase in illiteracy rate yields a 0.68 stan- dard deviation increase in murder rate, when controlling for population, income, and temperature. Using standardized regression coefficients as our guide, Illiteracy is the most important predictor and Frost is the least. There have been many other attempts at quantifying relative importance. Relative importance can be thought of as the contribution each predictor makes to R-square, both alone and in combination with other predictors. Several possible approaches to relative importance are captured in the relaimpo package written by Ulrike Grömping (http://prof.beuth-hochschule.de/groemping/relaimpo/). Download from Wow! eBook 16 Chapter 8 Regression A new method called relative weights shows significant promise. The method closely approximates the average increase in R-square obtained by adding a predictor variable across all possible submodels (Johnson, 2004; Johnson and Lebreton, 2004; LeBreton and Tonidandel, 2008). A function for generating relative weights is provided in the next listing. Listing 8.16 relweights() function for calculating relative importance of predictors relweights <- function(fit,...){ R <- cor(fit$model) nvar <- ncol(R) rxx <- R[2:nvar, 2:nvar] rxy <- R[2:nvar, 1] svd <- eigen(rxx) evec <- svd$vectors ev <- svd$values delta <- diag(sqrt(ev)) lambda <- evec %*% delta %*% t(evec) lambdasq <- lambda ^ 2 beta <- solve(lambda) %*% rxy rsquare <- colSums(beta ^ 2) rawwgt <- lambdasq %*% beta ^ 2 import <- (rawwgt / rsquare) * 100 lbls <- names(fit$model[2:nvar]) rownames(import) <- lbls colnames(import) <- "Weights" barplot(t(import),names.arg=lbls, ylab="% of R-Square", xlab="Predictor Variables", main="Relative Importance of Predictor Variables", sub=paste("R-Square=", round(rsquare, digits=3)), ...) return(import) } NOTE The code in listing 8.16 is adapted from an SPSS program generously provided by Dr. Johnson. See Johnson (2000, Multivariate Behavioral Research, 35, 1–19) for an explanation of how the relative weights are derived. In listing 8.17 the relweights() function is applied to the states data with murder rate predicted by the population, illiteracy, income, and temperature. You can see from figure 8.19 that the total amount of variance accounted for by the model (R-square=0.567) has been divided among the predictor variables. Illiteracy accounts for 59 percent of the R-square, Frost accounts for 20.79 percent, and so forth. Based on the method of relative weights, Illiteracy has the greatest relative importance, followed by Frost, Population, and Income, in that order. Download from Wow! eBook aking the analysis further 217 Listing 8.17 Applying the relweights() function > fit <- lm(Murder ~ Population + Illiteracy + Income + Frost, data=states) > relweights(fit, col="lightgrey") Weights Population 14.72 Illiteracy 59.00 Income 5.49 Frost 20.79 Relative importance measures (and in particular, the method of relative weights) have wide applicability. They come much closer to our intuitive conception of relative im- portance than standardized regression coefficients do, and I expect to see their use increase dramatically in coming years. Population Illiteracy Income Frost Relative Importance of Predictor Variables R−Square = 0.567 Predictor Variables % o f R − S q u a r e 0 1 0 2 0 3 0 4 0 5 0 Figure 8.19 Bar plot of relative weights for the states multiple regression problem Download from Wow! eBook 18 Chapter 8 Regression 8.8 Summary Regression analysis is a term that covers a broad range of methodologies in statistics. You’ve seen that it’s a highly interactive approach that involves fitting models, assessing their fit to statistical assumptions, modifying both the data and the models, and refit- ting to arrive at a final result. In many ways, this final result is based on art and skill as much as science. This has been a long chapter, because regression analysis is a process with many parts. We’ve discussed fitting OLS regression models, using regression diagnostics to assess the data’s fit to statistical assumptions, and methods for modifying the data to meet these assumptions more closely. We looked at ways of selecting a final regression model from many possible models, and you learned how to evaluate its likely performance on new samples of data. Finally, we tackled the thorny problem of variable importance: identifying which variables are the most important for predicting an outcome. In each of the examples in this chapter, the predictor variables have been quantitative. However, there are no restrictions against using categorical variables as predictors as well. Using categorical predictors such as gender, treatment type, or manufacturing process allows you to examine group differences on a response or outcome variable. This is the focus of our next chapter. Download from Wow! eBook 219 9Analysis of variance This chapter covers .n Using R to model basic experimental designs .n Fitting and interpreting ANOVA type models .n Evaluating model assumptions In chapter 7, we looked at regression models for predicting a quantitative response variable from quantitative predictor variables. But there’s no reason that we couldn’t have included nominal or ordinal factors as predictors as well. When factors are included as explanatory variables, our focus usually shifts from prediction to under- standing group differences, and the methodology is referred to as analysis of variance (ANOVA). ANOVA methodology is used to analyze a wide variety of experimental and quasi-experimental designs. This chapter provides an overview of R functions for analyzing common research designs. First we’ll look at design terminology, followed by a general discussion of R’s approach to fitting ANOVA models. Then we’ll explore several examples that illustrate the analysis of common designs. Along the way, we’ll treat anxiety disorders, lower blood cholesterol levels, help pregnant mice have fat babies, assure that pigs grow long in the tooth, facilitate breathing in plants, and learn which grocery shelves to avoid. In addition to the base installation, we’ll be using the car, gplots, HH, rrcov, and mvoutlier packages in our examples. Be sure to install them before trying out the sample code. Download from Wow! eBook 20 Chapter 9 Analysis of variance 9.1 A crash course on terminology Experimental design in general, and analysis of variance in particular, has its own lan- guage. Before discussing the analysis of these designs, we’ll quickly review some impor- tant terms. We’ll use a series of increasingly complex study designs to introduce the most significant concepts. Say you’re interested in studying the treatment of anxiety. Two popular therapies for anxiety are cognitive behavior therapy (CBT) and eye movement desensitization and reprocessing (EMDR). You recruit 10 anxious individuals and randomly assign half of them to receive five weeks of CBT and half to receive five weeks of EMDR. At the conclusion of therapy, each patient is asked to complete the State-Trait Anxiety Inventory (STAI), a self-report measure of anxiety. The design is outlined in table 9.1. In this design, Treatment is a between-groups factor with two levels (CBT, EMDR). It’s called a between-groups factor because patients are assigned to one and only one group. No patient receives both CBT and EMDR. The s characters represent the subjects (patients). STAI is the dependent variable, and Treatment is the independent variable. Because there are an equal number of observations in each treatment condition, you have a balanced design. When the sample sizes are unequal across the cells of a design, you have an unbalanced design. The statistical design in table 9.1 is called a one-way ANOVA because there’s a single classification variable. Specifically, it’s a one- way between-groups ANOVA. Effects in ANOVA designs are primarily evaluated through F tests. If the F test for Treatment is significant, you can conclude that the mean STAI scores for two therapies differed after five weeks of treatment. If you were interested in the effect of CBT on anxiety over time, you could place all 10 patients in the CBT group and assess them at the conclusion of therapy and again six months later. This design is displayed in table 9.2. Time is a within-groups factor with two levels (five weeks, six months). It’s called a within-groups factor because each patient is measured under both levels. The statistical Table 9.1 One-way between-groups ANOVA Treatment CBTEMDR s1 s6 s2 s7 s3 s8 s4 s9 s5 s10 Table 9.2 One-way within-groups ANOVA Patient Time 5 weeks 6 months 1 s2 s3 s4 s5 s6 s7 s8 s9 s10 Download from Wow! eBook crash course on terminology 221 design is a one-way within-groups ANOVA. Because each subject is measured more than once, the design is also called repeated measures ANOVA. If the F test for Time is significant, you can conclude that patients’ mean STAI scores changed between five weeks and six months. If you were interested in both treatment differences and change over time, you could combine the first two study designs, and randomly assign five patients to CBT and five patients to EMDR, and assess their STAI results at the end of therapy (five weeks) and at six months (see table 9.3). By including both Therapy and Time as factors, you’re able to examine the impact of Therapy (averaged across time), Time (averaged across therapy type), and the interaction of Therapy and Time. The first two are called the main effects, whereas the interaction is (not surprisingly) called an interaction effect. When you cross two or more factors, as you’ve done here, you have a factorial ANOVA design. Crossing two factors produces a two-way ANOVA, crossing three factors produces a three-way ANOVA, and so forth. When a factorial design includes both between-groups and within-groups factors, it’s also called a mixed-model ANOVA. The current design is a two-way mixed-model factorial ANOVA (phew!). In this case you’ll have three F tests: one for Therapy, one for Time, and one for the Therapy x Time interaction. A significant result for Therapy indicates that CBT and EMDR differ in their impact on anxiety. A significant result for Time indicates that Table 9.3 Two-way factorial ANOVA with one between-groups and one within-groups factor Patient Time 5 weeks 6 months Therapy CBT s1 s2 s3 s4 s5 EMDR s6 s7 s8 s9 s10 Download from Wow! eBook 22 Chapter 9 Analysis of variance anxiety changed from week five to the six month follow-up. A significant Therapy x Time interaction indicates that the two treatments for anxiety had a differential impact over time (that is, the change in anxiety from five weeks to six months was different for the two treatments). Now let’s extend the design a bit. It’s known that depression can have an impact on therapy, and that depression and anxiety often co-occur. Even though subjects were randomly assigned to treatment conditions, it’s possible that the two therapy groups differed in patient depression levels at the initiation of the study. Any post- therapy differences might then be due to the preexisting depression differences and not to your experimental manipulation. Because depression could also explain the group differences on the dependent variable, it’s a confounding factor. And because you’re not interested in depression, it’s called a nuisance variable. If you recorded depression levels using a self-report depression measure such as the Beck Depression Inventory (BDI) when patients were recruited, you could statistically adjust for any treatment group differences in depression before assessing the impact of therapy type. In this case, BDI would be called a covariate, and the design would be called an analysis of covariance (ANCOVA). Finally, you’ve recorded a single dependent variable in this study (the STAI). You could increase the validity of this study by including additional measures of anxiety (such as family ratings, therapist ratings, and a measure assessing the impact of anxiety on their daily functioning). When there’s more than one dependent variable, the design is called a multivariate analysis of variance (MANOVA). If there are covariates present, it’s called a multivariate analysis of covariance (MANCOVA). Now that you have the basic terminology under your belt, you’re ready to amaze your friends, dazzle new acquaintances, and discuss how to fit ANOVA/ANCOVA/ MANOVA models with R. 9.2 Fitting ANOVA models Although ANOVA and regression methodologies developed separately, functionally they’re both special cases of the general linear model. We could analyze ANOVA models using the same lm() function used for regression in chapter 7. However, we’ll primarily use the aov() function in this chapter. The results of lm() and aov() are equivalent, but the aov() function presents these results in a format that’s more famil- iar to ANOVA methodologists. For completeness, I’ll provide an example using lm()at the end of this chapter. 9.2.1 The aov() function The syntax of the aov() function is aov(formula, data=dataframe). Table 9.4 de- scribes special symbols that can be used in the formulas. In this table, y is the depen- dent variable and the letters A, B, and C represent factors. Download from Wow! eBook itting ANOVA models 223 Table 9.4 Special symbols used in R formulas Symbol Usage ~ Separates response variables on the left from the explanatory variables on the right. For example, a prediction of y from A, B, and C would be coded y ~ A + B + C. + Separates explanatory variables. :Denotes an interaction between variables. A prediction of y from A, B, and the interaction between A and B would be coded y ~ A + B + A:B. *Denotes the complete crossing variables. The code y ~ A*B*C expands to y ~ A + B + C + A:B + A:C + B:C + A:B:C. ^ Denotes crossing to a specified degree. The code y ~ (A+B+C)^2 expands to y ~ A + B + C + A:B + A:C + A:B. . A place holder for all other variables in the data frame except the dependent variable. For example, if a data frame contained the variables y, A, B, and C, then the code y ~ . would expand to y ~ A + B + C. Table 9.5 provides formulas for several common research designs. In this table, low- ercase letters are quantitative variables, uppercase letters are grouping factors, and Subject is a unique identifier variable for subjects. Table 9.5 Formulas for common research designs Design Formula One-way ANOVA y ~ A One-way ANCOVA with one covariate y ~ x + A Two-way Factorial ANOVA y ~ A * B Two-way Factorial ANCOVA with two covariates y ~ x1 + x2 + A * B Randomized Block y ~ B + A (where B is a blocking factor) One-way within-groups ANOVA y ~ A + Error(Subject/A) Repeated measures ANOVA with one within-groups factor (W) and one between-groups factor (B) y ~ B * W + Error(Subject/W) We’ll explore in-depth examples of several of these designs later in this chapter. 9.2.2 The order of formula terms The order in which the effects appear in a formula matters when (a) there’s more than one factor and the design is unbalanced, or (b) covariates are present. When either of these two conditions is present, the variables on the right side of the equation will be correlated with each other. In this case, there’s no unambiguous way to divide up their impact on the dependent variable. Download from Wow! eBook 24 Chapter 9 Analysis of variance For example, in a two-way ANOVA with unequal numbers of observations in the treatment combinations, the model y ~ A*B will not produce the same results as the model y ~ B*A. By default, R employs the Type I (sequential) approach to calculating ANOVA effects (see the sidebar “Order counts!”). The first model can be written out as y ~ A + B + A:B. The resulting R ANOVA table will assess .n The impact of A on y .n The impact of B on y, controlling for A .n The interaction of A and B, controlling for the A and B main effects Order counts! When independent variables are correlated with each other or with covariates, there’s no unambiguous method for assessing the independent contributions of these variables to the dependent variable. Consider an unbalanced two-way factorial design with factors A and B and dependent variable y. There are three effects in this design: the A and B main effects and the A x B interaction. Assuming that you’re modeling the data using the formula Y ~ A + B + A:B there are three typical approaches for partitioning the variance in y among the effects on the right side of this equation. Type I (sequential) Effects are adjusted for those that appear earlier in the formula. A is unadjusted. B is adjusted for the A. The A:B interaction is adjusted for A and B. Type II (hierarchical) Effects are adjusted for other effects at the same or lower level. A is adjusted for B. B is adjusted for A. The A:B interaction is adjusted for both A and B. Type III (marginal) Each effect is adjusted for every other effect in the model. A is adjusted for B and A:B. B is adjusted for A and A:B. The A:B interaction is adjusted for A and B. R employs the Type I approach by default. Other programs such as SAS and SPSS employ the Type III approach by default. The greater the imbalance in sample sizes, the greater the impact that the order of the terms will have on the results. In general, more fundamental effects should be listed earlier in the formula. In particular, covariates should be listed first, followed by main effects, followed by two-way interactions, followed by three-way interactions, and so on. For main effects, more fundamental variables should be listed first. Thus gender would be listed before treatment. Here’s the bottom line: When the research design isn’t orthogonal (that is, when the factors and/or covariates are correlated), be careful when specifying the order of effects. Download from Wow! eBook ne-way ANOVA 225 Before moving on to specific examples, note that the Anova() function in the car package (not to be confused with the standard anova() function) provides the option of using the Type II or Type III approach, rather than the Type I approach used by the aov() function. You may want to use the Anova() function if you’re concerned about matching your results to those provided by other packages such as SAS and SPSS. See help(Anova, package="car") for details. 9.3 One-way ANOVA In a one-way ANOVA, you’re interested in comparing the dependent variable means of two or more groups defined by a categorical grouping factor. Our example comes from the cholesterol dataset in the multcomp package, and taken from Westfall, To- bia, Rom, & Hochberg (1999). Fifty patients received one of five cholesterol-reducing drug regiments (trt). Three of the treatment conditions involved the same drug administered as 20 mg once per day (1time), 10mg twice per day (2times), or 5 mg four times per day (4times). The two remaining conditions (drugD and drugE) rep- resented competing drugs. Which drug regimen produced the greatest cholesterol reduction (response)? The analysis is provided in the following listing. Listing 9.1 One-way ANOVA library(multcomp) > attach(cholesterol) > table(trt)  rt 1time 2times 4times drugD drugE 10 10 10 10 10 > aggregate(response, by=list(trt), FUN=mean)  Group.1 x 1 1time 5.78 2 2times 9.22 3 4times 12.37 4 drugD 15.36 5 drugE 20.95 > aggregate(response, by=list(trt), FUN=sd) Group.1 x  1time 2.88 2 2times 3.48 3 4times 2.92 4 drugD 3.45 5 drugE 3.35 > fit <- aov(response ~ trt)  > summary(fit) Df Sum Sq Mean Sq F value Pr(>F) trt 4 1351 338 32.4 9.8e-13 *** Residuals 45 469 10 --- Group sample sizes Group means Group standard deviations Test for group differences (ANOVA) Download from Wow! eBook 26 Chapter 9 Analysis of variance Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1  > library(gplots) > plotmeans(response ~ trt, xlab="Treatment", ylab="Response", main="Mean Plot\nwith 95% CI") > detach(cholesterol) Looking at the output, you can see that 10 patients received each of the drug regi- ments . From the means, it appears that drugE produced the greatest cholesterol reduction, whereas 1time produced the least . Standard deviations were relatively constant across the five groups, ranging from 2.88 to 3.48 . The ANOVA F test for treatment (trt) is significant (p < .0001), providing evidence that the five treatments aren’t all equally effective . The plotmeans() function in the gplots package can be used to produce a graph of group means and their confidence intervals . A plot of the treatment means, with 95 percent confidence limits, is provided in figure 9.1 and allows you to clearly see these treatment differences. 5 1 0 1 5 2 0 Mean Plot with 95% CI Treatment R e s p o n s e 1time 2times 4times drugD drugE n=10 n=10 n=10 n=10 n=10 Figure 9.1 Treatment group means with 95 percent confidence intervals for five cholesterol-reducing drug regiments Plot group means, confidence intervals Download from Wow! eBook ne-way ANOVA 227 9.3.1 Multiple comparisons The ANOVA F test for treatment tells you that the five drug regiments aren’t equally effective, but it doesn’t tell you which treatments differ from one another. You can use a multiple comparison procedure to answer this question. For example, the TukeyHSD() function provides a test of all pairwise differences between group means (see listing 9.2). Note that the TukeyHSD() function has compatibility issues with package HH also used in this chapter; if HH is loaded, TukeyHSD() will fail. In that case, use detach("package:HH") to remove it from the search path and then call TukeyHSD(). Listing 9.2 Tukey HSD pairwise group comparisons > TukeyHSD(fit) Tukey multiple comparisons of means 95% family-wise confidence level Fit: aov(formula = response ~ trt)$trt diff lwr upr p adj 2times-1time 3.44 -0.658 7.54 0.138 4times-1time 6.59 2.492 10.69 0.000 drugD-1time 9.58 5.478 13.68 0.000 drugE-1time 15.17 11.064 19.27 0.000 4times-2times 3.15 -0.951 7.25 0.205 drugD-2times 6.14 2.035 10.24 0.001 drugE-2times 11.72 7.621 15.82 0.000 drugD-4times 2.99 -1.115 7.09 0.251 drugE-4times 8.57 4.471 12.67 0.000 drugE-drugD 5.59 1.485 9.69 0.003 > par(las=2) > par(mar=c(5,8,4,2)) > plot(TukeyHSD(fit)) For example, the mean cholesterol reductions for 1time and 2times aren’t signifi- cantly different from each other (p = 0.138), whereas the difference between 1time and 4times is significantly different (p < .001). The pairwise comparisons are plotted in figure 9.2. The first par statement rotates the axis labels, and the second one increases the left margin area so that the labels fit (par options are covered in chapter 3). In this graph, confidence intervals that include 0 indicate treatments that aren’t significantly different (p > 0.5). The glht() function in the multcomp package provides a much more comprehen- sive set of methods for multiple mean comparisons that you can use for both linear models (such as those described in this chapter) and generalized linear models (cov- ered in chapter 13). The following code reproduces the Tukey HSD test, along with a different graphical representation of the results (figure 9.3): > library(multcomp) > par(mar=c(5,4,6,2)) > tuk <- glht(fit, linfct=mcp(trt="Tukey")) > plot(cld(tuk, level=.05),col="lightgrey") Download from Wow! eBook 28 Chapter 9 Analysis of variance Figure 9.2 Plot of Tukey HSD pairwise mean comparisons In this code, the par statement increased the top margin to fit the letter array. The level option in the cld() function provides the significance level to use (0.05, or 95 percent confidence in this case). Groups (represented by box plots) that have the same letter don’t have significantly different means. You can see that 1time and 2times aren’t significantly different (they 1time 2times 4times drugD drugE 5 1 0 1 5 2 0 2 5 trt r e s p o n s e a a b b c c d Figure 9.3 Tukey HSD tests provided by the multcomp package Download from Wow! eBook ne-way ANOVA 229 both have the letter a) and that 2times and 4times aren’t significantly different (they both have the letter b), but that 1time and 4times are different (they don’t share a letter). Personally, I find figure 9.3 easier to read than figure 9.2. It also has the advan- tage of providing information on the distribution of scores within each group. From these results, you can see that taking the cholesterol-lowering drug in 5 mg doses four times a day was better than taking a 20 mg dose once per day. The competitor drugD wasn’t superior to this four-times-per-day regimen. But competitor drugE was superior to both drugD and all three dosage strategies for our focus drug. Multiple comparisons methodology is a complex and rapidly changing area of study. To learn more, see Bretz, Hothorn, and Westfall (2010). 9.3.2 Assessing test assumptions As we saw in the previous chapter, our confidence in results depends on the degree to which our data satisfies the assumptions underlying the statistical tests. In a one-way ANOVA, the dependent variable is assumed to be normally distributed, and have equal variance in each group. You can use a Q-Q plot to assess the normality assumption: > library(car) > qqPlot(lm(response ~ trt, data=cholesterol), simulate=TRUE, main="Q-Q Plot", labels=FALSE) Note the qqPlot() requires an lm() fit. The graph is provided in figure 9.4. The data fall within the 95 percent confidence envelope, suggesting that the normality assumption has been met fairly well. −2 −1 0 1 2 − 2 − 1 01 2 QQ Plot t Quantiles S t u d e n t i z e d R e s i d u a l s ( f i t ) Figure 9.4 Test of normality Download from Wow! eBook 30 Chapter 9 Analysis of variance R provides several tests for the equality (homogeneity) of variances. For example, you can perform Bartlett’s test with this code: > bartlett.test(response ~ trt, data=cholesterol) Bartlett test of homogeneity of variances data: response by trt Bartlett's K-squared = 0.5797, df = 4, p-value = 0.9653 Bartlett’s test indicates that the variances in the five groups don’t differ significantly (p = 0.97). Other possible tests include the Fligner–Killeen test (provided by the fligner.test() function), and the Brown–Forsythe test (provided by the hov() function in the HH package). Although not shown, the other two tests reach the same conclusion. Finally, analysis of variance methodologies can be sensitive to the presence of outliers. You can test for outliers using the outlierTest() function in the car package: > library(car) > outlierTest(fit) No Studentized residuals with Bonferonni p < 0.05 Largest |rstudent|: rstudent unadjusted p-value Bonferonni p 19 2.251149 0.029422 NA From the output, you can see that there’s no indication of outliers in the cholesterol data (NA occurs when p > 1). Taking the Q-Q plot, Bartlett’s test, and outlier test to- gether, the data appear to fit the ANOVA model quite well. This, in turn, adds to your confidence in the results. 9.4 One-way ANCOVA A one-way analysis of covariance (ANCOVA) extends the one-way ANOVA to include one or more quantitative covariates. This example comes from the litter dataset in the multcomp package (see Westfall et al., 1999). Pregnant mice were divided into four treatment groups; each group received a different dose of a drug (0, 5, 50, or 500). The mean post-birth weight for each litter was the dependent variable and gestation time was included as a covariate. The analysis is given in the following listing. Listing 9.3 One-way ANCOVA > data(litter, package="multcomp") > attach(litter) > table(dose) dose 0 5 50 500 20 19 18 17 > aggregate(weight, by=list(dose), FUN=mean) Group.1 x 1 0 32.3 2 5 29.3 Download from Wow! eBook ne-way ANCOVA 231 3 50 29.9 4 500 29.6 > fit <- aov(weight ~ gesttime + dose) > summary(fit) Df Sum Sq Mean Sq F value Pr(>F) gesttime 1 134.30 134.30 8.0493 0.005971 ** dose 3 137.12 45.71 2.7394 0.049883 * Residuals 69 1151.27 16.69 --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 From the table() function you can see that there are an unequal number of litters at each dosage level, with 20 litters at zero dosage (no drug) and 17 litters at dosage 500. Based on the group means provided by the aggregate() function, the no-drug group had the highest mean litter weight (32.3). The ANCOVA F tests indicate that (a) gesta- tion time was related to birth weight, and (b) drug dosage was related to birth weight after controlling for gestation time. The mean birth weight isn’t the same for each of the drug dosages, after controlling for gestation time. Because you’re using a covariate, you may want to obtain adjusted group means— that is, the group means obtained after partialing out the effects of the covariate. You can use the effect() function in the effects library to calculate adjusted means: > library(effects) > effect("dose", fit) dose effect dose 0 5 50 500 32.4 28.9 30.6 29.3 In this case, the adjusted means are similar to the unadjusted means produced by the aggregate() function, but this won’t always be the case. The effects package provides a powerful method of obtaining adjusted means for complex research de- signs and presenting them visually. See the package documentation on CRAN for more details. As with the one-way ANOVA example in the last section, the F test for dose indicates that the treatments don’t have the same mean birth weight, but it doesn’t tell you which means differ from one another. Again you can use the multiple comparison procedures provided by the multcomp package to compute all pairwise mean comparisons. Additionally, the multcomp package can be used to test specific user- defined hypotheses about the means. Suppose you’re interested in whether the no-drug condition differs from the three- drug condition. The code in the following listing can be used to test this hypothesis. Listing 9.4 Multiple comparisons employing user-supplied contrasts > library(multcomp) > contrast <- rbind("no drug vs. drug" = c(3, -1, -1, -1)) > summary(glht(fit, linfct=mcp(dose=contrast))) Multiple Comparisons of Means: User-defined Contrasts Download from Wow! eBook 32 Chapter 9 Analysis of variance Fit: aov(formula = weight ~ gesttime + dose) Linear Hypotheses: Estimate Std. Error t value Pr(>|t|) no drug vs. drug == 0 8.284 3.209 2.581 0.0120 * --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 The contrast c(3, -1, -1, -1) specifies a comparison of the first group with the av- erage of the other three. The hypothesis is tested with a t statistic (2.581 in this case), which is significant at the p < .05 level. Therefore, you can conclude that the no-drug group has a higher birth weight than drug conditions. Other contrasts can be added to the rbind() function (see help(glht) for details). 9.4.1 Assessing test assumptions ANCOVA designs make the same normality and homogeneity of variance assumptions described for ANOVA designs, and you can test these assumptions using the same pro- cedures described in section 9.3.2. In addition, standard ANCOVA designs assumes ho- mogeneity of regression slopes. In this case, it’s assumed that the regression slope for predicting birth weight from gestation time is the same in each of the four treatment groups. A test for the homogeneity of regression slopes can be obtained by including a gestation*dose interaction term in your ANCOVA model. A significant interaction would imply that the relationship between gestation and birth weight depends on the level of the dose variable. The code and results are provided in the following listing. Listing 9.5 Testing for homogeneity of regression slopes > library(multcomp) > fit2 <- aov(weight ~ gesttime*dose, data=litter) > summary(fit2) Df Sum Sq Mean Sq F value Pr(>F) gesttime 1 134 134 8.29 0.0054 ** dose 3 137 46 2.82 0.0456 * gesttime:dose 3 82 27 1.68 0.1789 Residuals 66 1069 16 --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 The interaction is nonsignificant, supporting the assumption of equality of slopes. If the assumption is untenable, you could try transforming the covariate or dependent variable, using a model that accounts for separate slopes, or employing a nonparamet- ric ANCOVA method that doesn’t require homogeneity of regression slopes. See the sm.ancova() function in the sm package for an example of the latter. 9.4.2 Visualizing the results The ancova() function in the HH package provides a plot of the relationship between the dependent variable, the covariate, and the factor. For example: Download from Wow! eBook ne-way ANCOVA 233 > library(HH) > ancova(weight ~ gesttime + dose, data=litter) produces the plot shown in the following figure 9.5. Note: the figure has been modi- fied to display better in black and white and will look slightly different when you run the code yourself. Here you can see that the regression lines for predicting birth weight from gestation time are parallel in each group but have different intercepts. As gestation time increases, birth weight increases. Additionally, you can see that the 0-dose group has the largest intercept and the 5-dose group has the lowest intercept. The lines are parallel because you’ve specified them to be. If you’d used the statement ancova(weight ~ gesttime*dose) instead, you’d generate a plot that allows both the slopes and intercepts to vary by group. This approach is useful for visualizing the case where the homogeneity of regression slopes doesn’t hold. weight ~ gesttime + dose gesttime w e i g h t 20 25 30 35 21.5 22.5 0 21.5 22.5 5 21.5 22.5 50 21.5 22.5 500 21.5 22.5 superpose dose 0 5 50 500 Figure 9.5 Plot of the relationship between gestation time and birth weight for each of four drug treatment groups Download from Wow! eBook 34 Chapter 9 Analysis of variance 9.5 Two-way factorial ANOVA In a two-way factorial ANOVA, subjects are assigned to groups that are formed from the cross-classification of two factors. This example uses the ToothGrowth dataset in the base installation to demonstrate a two-way between-groups ANOVA. Sixty guinea pigs are randomly assigned to receive one of three levels of ascorbic acid (0.5, 1, or 2mg), and one of two delivery methods (orange juice or Vitamin C), under the restriction that each treatment combination has 10 guinea pigs. The dependent variable is tooth length. The following listing shows the code for the analysis. Listing 9.6 Two-way ANOVA > attach(ToothGrowth) > table(supp, dose) dose supp 0.5 1 2 OJ 10 10 10 VC 10 10 10 > aggregate(len, by=list(supp, dose), FUN=mean) Group.1 Group.2 x 1 OJ 0.5 13.23 2 VC 0.5 7.98 3 OJ 1.0 22.70 4 VC 1.0 16.77 5 OJ 2.0 26.06 6 VC 2.0 26.14 > aggregate(len, by=list(supp, dose), FUN=sd) Group.1 Group.2 x 1 OJ 0.5 4.46 2 VC 0.5 2.75 3 OJ 1.0 3.91 4 VC 1.0 2.52 5 OJ 2.0 2.66 6 VC 2.0 4.80 > fit <- aov(len ~ supp*dose) > summary(fit) Df Sum Sq Mean Sq F value Pr(>F) supp 1 205 205 12.32 0.0009 *** dose 1 2224 2224 133.42 <2e-16 *** supp:dose 1 89 89 5.33 0.0246 * Residuals 56 934 17 --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 The table statement indicates that you have a balanced design (equal sample sizes in each cell of the design), and the aggregate statements provide the cell means and standard deviations. The ANOVA table provided by the summary() function indicates that both main effects (supp and dose) and the interaction between these factors are significant. Download from Wow! eBook wo-way factorial ANOVA 235 1 0 1 5 2 0 2 5 Interaction between Dose and Supplement T ype dose m e a n o f l e n 0.5 1 2 supp VC OJ Figure 9.6 Interaction between dose and delivery mechanism on tooth growth. The plot of means was created using the interaction. plot() function. You can visualize the results in several ways. You can use the interaction.plot() function to display the interaction in a two-way ANOVA. The code is interaction.plot(dose, supp, len, type="b", col=c("red","blue"), pch=c(16, 18), main = "Interaction between Dose and Supplement Type") and the resulting plot is presented in figure 9.6. The plot provides the mean tooth length for each supplement at each dosage. With a little finesse, you can get an interaction plot out of the plotmeans() function in the gplots package. The following code produces the graph in figure 9.7: library(gplots) plotmeans(len ~ interaction(supp, dose, sep=" "), connect=list(c(1,3,5),c(2,4,6)), col=c("red", "darkgreen"), main = "Interaction Plot with 95% CIs", xlab="Treatment and Dose Combination") The graph includes the means, as well as error bars (95 percent confidence intervals) and sample sizes. Finally, you can use the interaction2wt() function in the HH package to produce a plot of both main effects and two-way interactions for any factorial design of any order (figure 9.8): library(HH) interaction2wt(len~supp*dose) Again, this figure has been modified to display more clearly in black and white and will look slightly different when you run the code yourself. All three graphs indicate that tooth growth increases with the dose of ascorbic acid for both orange juice and Vitamin C. For the 0.5 and 1mg doses, orange juice produced Download from Wow! eBook 36 Chapter 9 Analysis of variance 1 0 1 5 2 0 2 5 3 0 Interaction Plot with 95% CIs T reatment and Dose Combination l e n OJ 0.5 VC 0.5 OJ 1 VC 1 OJ 2 VC 2 n=10 n=10 n=10 n=10 n=10 n=10 Figure 9.7 Interaction between dose and delivery mechanism on tooth growth. The mean plot with 95 percent confidence intervals was created by the plotmeans() function. more tooth growth than Vitamin C. For 2mg of ascorbic acid, both delivery methods produced identical growth. Of the three plotting methods provided, I prefer the in- teraction2wt() function in the HH package. It displays both the main effects (the box plots) and the two-way interactions for designs of any complexity (two-way ANOVA, three-way ANOVA, etc.). Although I don’t cover the tests of model assumptions and mean comparison procedures, they’re a natural extension of the methods you’ve seen so far. Additionally, the design is balanced, so you don’t have to worry about the order of effects. len: main effects and 2−way interactions x.values r e s p o n s e . v a r OJVC sssuuupppppp len ~ supp | supp 0.5 1 2 dddooossseee 5 10 15 20 25 30 llleeennn len ~ dose | supp len ~ supp | dose 5 10 15 20 25 30 llleeennn len ~ dose | dose dose 0.5 1 2 supp OJ VC Figure 9.8 Main effects and two-way interaction for the ToothGrowth dataset. This plot was created by the interaction2way() function. Download from Wow! eBook epeated measures ANOVA 237 9.6 Repeated measures ANOVA In repeated measures ANOVA, subjects are measured more than once. This section fo- cuses on a repeated measures ANOVA with one within-groups and one between-groups factor (a common design). We’ll take our example from the field of physiological ecol- ogy. Physiological ecologists study how the physiological and biochemical processes of living systems respond to variations in environmental factors (a crucial area of study given the realities of global warming). The CO2 dataset included in the base installa- tion contains the results of a study of cold tolerance in Northern and Southern plants of the grass species Echinochloa crus-galli (Potvin, Lechowicz, & Tardif, 1990). The photosynthetic rates of chilled plants were compared with the photosynthetic rates of nonchilled plants at several ambient CO2 concentrations. Half the plants were from Quebec and half were from Mississippi. In this example, we’ll focus on chilled plants. The dependent variable is carbon dioxide uptake (uptake) in ml/L, and the independent variables are Type (Quebec versus Mississippi) and ambient CO2 concentration (conc) with seven levels (ranging from 95 to 1000 umol/m^2 sec). Type is a between-groups factor and conc is a within- groups factor. The analysis is presented in the next listing. Listing 9.7 Repeated measures ANOVA with one between- and within-groups factor > w1b1 <- subset(CO2, Treatment=='chilled') > fit <- aov(uptake ~ conc*Type + Error(Plant/(conc), w1b1) > summary(fit) Error: Plant Df Sum Sq Mean Sq F value Pr(>F) Type 1 2667.24 2667.24 60.414 0.001477 ** Residuals 4 176.60 44.15 --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Error: Plant:conc Df Sum Sq Mean Sq F value Pr(>F) conc 1 888.57 888.57 215.46 0.0001253 *** conc:Type 1 239.24 239.24 58.01 0.0015952 ** Residuals 4 16.50 4.12 --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Error: Within Df Sum Sq Mean Sq F value Pr(>F) Residuals 30 869.05 28.97 > par(las=2) > par(mar=c(10,4,4,2)) > with(w1b1, interaction.plot(conc,Type,uptake, type="b", col=c("red","blue"), pch=c(16,18), main="Interaction Plot for Plant Type and Concentration")) > boxplot(uptake ~ Type*conc, data=w1b1, col=(c("gold", "green")), main=”Chilled Quebec and Mississippi Plants”, ylab=”Carbon dioxide uptake rate (umol/m^2 sec)”) Download from Wow! eBook 38 Chapter 9 Analysis of variance 10 15 20 25 30 35 40 Interaction Plot f or Plant T ype and Concentration conc m e a n o f u p t a k e 9 5 1 7 5 2 5 0 3 5 0 5 0 0 6 7 5 1 0 0 0 T ype Quebec Mississippi Figure 9.9 Interaction of ambient CO2 concentration and plant type on CO2 uptake. Graph produced by the interaction. plot() function. The ANOVA table indicates that the Type and concentration main effects and the Type x concentration interaction are all significant at the 0.01 level. The interaction is plot- ted via the interaction.plot() function in figure 9.9. In order to demonstrate a different presentation of the interaction, the boxplot() function is used to plot the same data. The results are provided in figure 9.10. Q u e b e c . 9 5 M i s s i s s i p p i . 9 5 Q u e b e c . 1 7 5 M i s s i s s i p p i . 1 7 5 Q u e b e c . 2 5 0 M i s s i s s i p p i . 2 5 0 Q u e b e c . 3 5 0 M i s s i s s i p p i . 3 5 0 Q u e b e c . 5 0 0 M i s s i s s i p p i . 5 0 0 Q u e b e c . 6 7 5 M i s s i s s i p p i . 6 7 5 Q u e b e c . 1 0 0 0 M i s s i s s i p p i . 1 0 0 0 10 15 20 25 30 35 40 Chilled Quebec and Mississippi Plants C a r b o n d i o x i d e u p t a k e r a t e ( u m o l / m ^ 2 s e c ) Figure 9.10 Interaction of ambient CO2 concentration and plant type on CO2 uptake. Graph produced by the boxplot() function. Download from Wow! eBook ultivariate analysis of variance (MANOVA) 239 From either graph, you can see that there’s a greater carbon dioxide uptake in plants from Quebec compared to Mississippi. The difference is more pronounced at higher ambient CO2 concentrations. NOTE The datasets that you work with are typically in wide format, where columns are variables and rows are observations, and there’s a single row for each subject. The litter data frame from section 9.4 is a good example. When dealing with repeated measures designs, you typically need the data in long format before fitting your models. In long format, each measurement of the dependent variable is placed in its own row. The CO2 dataset follows this form. Luckily, the reshape package described in chapter 5 (section 5.6.3) can easily reorganize your data into the required format. The many approaches to mixed-model designs The CO2 example in this section was analyzed using a traditional repeated measures ANOVA. The approach assumes that the covariance matrix for any within-groups factor follows a specified form known as sphericity. Specifically, it assumes that the variances of the differences between any two levels of the within-groups factor are equal. In real-world data, it’s unlikely that this assumption will be met. This has led to a number of alternative approaches, including the following: .n Using the lmer() function in the lme4 package to fit linear mixed models (Bates, 2005) .n Using the Anova() function in the car package to adjust traditional test sta- tistics to account for lack of sphericity (for example, Geisser–Greenhouse cor- rection) .n Using the gls() function in the nlme package to fit generalized least squares models with specified variance-covariance structures (UCLA, 2009) .n Using multivariate analysis of variance to model repeated measured data (Hand, 1987) Coverage of these approaches is beyond the scope of this text. If you’re interested in learning more, check out Pinheiro and Bates (2000) and Zuur et al. (2009). Up to this point, all the methods in this chapter have assumed that there’s a single de- pendent variable. In the next section, we’ll briefly consider designs that include more than one outcome variable. 9.7 Multivariate analysis of variance (MANOVA) If there’s more than one dependent (outcome) variable, you can test them simultane- ously using a multivariate analysis of variance (MANOVA). The following example is based on the UScereal dataset in the MASS package. The dataset comes from Venables Download from Wow! eBook 40 Chapter 9 Analysis of variance & Ripley (1999). In this example, we’re interested in whether the calories, fat, and sugar content of US cereals vary by store shelf, where 1 is the bottom shelf, 2 is the middle shelf, and 3 is the top shelf. Calories, fat, and sugars are the dependent vari- ables, and shelf is the independent variable with three levels (1, 2, and 3). The analysis is presented in the following listing. Listing 9.8 One-way MANOVA > library(MASS) > attach(UScereal) > y <- cbind(calories, fat, sugars) > aggregate(y, by=list(shelf), FUN=mean) Group.1 calories fat sugars 1 1 119 0.662 6.3 2 2 130 1.341 12.5 3 3 180 1.945 10.9 > cov(y) calories fat sugars calories 3895.2 60.67 180.38 fat 60.7 2.71 4.00 sugars 180.4 4.00 34.05 > fit <- manova(y ~ shelf) > summary(fit) Df Pillai approx F num Df den Df Pr(>F) shelf 1 0.1959 4.9550 3 61 0.00383 ** Residuals 63 --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 > summary.aov(fit) Response calories : Df Sum Sq Mean Sq F value Pr(>F) shelf 1 45313 45313 13.995 0.0003983 *** Residuals 63 203982 3238 --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Response fat : Df Sum Sq Mean Sq F value Pr(>F) shelf 1 18.421 18.421 7.476 0.008108 ** Residuals 63 155.236 2.464 --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Response sugars : Df Sum Sq Mean Sq F value Pr(>F) shelf 1 183.34 183.34 5.787 0.01909 * Residuals 63 1995.87 31.68 --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 This listing uses the cbind() function to form a matrix of the three dependent vari- ables (calories, fat, and sugars). The aggregate() function provides the shelf means, and the cov() function provides the variance and the covariances across cereals. Print univariate results Download from Wow! eBook ultivariate analysis of variance (MANOVA) 241 The manova() function provides the multivariate test of group differences. The significant F value indicates that the three groups differ on the set of nutritional measures. Because the multivariate test is significant, you can use the summary.aov() function to obtain the univariate one-way ANOVAs. Here, you see that the three groups differ on each nutritional measure considered separately. Finally, you can use a mean comparison procedure (such as TukeyHSD) to determine which shelves differ from each other for each of the three dependent variables (omitted here to save space). 9.7.1 Assessing test assumptions The two assumptions underlying a one-way MANOVA are multivariate normality and homogeneity of variance-covariance matrices. The first assumption states that the vector of dependent variables jointly follows a multivariate normal distribution. You can use a Q-Q plot to assess this assumption (see the sidebar “A Theory Interlude” for a statistical explanation of how this works). A theory interlude If you have p x 1 multivariate normal random vector x with mean μ and covariance matrix Σ, then the squared Mahalanobis distance between x and μ is chi-square distributed with p degrees of freedom. The Q-Q plot graphs the quantiles of the chi- square distribution for the sample against the Mahalanobis D-squared values. To the degree that the points fall along a line with slope 1 and intercept 0, there’s evidence that the data is multivariate normal. The code is provided in the following listing and the resulting graph is displayed in figure 9.11. Listing 9.9 Assessing multivariate normality > center <- colMeans(y) > n <- nrow(y) > p <- ncol(y) > cov <- cov(y) > d <- mahalanobis(y,center,cov) > coord <- qqplot(qchisq(ppoints(n),df=p), d, main="Q-Q Plot Assessing Multivariate Normality", ylab="Mahalanobis D2") > abline(a=0,b=1) > identify(coord$x, coord$y, labels=row.names(UScereal)) If the data follow a multivariate normal distribution, then points will fall on the line. The identify() function allows you to interactively identify points in the graph. (The identify() function is covered in chapter 16, section 16.4.) Here, the dataset appears to violate multivariate normality, primarily due to the observations for Wheaties Honey Gold and Wheaties. You may want to delete these two cases and rerun the analyses. Download from Wow! eBook 42 Chapter 9 Analysis of variance 0 2 4 6 8 10 12 0 1 0 2 0 3 0 4 0 QQ Plot Assessing Multivariate Normality qchisq(ppoints(n), df = p) M a h a l a n o b i s D 2 Wheaties Wheaties Honey Gold Figure 9.11 A Q-Q plot for assessing multivariate normality The homogeneity of variance-covariance matrices assumption requires that the covari- ance matrix for each group are equal. The assumption is usually evaluated with a Box’s M test. R doesn’t include a function for Box’s M, but an internet search will provide the appropriate code. Unfortunately, the test is sensitive to violations of normality, leading to rejection in most typical cases. This means that we don’t yet have a good working method for evaluating this important assumption (but see Anderson [2006] and Silva et al. [2008] for interesting alternative approaches not yet available in R). Finally, you can test for multivariate outliers using the aq.plot() function in the mvoutlier package. The code in this case looks like this: library(mvoutlier) outliers <- aq.plot(y) outliers Try it out and see what you get! 9.7.2 Robust MANOVA If the assumptions of multivariate normality or homogeneity of variance-covariance matrices are untenable, or if you’re concerned about multivariate outliers, you may want to consider using a robust or nonparametric version of the MANOVA test instead. A robust version of the one-way MANOVA is provided by the Wilks.test() function in the rrcov package. The adonis() function in the vegan package can provide the equivalent of a nonparametric MANOVA. Listing 9.10 applies Wilks.test() to our example. Download from Wow! eBook NOVA as regression 243 Listing 9.10 Robust one-way MANOVA library(rrcov) > Wilks.test(y,shelf,method="mcd") Robust One-way MANOVA (Bartlett Chi2) data: x Wilks' Lambda = 0.511, Chi2-Value = 23.71, DF = 4.85, p-value = 0.0002143 sample estimates: calories fat sugars 1 120 0.701 5.66 2 128 1.185 12.54 3 161 1.652 10.35 From the results, you can see that using a robust test that’s insensitive to both outli- ers and violations of MANOVA assumptions still indicates that the cereals on the top, middle, and bottom store shelves differ in their nutritional profiles. 9.8 ANOVA as regression In section 9.2, we noted that ANOVA and regression are both special cases of the same general linear model. As such, the designs in this chapter could have been analyzed using the lm() function. However, in order to understand the output, you need to understand how R deals with categorical variables when fitting models. Consider the one-way ANOVA problem in section 9.3, which compares the impact of five cholesterol-reducing drug regiments (trt). > library(multcomp) > levels(cholesterol$trt) [1] "1time" "2times" "4times" "drugD" "drugE" First, let’s fit the model using the aov() function: > fit.aov <- aov(response ~ trt, data=cholesterol) > summary(fit.aov) Df Sum Sq Mean Sq F value Pr(>F) trt 4 1351.37 337.84 32.433 9.819e-13 *** Residuals 45 468.75 10.42 Now, let’s fit the same model using lm(). In this case you get the results shown in the next listing. Listing 9.11 A regression approach to the ANOVA problem in section 9.3 > fit.lm <- lm(response ~ trt, data=cholesterol) > summary(fit.lm) Coefficients: Estimate Std. Error t value Pr(>|t|) (Intercept) 5.782 1.021 5.665 9.78e-07 *** trt2times 3.443 1.443 2.385 0.0213 * Download from Wow! eBook 44 Chapter 9 Analysis of variance trt4times 6.593 1.443 4.568 3.82e-05 *** trtdrugD 9.579 1.443 6.637 3.53e-08 *** trtdrugE 15.166 1.443 10.507 1.08e-13 *** Residual standard error: 3.227 on 45 degrees of freedom Multiple R-squared: 0.7425, Adjusted R-squared: 0.7196 F-statistic: 32.43 on 4 and 45 DF, p-value: 9.819e-13 What are we looking at? Because linear models require numeric predictors, when the lm() function encounters a factor, it replaces that factor with a set of numeric variables representing contrasts among the levels. If the factor has k levels, k-1 contrast variables will be created. R provides five built-in methods for creating these contrast variables (see table 9.6). You can also create your own (we won’t cover that here). By default, treatment contrasts are used for unordered factors and orthogonal polynomials are used for ordered factors. Table 9.6 Built-in contrasts Contrast Description contr.helmert Contrasts the second level with the first, the third level with the average of the first two, the fourth level with the average of the first three, and so on. contr.poly Contrasts used for trend analysis (linear, quadratic, cubic, and so on.) based on orthogonal polynomials. Use for ordered factors with equally spaced levels. contr.sum Contrasts are constrained to sum to zero. Also called deviation contrasts, they compare the mean of each level to the overall mean across levels. contr.treatment Contrasts each level with the baseline level (first level by default). Also called dummy coding. contr.SASSimilar to contr.treatment but the baseline level is the last level. This produces coefficients similar to contrasts used in most SAS procedures. With treatment contrasts, the first level of the factor becomes the reference group and each subsequent level is compared with it. You can see the coding scheme via the contrasts() function: > contrasts(cholesterol$trt) 2times 4times drugD drugE 1time 0 0 0 0 2times 1 0 0 0 4times 0 1 0 0 drugD 0 0 1 0 drugE 0 0 0 1 If a patient is in the drugD condition, then the variable drugD equals 1, and the vari- ables 2times, 4times, and drugE will each equal zero. You don’t need a variable for the first group, because a zero on each of the four indicator variables uniquely deter- mines that the patient is in the 1times condition. Download from Wow! eBook ummary 245 In listing 9.11, the variable trt2times represents a contrast between the levels 1time and 2time. Similarly, trt4times is a contrast between 1time and 4times, and so on. You can see from the probability values in the output that each drug condition is significantly different from the first (1time). You can change the default contrasts used in lm() by specifying a contrasts option. For example, you can specify Helmert contrasts by using fit.lm <- lm(response ~ trt, data=cholesterol, contrasts="contr.helmert") You can change the default contrasts used during an R session via the options() func- tion. For example, options(contrasts = c("contr.SAS", "contr.helmert")) would set the default contrast for unordered factors to contr.SAS and for ordered fac- tors to contr.helmert. Although we’ve limited our discussion to the use of contrasts in linear models, note that they’re applicable to other modeling functions in R. This includes the generalized linear models covered in chapter 13. 9.9 Summary In this chapter, we reviewed the analysis of basic experimental and quasi-experimental designs using ANOVA/ANCOVA/MANOVA methodology. We reviewed the basic termi- nology used, and looked at examples of between and within-groups designs, including the one-way ANOVA, one-way ANCOVA, two-way factorial ANOVA, repeated measures ANOVA, and one-way MANOVA. In addition to the basic analyses, we reviewed methods of assessing model assumptions and applying multiple comparison procedures following significant omnibus tests. Finally, we explored a wide variety of methods for displaying the results visually. If you’re interested in learning more about the design of experiments (DOE) using R, be sure to see the CRAN View provided by Groemping (2009). Chapters 8 and 9 have covered the statistical methods most often used by researchers in a wide variety of fields. In the next chapter, we’ll address issues of power analysis. Power analysis helps us to determine the sample sizes needed to detect an effect of a given size with a given degree of confidence, and is a crucial component of research design. Download from Wow! eBook 246 10Power analysis This chapter covers .n Determining sample size requirements .n Calculating effect sizes .n Assessing statistical power As a statistical consultant, I am often asked the question, “How many subjects do I need for my study?” Sometimes the question is phrased this way: “I have x number of people available for this study. Is the study worth doing?” Questions like these can be answered through power analysis, an important set of techniques in experimental design. Power analysis allows you to determine the sample size required to detect an effect of a given size with a given degree of confidence. Conversely, it allows you to determine the probability of detecting an effect of a given size with a given level of confidence, under sample size constraints. If the probability is unacceptably low, you’d be wise to alter or abandon the experiment. In this chapter, you’ll learn how to conduct power analyses for a variety of statistical tests, including tests of proportions, t-tests, chi-square tests, balanced one- way ANOVA, tests of correlations, and linear models. Because power analysis applies to hypothesis testing situations, we’ll start with a brief review of null hypothesis significance testing (NHST). Then we’ll review conducting power analyses within R, focusing primarily on the pwr package. Finally, we’ll consider other approaches to power analysis available with R. Download from Wow! eBook quick review of hypothesis testing 247 10.1 A quick review of hypothesis testing To help you understand the steps in a power analysis, we’ll briefly review statistical hypothesis testing in general. If you have a statistical background, feel free to skip to section 10.2. In statistical hypothesis testing, you specify a hypothesis about a population parameter (your null hypothesis, or H0). You then draw a sample from this population and calculate a statistic that’s used to make inferences about the population parameter. Assuming that the null hypothesis is true, you calculate the probability of obtaining the observed sample statistic or one more extreme. If the probability is sufficiently small, you reject the null hypothesis in favor of its opposite (referred to as the alternative or research hypothesis, H1). An example will clarify the process. Say you’re interested in evaluating the impact of cell phone use on driver reaction time. Your null hypothesis is Ho: µ1 – µ2 = 0, where µ1 is the mean response time for drivers using a cell phone and µ2 is the mean response time for drivers that are cell phone free (here, µ1 – µ2 is the population parameter of interest). If you reject this null hypothesis, you’re left with the alternate or research hypothesis, namely H1: µ1 – µ2 ≠ 0. This is equivalent to µ1 ≠ µ2, that the mean reaction times for the two conditions are not equal. A sample of individuals is selected and randomly assigned to one of two conditions. In the first condition, participants react to a series of driving challenges in a simulator while talking on a cell phone. In the second condition, participants complete the same series of challenges but without a cell phone. Overall reaction time is assessed for each individual. Based on the sample data, you can calculate the statistic where X1 and X2 are the sample reaction time means in the two conditions, s is the pooled sample standard deviation, and n is the number of participants in each condi- tion. If the null hypothesis is true and you can assume that reaction times are normally distributed, this sample statistic will follow a t distribution with 2n-2 degrees of free- dom. Using this fact, you can calculate the probability of obtaining a sample statistic this large or larger. If the probability (p) is smaller than some predetermined cutoff (say p < .05), you reject the null hypothesis in favor of the alternate hypothesis. This predetermined cutoff (0.05) is called the significance level of the test. Note that you use sample data to make an inference about the population it’s drawn from. Your null hypothesis is that the mean reaction time of all drivers talking on cell phones isn’t different from the mean reaction time of all drivers who aren’t talking on cell phones, not just those drivers in your sample. The four possible outcomes from your decision are as follows: .n If the null hypothesis is false and the statistical test leads us to reject it, you’ve made a correct decision. You’ve correctly determined that reaction time is affected by cell phone use. Download from Wow! eBook 48 Chapter 10 Power analysis .n If the null hypothesis is true and you don’t reject it, again you’ve made a correct decision. Reaction time isn’t affected by cell phone use. .n If the null hypothesis is true but you reject it, you’ve committed a Type I error. You’ve concluded that cell phone use affects reaction time when it doesn’t. .n If the null hypothesis is false and you fail to reject it, you’ve committed a Type II error. Cell phone use affects reaction time, but you’ve failed to discern this. Each of these outcomes is illustrated in the table below. Decision Reject H0 Fail to Reject H0 Actual H0 true Type I error correct H0 false correct Type II error Controversy surrounding null hypothesis significance testing Null hypothesis significance testing is not without controversy and detractors have raised numerous concerns about the approach, particularly as practiced in the field of psychology. They point to a widespread misunderstanding of p values, reliance on statistical significance over practical significance, the fact that the null hypothesis is never exactly true and will always be rejected for sufficient sample sizes, and a number of logical inconsistencies in NHST practices. An in-depth discussion of this topic is beyond the scope of this book. Interested readers are referred to Harlow, Mulaik, and Steiger (1997). In planning research, the researcher typically pays special attention to four quantities: sample size, significance level, power, and effect size (see figure 10.1). Specifically: .n Sample size refers to the number of observations in each condition/group of the experimental design. .n The significance level (also referred to as alpha) is defined as the probability of making a Type I error. The significance level can also be thought of as the prob- ability of finding an effect that is not there. .n Power is defined as one minus the probability of making a Type II error. Power can be thought of as the probability of finding an effect that is there. .n Effect size is the magnitude of the effect under the alternate or research hypothe- sis. The formula for effect size depends on the statistical methodology employed in the hypothesis testing. Download from Wow! eBook mplementing power analysis with the pwr package 249 Figure 10.1 Four primary quantities considered in a study design power analysis. Given any three, you can calculate the fourth. Power 1-P(Type II Error) Sample Size n Significance Level P(Type I Error) Effect Size ES Although the sample size and significance level are under the direct control of the researcher, power and effect size are affected more indirectly. For example, as you re- lax the significance level (in other words, make it easier to reject the null hypothesis), power increases. Similarly, increasing the sample size increases power. Your research goal is typically to maximize the power of your statistical tests while maintaining an acceptable significance level and employing as small a sample size as possible. That is, you want to maximize the chances of finding a real effect and minimize the chances of finding an effect that isn’t really there, while keeping study costs within reason. The four quantities (sample size, significance level, power, and effect size) have an intimate relationship. Given any three, you can determine the fourth. We’ll use this fact to carry out various power analyses throughout the remainder of the chapter. In the next section, we’ll look at ways of implementing power analyses using the R package pwr. Later, we’ll briefly look at some highly specialized power functions that are used in biology and genetics. 10.2 Implementing power analysis with the pwr package The pwr package, developed by Stéphane Champely, implements power analysis as outlined by Cohen (1988). Some of the more important functions are listed in table 10.1. For each function, the user can specify three of the four quantities (sample size, significance level, power, effect size) and the fourth will be calculated. Download from Wow! eBook 50 Chapter 10 Power analysis Table 10.1 pwr package functions Function Power calculations for pwr.2p.test()Two proportions (equal n) pwr.2p2n.test()Two proportions (unequal n) pwr.anova.test()Balanced one-way ANOVA pwr.chisq.test()Chi-square test pwr.f2.test()General linear model pwr.p.test()Proportion (one sample) pwr.r.test()Correlation pwr.t.test() t-tests (one sample, two sample, paired) pwr.t2n.test() t-test (two samples with unequal n) Of the four quantities, effect size is often the most difficult to specify. Calculating effect size typically requires some experience with the measures involved and knowledge of past research. But what can you do if you have no clue what effect size to expect in a given study? You’ll look at this difficult question in section 10.2.7. In the remainder of this section, you’ll look at the application of pwr functions to common statistical tests. Before invoking these functions, be sure to install and load the pwr package.        t-tests When the statistical test to be used is a t-test, the pwr.t.test() function provides a number of useful power analysis options. The format is pwr.t.test(n=, d=, sig.level=, power=, alternative=) where .n n is the sample size. .n d is the effect size defined as the standardized mean difference. d = m1– m2 s where m1 = mean of group 1 m2 = mean of group 2 s2 = common error variance .n sig.level is the significance level (0.05 is the default). .n power is the power level. .n type is two-sample t-test ("two.sample"), a one-sample t-test ("one.sample"), or a dependent sample t-test ( "paired"). A two-sample test is the default. .n alternative indicates whether the statistical test is two-sided ("two.sided") or one-sided ("less" or "greater"). A two-sided test is the default. Download from Wow! eBook mplementing power analysis with the pwr package 251 Let’s work through an example. Continuing the cell phone use and driving reaction time experiment from section 10.1, assume that you’ll be using a two-tailed indepen- dent sample t-test to compare the mean reaction time for participants in the cell phone condition with the mean reaction time for participants driving unencumbered. Let’s assume that you know from past experience that reaction time has a standard deviation of 1.25 seconds. Also suppose that a 1-second difference in reaction time is considered an important difference. You’d therefore like to conduct a study in which you’re able to detect an effect size of d = 1/1.25 = 0.8 or larger. Additionally, you want to be 90 percent sure to detect such a difference if it exists, and 95 percent sure that you won’t declare a difference to be significant when it’s actually due to random variability. How many participants will you need in your study? Entering this information in the pwr.t.test() function, you have the following: > library(pwr) > pwr.t.test(d=.8, sig.level=.05, power=.9, type="two.sample", alternative="two.sided") Two-sample t test power calculation n = 34 d = 0.8 sig.level = 0.05 power = 0.9 alternative = two.sided NOTE: n is number in *each* group The results suggest that you need 34 participants in each group (for a total of 68 par- ticipants) in order to detect an effect size of 0.8 with 90 percent certainty and no more than a 5 percent chance of erroneously concluding that a difference exists when, in fact, it doesn’t. Let’s alter the question. Assume that in comparing the two conditions you want to be able to detect a 0.5 standard deviation difference in population means. You want to limit the chances of falsely declaring the population means to be different to 1 out of 100. Additionally, you can only afford to include 40 participants in the study. What’s the probability that you’ll be able to detect a difference between the population means that’s this large, given the constraints outlined? Assuming that an equal number of participants will be placed in each condition, you have > pwr.t.test(n=20, d=.5, sig.level=.01, type="two.sample", alternative="two.sided") Two-sample t test power calculation n = 20 d = 0.5 sig.level = 0.01 power = 0.14 Download from Wow! eBook 52 Chapter 10 Power analysis alternative = two.sided NOTE: n is number in *each* group With 20 participants in each group, an a priori significance level of 0.01, and a de- pendent variable standard deviation of 1.25 seconds, you have less than a 14 per- cent chance of declaring a difference of 0.625 seconds or less significant (d = 0.5 = 0.625/1.25). Conversely, there’s a 86 percent chance that you’ll miss the effect that you’re looking for. You may want to seriously rethink putting the time and effort into the study as it stands. The previous examples assumed that there are equal sample sizes in the two groups. If the sample sizes for the two groups are unequal, the function pwr.t2n.test(n1=, n2=, d=, sig.level=, power=, alternative=) can be used. Here, n1 and n2 are the sample sizes and the other parameters are the same as for pwer.t.test. Try varying the values input to the pwr.t2n.test function and see the effect on the output. 10.2.2 ANOVA The pwr.anova.test() function provides power analysis options for a balanced one- way analysis of variance. The format is pwr.anova.test(k=, n=, f=, sig.level=, power=) where k is the number of groups and n is the common sample size in each group. For a one-way ANOVA, effect size is measured by f, where where p i = ni/N, ni = number of observations in group i N = total number of observations mi = mean of group i m = grand mean s2 = error variance within groups Let’s try an example. For a one-way ANOVA comparing five groups, calculate the sam- ple size needed in each group to obtain a power of 0.80, when the effect size is 0.25 and a significance level of 0.05 is employed. The code looks like this: > pwr.anova.test(k=5, f=.25, sig.level=.05, power=.8) Balanced one-way analysis of variance power calculation k = 5 n = 39 f = 0.25 sig.level = 0.05 power = 0.8 NOTE: n is number in each group Download from Wow! eBook mplementing power analysis with the pwr package 253 The total sample size is therefore 5 × 39, or 195. Note that this example requires you to estimate what the means of the five groups will be, along with the common variance. When you have no idea what to expect, the approaches described in section 10.2.7 may help. 10.2.3 Correlations The pwr.r.test() function provides a power analysis for tests of correlation coef- ficients. The format is as follows: pwr.r.test(n=, r=, sig.level=, power=, alternative=) where n is the number of observations, r is the effect size (as measured by a linear cor- relation coefficient), sig.level is the significance level, power is the power level, and alternative specifies a two-sided ("two.sided") or a one-sided ("less" or "great- er") significance test. For example, let’s assume that you’re studying the relationship between depression and loneliness. Your null and research hypotheses are H0: ρ ≤ 0.25 versus H1: ρ > 0.25 where ρ is the population correlation between these two psychological variables. You’ve set your significance level to 0.05 and you want to be 90 percent confident that you’ll reject H0 if it’s false. How many observations will you need? This code provides the answer: > pwr.r.test(r=.25, sig.level=.05, power=.90, alternative="greater") approximate correlation power calculation (arctangh transformation) n = 134 r = 0.25 sig.level = 0.05 power = 0.9 alternative = greater Thus, you need to assess depression and loneliness in 134 participants in order to be 90 percent confident that you’ll reject the null hypothesis if it’s false. 10.2.4 Linear models For linear models (such as multiple regression), the pwr.f2.test() function can be used to carry out a power analysis. The format is pwr.f2.test(u=, v=, f2=, sig.level=, power=) where u and v are the numerator and denominator degrees of freedom and f2 is the effect size. f R R 2 2 21= − where R2 = population squared multiple correlation Download from Wow! eBook 54 Chapter 10 Power analysis where R2 A = variance accounted for in the population by variable set A R2 AB = variance accounted for in the population by variable set A and B together f RR R ABA AB 2 2 2 2= − 1− The first formula for f2 is appropriate when you’re evaluating the impact of a set of predictors on an outcome. The second formula is appropriate when you’re evaluating the impact of one set of predictors above and beyond a second set of predictors (or covariates). Let’s say you’re interested in whether a boss’s leadership style impacts workers’ satisfaction above and beyond the salary and perks associated with the job. Leadership style is assessed by four variables, and salary and perks are associated with three variables. Past experience suggests that salary and perks account for roughly 30 percent of the variance in worker satisfaction. From a practical standpoint, it would be interesting if leadership style accounted for at least 5 percent above this figure. Assuming a significance level of 0.05, how many subjects would be needed to identify such a contribution with 90 percent confidence? Here, sig.level=0.05, power=0.90, u=3 (total number of predictors minus the number of predictors in set B), and the effect size is f2 = (.35-.30)/(1-.35) = 0.0769. Entering this into the function yields the following: > pwr.f2.test(u=3, f2=0.0769, sig.level=0.05, power=0.90) Multiple regression power calculation u = 3 v = 184.2426 f2 = 0.0769 sig.level = 0.05 power = 0.9 In multiple regression, the denominator degrees of freedom equals N-k-1, where N is the number of observations and k is the number of predictors. In this case, N-7-1=185, which means the required sample size is N = 185 + 7 + 1 = 193. 10.2.5 Tests of proportions The pwr.2p.test() function can be used to perform a power analysis when compar- ing two proportions. The format is pwr.2p.test(h=, n=, sig.level=, power=) where h is the effect size and n is the common sample size in each group. The effect size h is defined as h p p= ()− ()2 21 2arcsin arcsin and can be calculated with the function ES.h(p1, p2). Download from Wow! eBook mplementing power analysis with the pwr package 255 For unequal ns the desired function is pwr.2p2n.test(h =, n1 =, n2 =, sig.level=, power=). The alternative= option can be used to specify a two-tailed ("two.sided") or one- tailed ("less" or "greater") test. A two-tailed test is the default. Let’s say that you suspect that a popular medication relieves symptoms in 60 percent of users. A new (and more expensive) medication will be marketed if it improves symptoms in 65 percent of users. How many participants will you need to include in a study comparing these two medications if you want to detect a difference this large? Assume that you want to be 90 percent confident in a conclusion that the new drug is better and 95 percent confident that you won’t reach this conclusion erroneously. You’ll use a one-tailed test because you’re only interested in assessing whether the new drug is better than the standard. The code looks like this: > pwr.2p.test(h=ES.h(.65, .6), sig.level=.05, power=.9, alternative="greater") Difference of proportion power calculation for binomial distribution (arcsine transformation) h = 0.1033347 n = 1604.007 sig.level = 0.05 power = 0.9 alternative = greater NOTE: same sample sizes Based on these results, you’ll need to conduct a study with 1,605 individuals receiving the new drug and 1,605 receiving the existing drug in order to meet the criteria. 10.2.6 Chi-square tests Chi-square tests are often used to assess the relationship between two categorical vari- ables. The null hypothesis is typically that the variables are independent versus a re- search hypothesis that they aren’t. The pwr.chisq.test() function can be used to evaluate the power, effect size, or requisite sample size when employing a chi-square test. The format is pwr.chisq.test(w =, N = , df = , sig.level =, power = ) where w is the effect size, N is the total sample size, and df is the degrees of freedom. Here, effect size w is defined as where p0i = cell probability in ith cell under H0 p1i = cell probability in ith cell under H1 The summation goes from 1 to m, where m is the number of cells in the contingency table. The function ES.w2(P) can be used to calculate the effect size corresponding Download from Wow! eBook 56 Chapter 10 Power analysis the alternative hypothesis in a two-way contingency table. Here, P is a hypothesized two-way probability table. As a simple example, let’s assume that you’re looking the relationship between ethnicity and promotion. You anticipate that 70 percent of your sample will be Caucasian, 10 percent will be African American, and 20 percent will be Hispanic. Further, you believe that 60 percent of Caucasians tend to be promoted, compared with 30 percent for African Americans, and 50 percent for Hispanics. Your research hypothesis is that the probability of promotion follows the values in table 10.2. Table 10.2 Proportion of individuals expected to be promoted based on the research hypothesis Ethnicity Promoted Not promoted Caucasian 0.42 0.28 African American 0.03 0.07 Hispanic 0.10 0.10 For example, you expect that 42 percent of the population will be promoted Cauca- sians (.42 = .70 × .60) and 7 percent of the population will be nonpromoted African Americans (.07 = .10 × .70). Let’s assume a significance level of 0.05 and the de- sired power level is 0.90. The degrees of freedom in a two-way contingency table are (r-1)*(c-1), where r is the number of rows and c is the number of columns. You can calculate the hypothesized effect size with the following code: > prob <- matrix(c(.42, .28, .03, .07, .10, .10), byrow=TRUE, nrow=3) > ES.w2(prob) [1] 0.1853198 Using this information, you can calculate the necessary sample size like this: > pwr.chisq.test(w=.1853, df=2, sig.level=.05, power=.9) Chi squared power calculation w = 0.1853 N = 368.5317 df = 2 sig.level = 0.05 power = 0.9 NOTE: N is the number of observations The results suggest that a study with 369 participants will be adequate to detect a relationship between ethnicity and promotion given the effect size, power, and signifi- cance level specified. Download from Wow! eBook mplementing power analysis with the pwr package 257 10.2.7 Choosing an appropriate effect size in novel situations In power analysis, the expected effect size is the most difficult parameter to determine. It typically requires that you have experience with the subject matter and the measures employed. For example, the data from past studies can be used to calculate effect sizes, which can then be used to plan future studies. But what can you do when the research situation is completely novel and you have no past experience to call upon? In the area of behavioral sciences, Cohen (1988) attempted to provide benchmarks for “small,” “medium,” and “large” effect sizes for various statistical tests. These guidelines are provided in table 10.3. Table 10.3 Cohen’s effect size benchmarks Statistical method Effect size measures Suggested guidelines for effect size Small Medium Large t-test d 0.20 0.50 0.80 ANOVA f 0.10 0.25 0.40 Linear models f2 0.02 0.15 0.35 Test of proportions h 0.20 0.50 0.80 Chi-square w 0.10 0.30 0.50 When you have no idea what effect size may be present, this table may provide some guidance. For example, what’s the probability of rejecting a false null hypothesis (that is, finding a real effect), if you’re using a one-way ANOVA with 5 groups, 25 subjects per group, and a significance level of 0.05? Using the pwr.anova.test() function and the suggestions in f row of table 10.3, the power would be 0.118 for detecting a small effect, 0.574 for detecting a moderate effect, and 0.957 for detecting a large effect. Given the sample size limitations, you’re only likely to find an effect if it’s large. It’s important to keep in mind that Cohen’s benchmarks are just general suggestions derived from a range of social research studies and may not apply to your particular field of research. An alternative is to vary the study parameters and note the impact on such things as sample size and power. For example, again assume that you want to compare five groups using a one-way ANOVA and a 0.05 significance level. The following listing computes the sample sizes needed to detect a range of effect sizes and plots the results in figure 10.2. Download from Wow! eBook 58 Chapter 10 Power analysis 50 100 150 200 250 300 0 . 1 0 . 2 0 . 3 0 . 4 0 . 5 One Way ANOVA with Power=.90 and Alpha=.05 Sample Size (per cell) E f f e c t S i z e Figure 10.2 Sample size needed to detect various effect sizes in a one-way ANOVA with five groups (assuming a power of 0.90 and significance level of 0.05) Listing 10.1 Sample sizes for detecting significant effects in a one-way ANOVA library(pwr) es <- seq(.1, .5, .01) nes <- length(es) samsize <- NULL for (i in 1:nes){ result <- pwr.anova.test(k=5, f=es[i], sig.level=.05, power=.9) samsize[i] <- ceiling(result$n) } plot(samsize,es, type="l", lwd=2, col="red", ylab="Effect Size", xlab="Sample Size (per cell)", main="One Way ANOVA with Power=.90 and Alpha=.05") Graphs such as these can help you estimate the impact of various conditions on your experimental design. For example, there appears to be little bang for the buck increas- ing the sample size above 200 observations per group. We’ll look at another plotting example in the next section. 10.3 Creating power analysis plots Before leaving the pwr package, let’s look at a more involved graphing example. Sup- pose you’d like to see the sample size necessary to declare a correlation coefficient statistically significant for a range of effect sizes and power levels. You can use the pwr.r.test() function and for loops to accomplish this task, as shown in the follow- ing listing. Download from Wow! eBook reating power analysis plots 259 Listing 10.2 Sample size curves for detecting correlations of various sizes library(pwr) r <- seq(.1,.5,.01) nr <- length(r) p <- seq(.4,.9,.1) np <- length(p)  amsize <- array(numeric(nr*np), dim=c(nr,np))  or (i in 1:np){ for (j in 1:nr){ result <- pwr.r.test(n = NULL, r = r[j], sig.level = .05, power = p[i], alternative = "two.sided") samsize[j,i] <- ceiling(result$n) } } xrange <- range(r)  range <- round(range(samsize)) colors <- rainbow(length(p)) plot(xrange, yrange, type="n", xlab="Correlation Coefficient (r)", ylab="Sample Size (n)" ) for (i in 1:np){  lines(r, samsize[,i], type="l", lwd=2, col=colors[i]) } abline(v=0, h=seq(0,yrange[2],50), lty=2, col="grey89")  abline(h=0, v=seq(xrange[1],xrange[2],.02), lty=2, col="gray89") title("Sample Size Estimation for Correlation Studies\n Sig=0.05 (Two-tailed)") legend("topright", title="Power", as.character(p), fill=colors) Listing 10.2 uses the seq function to generate a range of effect sizes r (correlation co- efficients under H1) and power levels p . It then uses two for loops to cycle through these effect sizes and power levels, calculating the corresponding sample sizes required and saving them in the array samsize . The graph is set up with the appropriate horizontal and vertical axes and labels . Power curves are added using lines rather than points . Finally, a grid and legend are added to aid in reading the graph . The resulting graph is displayed in figure 10.3. As you can see from the graph, you’d need a sample size of approximately 75 to detect a correlation of 0.20 with 40 percent confidence. You’d need approximately 185 additional observations (n=260) to detect the same correlation with 90 percent confidence. With simple modifications, the same approach can be used to create sample size and power curve graphs for a wide range of statistical tests. We’ll close this chapter by briefly looking at other R functions that are useful for power analysis. Set range of correlations & power values Obtain sample sizes Set up graph Add power curves Add annotations Download from Wow! eBook 60 Chapter 10 Power analysis 0.1 0.2 0.3 0.4 0.5 0 2 0 0 4 0 0 6 0 0 8 0 0 1 0 0 0 Correlation Coefficient (r) S a m p l e S i z e ( n ) Sample Size Estimation f or Correlation Studies Sig=0.05 (T w o−tailed) Po wer 0.4 0.5 0.6 0.7 0.8 0.9 Figure 10.3 Sample size curves for detecting a significant correlation at various power levels 10.4 Other packages There are several other packages in R that can be useful in the planning stages of stud- ies. Some contain general tools, whereas some are highly specialized. The piface package (see figure 10.4) provides a Java GUI for sample-size methods that interfaces with R. The GUI allows the user to vary study parameters interactively and see their impact on other parameters. Although the package is described as Pre-Alpha, it’s definitely worth checking out. You can download the package source and binaries for Windows and Mac OS X from http://r-forge.r-project.org/projects/piface/. In R, enter the code Figure 10.4 Sample dialog boxes from the piface program Download from Wow! eBook ummary 261 install.packages(“piface”, repos=”http://R-Forge.R-project.org”) library(piface) piface() The package is particularly useful for exploring the impact of changes in sample size, effect size, significance levels, and desired power on the other parameters. Other packages related to power analysis are described in table 10.4. The last five are particularly focused on power analysis in genetic studies. Genome-wide association studies (GWAS) are studies used to identify genetic associations with observable traits. For example, these studies would focus on why some people get a specific type of heart disease. Table 10.4 Specialized power analysis packages Package Purpose asypow Power calculations via asymptotic likelihood ratio methods PwrGSDPower analysis for group sequential designs pamm Power analysis for random effects in mixed models powerSurvEpi Power and sample size calculations for survival analysis in epidemiological studies powerpkg Power analyses for the affected sib pair and the TDT (transmission disequilibrium test) design powerGWASinteraction Power calculations for interactions for GWAS pedantics Functions to facilitate power analyses for genetic studies of natural populations gap Functions for power and sample size calculations in case-cohort designs ssize.fdr Sample size calculations for microarray experiments Finally, the MBESS package contains a wide range of functions that can be used for vari- ous forms of power analysis. The functions are particularly relevant for researchers in the behavioral, educational, and social sciences. 10.5 Summary In chapters 7, 8, and 9, we explored a wide range of R functions for statistical hypothesis testing. In this chapter, we focused on the planning stages of such research. Power analysis helps you to determine the sample sizes needed to discern an effect of a given size with a given degree of confidence. It can also tell you the probability of detecting such an effect for a given sample size. You can directly see the tradeoff between limit- ing the likelihood of wrongly declaring an effect significant (a Type I error) with the likelihood of rightly identifying a real effect (power). Download from Wow! eBook 62 Chapter 10 Power analysis The bulk of this chapter has focused on the use of functions provided by the pwr package. These functions can be used to carry out power and sample size determinations for common statistical methods (including t-tests, chi-square tests, and tests of proportions, ANOVA, and regression). Pointers to more specialized methods were provided in the final section. Power analysis is typically an interactive process. The investigator varies the parameters of sample size, effect size, desired significance level, and desired power to observe their impact on each other. The results are used to plan studies that are more likely to yield meaningful results. Information from past research (particularly regarding effect sizes) can be used to design more effective and efficient future research. An important side benefit of power analysis is the shift that it encourages, away from a singular focus on binary hypothesis testing (that is, does an effect exists or not), toward an appreciation of the size of the effect under consideration. Journal editors are increasingly requiring authors to include effect sizes as well as p values when reporting research results. This helps you to determine both the practical implications of the research and provides you with information that can be used to plan future studies. In the next chapter, we’ll look at additional and novel ways to visualize multivariate relationships. These graphic methods can complement and enhance the analytic methods that we’ve discussed so far and prepare you for the advanced methods covered in part 3. Download from Wow! eBook 263 11Intermediate graphs This chapter covers ■ Visualizing bivariate and multivariate relationships ■ Working with scatter and line plots ■ Understanding correlograms ■ Using mosaic and association plots In chapter 6 (basic graphs), we considered a wide range of graph types for dis- playing the distribution of single categorical or continuous variables. Chapter 8 (regression) reviewed graphical methods that are useful when predicting a con- tinuous outcome variable from a set of predictor variables. In chapter 9 (analysis of variance), we considered techniques that are particularly useful for visualizing how groups differ on a continuous outcome variable. In many ways, the current chapter is a continuation and extension of the topics covered so far. In this chapter, we’ll focus on graphical methods for displaying relationships between two variables (bivariate relationships) and between many variables (multivariate relationships). For example: ■ What’s the relationship between automobile mileage and car weight? Does it vary by the number of cylinders the car has? ■ How can you picture the relationships among an automobile’s mileage, weight, displacement, and rear axle ratio in a single graph? Download from Wow! eBook 264 CHAPTER 11 Intermediate graphs ■ When plotting the relationship between two variables drawn from a large dataset (say 10,000 observations), how can you deal with the massive overlap of data points you’re likely to see? In other words, what do you do when your graph is one big smudge? ■ How can you visualize the multivariate relationships among three variables at once (given a 2D computer screen or sheet of paper, and a budget slightly less than that for Avatar)? ■ How can you display the growth of several trees over time? ■ How can you visualize the correlations among a dozen variables in a single graph? How does it help you to understand the structure of your data? ■ How can you visualize the relationship of class, gender, and age with passenger survival on the Titanic? What can you learn from such a graph? These are the types of questions that can be answered with the methods described in this chapter. The datasets that we’ll use are examples of what’s possible. It’s the general techniques that are most important. If the topic of automobile characteristics or tree growth isn’t interesting to you, plug in your own data! We’ll start with scatter plots and scatter plot matrices. Then, we’ll explore line charts of various types. These approaches are well known and widely used in research. Next, we’ll review the use of correlograms for visualizing correlations and mosaic plots for visualizing multivariate relationships among categorical variables. These approaches are also useful but much less well known among researchers and data analysts. You’ll see examples of how you can use each of these approaches to gain a better understanding of your data and communicate these findings to others. 11.1 Scatter plots As you’ve seen in previous chapters, scatter plots describe the relationship between two continuous variables. In this section, we’ll start with a depiction of a single bivari- ate relationship (x versus y). We’ll then explore ways to enhance this plot by super- imposing additional information. Next, we’ll learn how to combine several scatter plots into a scatter plot matrix so that you can view many bivariate relationships at once. We’ll also review the special case where many data points overlap, limiting our ability to picture the data, and we’ll discuss a number of ways around this difficulty. Finally, we’ll extend the two-dimensional graph to three dimensions, with the ad- dition of a third continuous variable. This will include 3D scatter plots and bubble plots. Each can help you understand the multivariate relationship among three vari- ables at once. The basic function for creating a scatter plot in R is plot(x, y), where x and y are numeric vectors denoting the (x, y) points to plot. Listing 11.1 presents an example. Download from Wow! eBook Scatter plots 265 Listing 11.1 A scatter plot with best fit lines attach(mtcars) plot(wt, mpg, main="Basic Scatter plot of MPG vs. Weight", xlab="Car Weight (lbs/1000)", ylab="Miles Per Gallon ", pch=19) abline(lm(mpg~wt), col="red", lwd=2, lty=1) lines(lowess(wt,mpg), col="blue", lwd=2, lty=2) The resulting graph is provided in figure 11.1. The code in listing 11.1 attaches the mtcars data frame and creates a basic scatter plot using filled circles for the plotting symbol. As expected, as car weight increases, miles per gallon decreases, though the relationship isn’t perfectly linear. The a bline() function is used to add a linear line of best fit, while the l owess() function is used to add a smoothed line. This smoothed line is a nonparametric fit line based on locally weighted polynomial regression. See Cleveland (1981) for details on the algorithm. Figure 11.1 Scatter plot of car mileage versus weight, with superimposed linear and lowess fit lines. Download from Wow! eBook 266 CHAPTER 11 Intermediate graphs NOTE R has two functions for producing lowess fits: l owess() and l oess(). The loess() function is a newer, formula-based version of lowess() and is more powerful. The two functions have different defaults, so be careful not to confuse them. The s catterplot() function in the c ar package offers many enhanced features and convenience functions for producing scatter plots, including fit lines, marginal box plots, confidence ellipses, plotting by subgroups, and interactive point identification. For example, a more complex version of the previous plot is produced by the follow- ing code: library(car) scatterplot(mpg ~ wt | cyl, data=mtcars, lwd=2, main="Scatter Plot of MPG vs. Weight by # Cylinders", xlab="Weight of Car (lbs/1000)", ylab="Miles Per Gallon", legend.plot=TRUE, id.method="identify", labels=row.names(mtcars), boxplots="xy" ) Here, the scatterplot() function is used to plot miles per gallon versus weight for automobiles that have four, six, or eight cylinders. The formula mpg ~ wt | cyl indi- cates conditioning (that is, separate plots between mpg and wt for each level of cyl). The graph is provided in figure 11.2. By default, subgroups are differentiated by color and plotting symbol, and separate linear and loess lines are fit. By default, the loess fit requires five unique data points, so no smoothed fit is plotted for six- cylinder cars. The i d.method option indicates that points will be identified interactively by mouse clicks, until the user selects Stop (via the Graphics or context-sensitive menu) or the Esc key. The l abels option indicates that points will be identified with their row names. Here you see that the Toyota Corolla and Fiat 128 have unusually good gas mileage, given their weights. The l egend.plot option adds a legend to the upper-left margin and marginal box plots 1 0 1 5 2 0 2 5 3 0 Scatter Plot of MPG vs. W eight b y # Cylinder s We ight of Car (lbs/1000) M i l e s P e r G a l l o n cyl 4 6 8 Fiat 128 To yota Corolla Figure 11.2 Scatter plot with subgroups and separately estimated fit lines Download from Wow! eBook Scatter plots 267 for mpg and weight are requested with the b oxplots option. The scatterplot() function has many features worth investigating, including robust options and data concentration ellipses not covered here. See help(scatterplot) for more details. Scatter plots help you visualize relationships between quantitative variables, two at a time. But what if you wanted to look at the bivariate relationships between automobile mileage, weight, displacement (cubic inch), and rear axle ratio? One way is to arrange these six scatter plots in a matrix. When there are several quantitative variables, you can represent their relationships in a scatter plot matrix, which is covered next. 11.1.1 Scatter plot matrices There are at least four useful functions for creating scatter plot matrices in R. Analysts must love scatter plot matrices! A basic scatter plot matrix can be created with the p airs() function. The following code produces a scatter plot matrix for the variables mpg, disp, drat, and wt: pairs(~mpg+disp+drat+wt, data=mtcars, main="Basic Scatter Plot Matrix") All the variables on the right of the ~ are included in the plot. The graph is provided in figure 11.3. mpg 100 200 300 400 2 3 4 5 1 0 1 5 2 0 2 5 3 0 1 0 0 2 0 0 3 0 0 4 0 0 disp drat 3 . 0 3 . 5 4 . 0 4 . 5 5 . 0 10 15 20 25 30 2345 3.0 3.5 4.0 4.5 5.0 wt Basic Scatterplot Matrix Figure 11.3 Scatter plot matrix created by the pairs() function Download from Wow! eBook 268 CHAPTER 11 Intermediate graphs Here you can see the bivariate relationship among all the variables specified. For example, the scatter plot between mpg and disp is found at the row and column intersection of those two variables. Note that the six scatter plots below the principal diagonal are the same as those above the diagonal. This arrangement is a matter of convenience. By adjusting the options, you could display just the lower or upper tri- angle. For example, the option upper.panel=NULL would produce a graph with just the lower triangle of plots. The s catterplotMatrix() function in the c ar package can also produce scatter plot matrices and can optionally do the following: ■ Condition the scatter plot matrix on a factor ■ Include linear and loess fit lines ■ Place box plots, densities, or histograms in the principal diagonal ■ Add rug plots in the margins of the cells Here’s an example: library(car) scatterplotMatrix(~ mpg + disp + drat + wt, data=mtcars, spread=FALSE, lty.smooth=2, main="Scatter Plot Matrix via car Package") The graph is provided in figure 11.4. Here you can see that linear and smoothed (loess) fit lines are added by default and that kernel density and rug plots are mpg 100 200 300 400 2 3 4 5 1 0 1 5 2 0 2 5 3 0 1 0 0 2 0 0 3 0 0 4 0 0 disp drat 3 . 0 3 . 5 4 . 0 4 . 5 5 . 0 10 15 20 25 30 23 4 5 3.0 3.5 4.0 4.5 5.0 wt Scatterplot Matrix via car pac kage Figure 11.4 Scatter plot matrix created with the scatterplotMatrix() function. The graph includes kernel density and rug plots in the principal diagonal and linear and loess fit lines. Download from Wow! eBook Scatter plots 269 added to the principal diagonal. The s pread=FALSE option suppresses lines show- ing spread and asymmetry, and the lty.smooth=2 option displays the loess fit lines using dashed rather than solid lines. As a second example of the scatterplotMatrix() function, consider the following code: library(car) scatterplotMatrix(~ mpg + disp + drat + wt | cyl, data=mtcars, spread=FALSE, diagonal="histogram", main="Scatter Plot Matrix via car Package") Here, you change the kernel density plots to histograms and condition the results on the number of cylinders for each car. The results are displayed in figure 11.5. By default, the regression lines are fit for the entire sample. Including the option by.groups = TRUE would have produced separate fit lines by subgroup. An interesting variation on the scatter plot matrix is provided by the c pairs() function in the g clus package. The cpairs() function provides options to rearrange 4 6 8 mpg 100 200 300 400 2 3 4 5 1 0 1 5 2 0 2 5 3 0 1 0 0 2 0 0 3 0 0 4 0 0 disp drat 3 . 0 3 . 5 4 . 0 4 . 5 5 . 0 10 15 20 25 30 23 4 5 3.0 3.5 4.0 4.5 5.0 wt Scatterplot Matrix via car pac kage Figure 11.5 Scatter plot matrix produced by the scatterplot.Matrix() function. The graph includes histograms in the principal diagonal and linear and loess fit lines. Additionally, subgroups (defined by number of cylinders) are indicated by symbol type and color. Download from Wow! eBook 270 CHAPTER 11 Intermediate graphs variables in the matrix so that variable pairs with higher correlations are closer to the principal diagonal. The function can also color-code the cells to reflect the size of these correlations. Consider the correlations among mpg, wt, disp, and drat: > cor(mtcars[c("mpg", "wt", "disp", "drat")]) mpg wt disp drat mpg 1.000 -0.868 -0.848 0.681 wt -0.868 1.000 0.888 -0.712 disp -0.848 0.888 1.000 -0.710 drat 0.681 -0.712 -0.710 1.000 You can see that the highest correlations are between weight and displacement (0.89) and between weight and miles per gallon (–0.87). The lowest correlation is between miles per gallon and rear axle ratio (0.68). You can reorder and color the scatter plot matrix among these variables using the code in the following listing. Listing 11.2 Scatter plot matrix produced with the gclus package library(gclus) mydata <- mtcars[c(1, 3, 5, 6)] mydata.corr <- abs(cor(mydata)) mycolors <- dmat.color(mydata.corr) myorder <- order.single(mydata.corr) cpairs(mydata, myorder, panel.colors=mycolors, gap=.5, main="Variables Ordered and Colored by Correlation" ) The code in listing 11.2 uses the d mat.color(), o rder.single(), and c pairs() functions from the g clus package. First, you select the desired variables from the mtcars data frame and calculate the absolute values of the correlations among them. Next, you obtain the colors to plot using the dmat.color() function. Given a sym- metric matrix (a correlation matrix in this case), dmat.color() returns a matrix of colors. You also sort the variables for plotting. The order.single() function sorts objects so that similar object pairs are adjacent. In this case, the variable ordering is based on the similarity of the correlations. Finally, the scatter plot matrix is plotted and colored using the new ordering (myorder) and the color list (mycolors). The gap option adds a small space between cells of the matrix. The resulting graph is provided in figure 11.6. You can see from the figure that the highest correlations are between weight and displacement and weight and miles per gallon (red and closest to the principal diagonal). The lowest correlation is between rear axle ratio and miles per gallon Download from Wow! eBook Scatter plots 271 drat 100 200 300 400 10 15 20 25 30 3 . 0 3 . 5 4 . 0 4 . 5 5 . 0 1 0 0 2 0 0 3 0 0 4 0 0 disp wt 234 5 3.0 3.5 4.0 4.5 5.0 1 0 1 5 2 0 2 5 3 0 2 3 4 5 mpg V ariables Or dered and Colored b y Correlation Figure 11.6 Scatter plot matrix produced with the cpairs() function in the gclus package. Variables closer to the principal diagonal are more highly correlated. (yellow and far from the principal diagonal). This method is particularly useful when many variables, with widely varying inter-correlations, are considered. You’ll see other examples of scatter plot matrices in chapter 16. 11.1.2 High-density scatter plots When there’s a significant overlap among data points, scatter plots become less use- ful for observing relationships. Consider the following contrived example with 10,000 observations falling into two overlapping clusters of data: set.seed(1234) n <- 10000 c1 <- matrix(rnorm(n, mean=0, sd=.5), ncol=2) c2 <- matrix(rnorm(n, mean=3, sd=2), ncol=2) mydata <- rbind(c1, c2) mydata <- as.data.frame(mydata) names(mydata) <- c("x", "y") Download from Wow! eBook 272 CHAPTER 11 Intermediate graphs Figure 11.7 Scatter plot with 10,000 observations and significant overlap of data points. Note that the overlap of data points makes it difficult to discern where the concentration of data is greatest. If you generate a standard scatter plot between these variables using the following code with(mydata, plot(x, y, pch=19, main="Scatter Plot with 10,000 Observations")) you’ll obtain a graph like the one in figure 11.7. The overlap of data points in figure 11.7 makes it difficult to discern the relationship between x and y. R provides several graphical approaches that can be used when this occurs. They include the use of binning, color, and transparency to indicate the number of overprinted data points at any point on the graph. The s moothScatter() function uses a kernel density estimate to produce smoothed color density representations of the scatterplot. The following code with(mydata, smoothScatter(x, y, main="Scatterplot Colored by Smoothed Densities")) produces the graph in figure 11.8. Using a different approach, the h exbin() function in the h exbin package provides bivariate binning into hexagonal cells (it looks better than it sounds). Applying this function to the dataset library(hexbin) with(mydata, { bin <- hexbin(x, y, xbins=50) plot(bin, main="Hexagonal Binning with 10,000 Observations") }) Download from Wow! eBook Scatter plots 273 Figure 11.8 Scatterplot using smoothScatter() to plot smoothed density estimates. Densities are easy to read from the graph. you get the scatter plot in figure 11.9. Finally, the i plot() function in the I DPmisc package can be used to display density (the number of data points at a specific spot) using color. The code library(IDPmisc) with(mydata, iplot(x, y, main="Image Scatter Plot with Color Indicating Density")) produces the graph in figure 11.10. Figure 11.9 Scatter plot using hexagonal binning to display the number of observations at each point. Data concentrations are easy to see and counts can be read from the legend. Download from Wow! eBook 274 CHAPTER 11 Intermediate graphs Image Scatter Plot with Color Indicating Density 0 max x y 0 5 10 −5 0 5 10 Figure 11.10 Scatter plot of 10,000 observations, where density is indicated by color. The data concentrations are easily discernable. It’s useful to note that the s moothScatter() function in the b ase package, along with the i pairs() function in the I DPmisc package, can be used to create readable scat- ter plot matrices for large datasets as well. See ?smoothScatter and ?ipairs for ex- amples. 11.1.3 3D scatter plots Scatter plots and scatter plot matrices display bivariate relationships. What if you want to visualize the interaction of three quantitative variables at once? In this case, you can use a 3D scatter plot. For example, say that you’re interested in the relationship between automobile mileage, weight, and displacement. You can use the s catterplot3d() function in the s catterplot3d package to picture their relationship. The format is scatterplot3d(x, y, z) where x is plotted on the horizontal axis, y is plotted on the vertical axis, and z is plot- ted in perspective. Continuing our example library(scatterplot3d) attach(mtcars) scatterplot3d(wt, disp, mpg, main="Basic 3D Scatter Plot") produces the 3D scatter plot in figure 11.11. Download from Wow! eBook Scatter plots 275 Basic 3D Scatterplot 1 2 3 4 5 6 1 0 1 5 2 0 2 5 3 0 3 5 0 100 200 300 400 500 wt d i s p m p g Figure 11.11 3D scatter plot of miles per gallon, auto weight, and displacement The scatterplot3d() function offers many options, including the ability to specify symbols, axes, colors, lines, grids, highlighting, and angles. For example, the code library(scatterplot3d) attach(mtcars) scatterplot3d(wt, disp, mpg, pch=16, highlight.3d=TRUE, type="h", main="3D Scatter Plot with Vertical Lines") produces a 3D scatter plot with highlighting to enhance the impression of depth, and vertical lines connecting points to the horizontal plane (see figure 11.12). As a final example, let’s take the previous graph and add a regression plane. The necessary code is: library(scatterplot3d) attach(mtcars) s3d <-scatterplot3d(wt, disp, mpg, pch=16, highlight.3d=TRUE, type="h", main="3D Scatter Plot with Vertical Lines and Regression Plane") fit <- lm(mpg ~ wt+disp) s3d$plane3d(fit) The resulting graph is provided in figure 11.13. Download from Wow! eBook 276 CHAPTER 11 Intermediate graphs 3D Scatterplot with V er tical Lines 1 2 3 4 5 6 1 0 1 5 2 0 2 5 3 0 3 5 0 100 200 300 400 500 wt d i s p m p g Figure 11.12 3D scatter plot with vertical lines and shading The graph allows you to visualize the prediction of miles per gallon from automobile weight and displacement using a multiple regression equation. The plane represents the predicted values, and the points are the actual values. The vertical distances from the plane to the points are the residuals. Points that lie above the plane are under- predicted, while points that lie below the line are over-predicted. Multiple regression is covered in chapter 8. 3D Scatter Plot with V erical Lines and Regression Plane 1 2 3 4 5 6 1 0 1 5 2 0 2 5 3 0 3 5 0 100 200 300 400 500 wt d i s p m p g Figure 11.13 3D scatter plot with vertical lines, shading, and overlaid regression plane Download from Wow! eBook Scatter plots 277 SPINNING 3D SCATTER PLOTS Three-dimensional scatter plots are much easier to interpret if you can interact with them. R provides several mechanisms for rotating graphs so that you can see the plot- ted points from more than one angle. For example, you can create an interactive 3D scatter plot using the p lot3d() function in the r gl package. It creates a spinning 3D scatter plot that can be rotated with the mouse. The format is plot3d(x, y, z) where x, y, and z are numeric vectors representing points. You can also add options like col and size to control the color and size of the points, respectively. Continuing our example, try the code library(rgl) attach(mtcars) plot3d(wt, disp, mpg, col="red", size=5) You should get a graph like the one depicted in figure 11.14. Use the mouse to rotate the axes. I think that you’ll find that being able to rotate the scatter plot in three di- mensions makes the graph much easier to understand. You can perform a similar function with the s catter3d() in the R cmdr package: library(Rcmdr) attach(mtcars) scatter3d(wt, disp, mpg) The results are displayed in figure 11.15. The scatter3d() function can include a variety of regression surfaces, such as linear, quadratic, smooth, and additive. The linear surface depicted is the default. Additionally, there are options for interactively identifying points. See help(scatter3d) for more details. I’ll have more to say about the Rcmdr package in appendix A. Figure 11.14 Rotating 3D scatter plot produced by the plot3d() function in the rgl package Download from Wow! eBook 278 CHAPTER 11 Intermediate graphs Figure 11.15 Spinning 3D scatter plot produced by the scatter3d() function in the Rcmdr package 11.1.4 Bubble plots In the previous section, you displayed the relationship between three quantitative vari- ables using a 3D scatter plot. Another approach is to create a 2D scatter plot and use the size of the plotted point to represent the value of the third variable. This approach is referred to as a bubble plot. You can create a bubble plot using the s ymbols() function. This function can be used to draw circles, squares, stars, thermometers, and box plots at a specified set of (x, y) coordinates. For plotting circles, the format is symbols(x, y, circle=radius) where x and y and radius are vectors specifying the x and y coordinates and circle radiuses, respectively. You want the areas, rather than the radiuses of the circles, to be proportional to the values of a third variable. Given the formula for the radius of a circle (r A= π ) the proper call is symbols(x, y, circle=sqrt(z/pi)) where z is the third variable to be plotted. Let’s apply this to the mtcars data, plotting car weight on the x-axis, miles per gallon on the y-axis, and engine displacement as the bubble size. The following code attach(mtcars) r <- sqrt(disp/pi) symbols(wt, mpg, circle=r, inches=0.30, fg="white", bg="lightblue", Download from Wow! eBook Scatter plots 279 main="Bubble Plot with point size proportional to displacement", ylab="Miles Per Gallon", xlab="Weight of Car (lbs/1000)") text(wt, mpg, rownames(mtcars), cex=0.6) detach(mtcars) produces the graph in figure 11.16. The option inches is a scaling factor that can be used to control the size of the circles (the default is to make the largest circle 1 inch). The text() function is optional. Here it is used to add the names of the cars to the plot. From the figure, you can see that increased gas mileage is associated with both decreased car weight and engine displacement. In general, statisticians involved in the R project tend to avoid bubble plots for the same reason they avoid pie charts. Humans typically have a harder time making judgments about volume than distance. But bubble charts are certainly popular in the business world, so I’m including them here for completeness. l’ve certainly had a lot to say about scatter plots. This attention to detail is due, in part, to the central place that scatter plots hold in data analysis. While simple, they can help you visualize your data in an immediate and straightforward manner, uncovering relationships that might otherwise be missed. 1 0 1 5 2 0 2 5 3 0 3 5 Bubble Plot with point size pr opor tional to displacement W eight of Car (lbs/1000) M i l e s P e r G a l l o n Mazda RX4 Mazda RX4 W ag Datsun 710 Hor net 4 D ri ve Hor net Spor tabout V aliant Duster 360 Merc 240D Merc 230 Merc 280 Merc 280C Merc 450S E Merc 450S L Merc 450SLC Cadillac FllleetwoodLinco n Continental Chr ysler Imper ial Fiat 128 Honda Civic To y ota Corolla To y ota Corona Dodge Challenger AMC Jav elin Camaro Z28 P ontiac Firebird Fiat X1−9 P orsche 914−2 Lotus Europa F ord P antera L F errar i Dino Maserati Bor a V olv o 142E Figure 11.16 Bubble plot of car weight versus mpg where point size is proportional to engine displacement Download from Wow! eBook 280 CHAPTER 11 Intermediate graphs 11.2 Line charts If you connect the points in a scatter plot moving from left to right, you have a line plot. The dataset Orange that come with the base installation contains age and cir- cumference data for five orange trees. Consider the growth of the first orange tree, depicted in figure 11.17. The plot on the left is a scatter plot, and the plot on the right is a line chart. As you can see, line charts are particularly good vehicles for conveying change. The graphs in figure 11.17 were created with the code in the following listing. Listing 11.3 Creating side-by-side scatter and line plots opar <- par(no.readonly=TRUE) par(mfrow=c(1,2)) t1 <- subset(Orange, Tree==1) plot(t1$age, t1$circumference, xlab="Age (days)", ylab="Circumference (mm)", main="Orange Tree 1 Growth") plot(t1$age, t1$circumference, xlab="Age (days)", ylab="Circumference (mm)", main="Orange Tree 1 Growth", type="b") par(opar) You’ve seen the elements that make up this code in chapter 3, so I won’t go into details here. The main difference between the two plots in figure 11.17 is produced by the option type="b". In general, line charts are created with one of the following two functions plot(x, y, type=) lines(x, y, type=) 500 1000 1500 4 0 6 0 8 0 1 0 0 1 2 0 1 4 0 Orange Tree 1 Growth Age (days) C i r c u m f e r e n c e ( m m ) 500 1000 1500 4 0 6 0 8 0 1 0 0 1 2 0 1 4 0 Orange Tree 1 Growth Age (days) C i r c u m f e r e n c e ( m m ) Figure 11.17 Comparison of a scatter plot and a line plot Download from Wow! eBook Line charts 281 where x and y are numeric vectors of (x,y) points to connect. The option type= can take the values described in table 11.1. Table 11.1 Line chart options Type What is plotted p Points only l Lines only o Over-plotted points (that is, lines overlaid on top of points) b, c Points (empty if c) joined by lines s, SStair steps h Histogram-line vertical lines n Doesn’t produce any points or lines (used to set up the axes for later commands) Examples of each type are given in figure 11.18. As you can see, type="p" produces the typical scatter plot. The option type="b" is the most common for line charts. The difference between b and c is whether the points appear or gaps are left instead. Both type="s" and type="S" produce stair steps (step functions). The first runs, then rises, whereas the second rises, then runs. 1 2 3 4 5 12345 type= "p" x y 1 2 3 4 5 12345 type= "l" x y 1 2 3 4 5 12345 type= "o" x y 1 2 3 4 5 12345 type= "b" x y 1 2 3 4 5 12345 type= "c" x y 1 2 3 4 5 12345 type= "s" x y 1 2 3 4 5 12345 type= "S" x y 1 2 3 4 5 12345 type= "h" x y Figure 11.18 type= options in the plot() and lines() functions Download from Wow! eBook 282 CHAPTER 11 Intermediate graphs There’s an important difference between the p lot() and l ines() functions. The plot() function will create a new graph when invoked. The lines() function adds information to an existing graph but can’t produce a graph on its own. Because of this, the lines() function is typically used after a plot() command has produced a graph. If desired, you can use the type="n" option in the plot() function to set up the axes, titles, and other graph features, and then use the lines() function to add various lines to the plot. To demonstrate the creation of a more complex line chart, let’s plot the growth of all five orange trees over time. Each tree will have its own distinctive line. The code is shown in the next listing and the results in figure 11.19. Listing 11.4 Line chart displaying the growth of five orange trees over time Orange$Tree <- as.numeric(Orange$Tree) ntrees <- max(Orange$Tree) xrange <- range(Orange$age) yrange <- range(Orange$circumference) plot(xrange, yrange, type="n", xlab="Age (days)", ylab="Circumference (mm)" ) colors <- rainbow(ntrees) linetype <- c(1:ntrees) plotchar <- seq(18, 18+ntrees, 1) for (i in 1:ntrees) { tree <- subset(Orange, Tree==i) lines(tree$age, tree$circumference, type="b", lwd=2, lty=linetype[i], col=colors[i], pch=plotchar[i] ) } title("Tree Growth", "example of line plot") legend(xrange[1], yrange[2], 1:ntrees, cex=0.8, col=colors, pch=plotchar, lty=linetype, title="Tree" ) Convert factor to numeric for convenience Set up plot Add lines Add legend Download from Wow! eBook Correlograms 283 500 1000 1500 5 0 1 0 0 1 5 0 2 0 0 Age (da ys) C i r c u m f e r e n c e ( m m ) T ree Gr o wth e xample of line plot Tr ee 1 2 3 4 5 Figure 11.19 Line chart displaying the growth of five orange trees In listing 11.4, the plot() function is used to set up the graph and specify the axis labels and ranges but plots no actual data. The lines() function is then used to add a separate line and set of points for each orange tree. You can see that tree 4 and tree 5 demonstrated the greatest growth across the range of days measured, and that tree 5 overtakes tree 4 at around 664 days. Many of the programming conventions in R that I discussed in chapters 2, 3, and 4 are used in listing 11.4. You may want to test your understanding by working through each line of code and visualizing what it’s doing. If you can, you are on your way to becoming a serious R programmer (and fame and fortune is near at hand)! In the next section, you’ll explore ways of examining a number of correlation coefficients at once. 11.3 Correlograms Correlation matrices are a fundamental aspect of multivariate statistics. Which vari- ables under consideration are strongly related to each other and which aren’t? Are there clusters of variables that relate in specific ways? As the number of variables grow, such questions can be harder to answer. Correlograms are a relatively recent tool for visualizing the data in correlation matrices. It’s easier to explain a correlogram once you’ve seen one. Consider the correlations among the variables in the mtcars data frame. Here you have 11 variables, each measuring some aspect of 32 automobiles. You can get the correlations using the following code: > options(digits=2) > cor(mtcars) Download from Wow! eBook 284 CHAPTER 11 Intermediate graphs mpg cyl disp hp drat wt qsec vs am gear carb mpg 1.00 -0.85 -0.85 -0.78 0.681 -0.87 0.419 0.66 0.600 0.48 -0.551 cyl -0.85 1.00 0.90 0.83 -0.700 0.78 -0.591 -0.81 -0.523 -0.49 0.527 disp -0.85 0.90 1.00 0.79 -0.710 0.89 -0.434 -0.71 -0.591 -0.56 0.395 hp -0.78 0.83 0.79 1.00 -0.449 0.66 -0.708 -0.72 -0.243 -0.13 0.750 drat 0.68 -0.70 -0.71 -0.45 1.000 -0.71 0.091 0.44 0.713 0.70 -0.091 wt -0.87 0.78 0.89 0.66 -0.712 1.00 -0.175 -0.55 -0.692 -0.58 0.428 qsec 0.42 -0.59 -0.43 -0.71 0.091 -0.17 1.000 0.74 -0.230 -0.21 -0.656 vs 0.66 -0.81 -0.71 -0.72 0.440 -0.55 0.745 1.00 0.168 0.21 -0.570 am 0.60 -0.52 -0.59 -0.24 0.713 -0.69 -0.230 0.17 1.000 0.79 0.058 gear 0.48 -0.49 -0.56 -0.13 0.700 -0.58 -0.213 0.21 0.794 1.00 0.274 carb -0.55 0.53 0.39 0.75 -0.091 0.43 -0.656 -0.57 0.058 0.27 1.000 Which variables are most related? Which variables are relatively independent? Are there any patterns? It isn’t that easy to tell from the correlation matrix without signifi- cant time and effort (and probably a set of colored pens to make notations). You can display that same correlation matrix using the c orrgram() function in the c orrgram package (see figure 11.20). The code is: library(corrgram) corrgram(mtcars, order=TRUE, lower.panel=panel.shade, upper.panel=panel.pie, text.panel=panel.txt, main="Correlogram of mtcars intercorrelations") To interpret this graph, start with the lower triangle of cells (the cells below the princi- pal diagonal). By default, a blue color and hashing that goes from lower left to upper right represents a positive correlation between the two variables that meet at that cell. Conversely, a red color and hashing that goes from the upper left to the lower right rep- resents a negative correlation. The darker and more saturated the color, the greater the magnitude of the correlation. Weak correlations, near zero, will appear washed out. In the current graph, the rows and columns have been reordered (using principal compo- nents analysis) to cluster variables together that have similar correlation patterns. Figure 11.20 Correlogram of the correlations among the variables in the mtcars data frame. Rows and columns have been reordered using principal components analysis. Download from Wow! eBook Correlograms 285 You can see from shaded cells that gear, am, drat, and mpg are positively correlated with one another. You can also see that wt, disp, cyl, hp, and carb are positively cor- related with one another. But the first group of variables is negatively correlated with the second group of variables. You can also see that the correlation between carb and am is weak, as is the correlation between vs and gear, vs and am, and drat and qsec. The upper triangle of cells displays the same information using pies. Here, color plays the same role, but the strength of the correlation is displayed by the size of the filled pie slice. Positive correlations fill the pie starting at 12 o’clock and moving in a clockwise direction. Negative correlations fill the pie by moving in a counterclockwise direction. The format of the corrgram() function is corrgram(x, order=, panel=, text.panel=, diag.panel=) where x is a data frame with one observation per row. When order=TRUE, the variables are reordered using a principal component analysis of the correlation matrix. Reor- dering can help make patterns of bivariate relationships more obvious. The option p anel specifies the type of off-diagonal panels to use. Alternatively, you can use the options l ower.panel and u pper.panel to choose different options below and above the main diagonal. The t ext.panel and d iag.panel options refer to the main diagonal. Allowable values for panel are described in table 11.2. Table 11.2 Panel options for the corrgram() function Placement Panel Option Description Off diagonal p anel.pie The filled portion of the pie indicates the magnitude of the correlation. p anel.shade The depth of the shading indicates the magnitude of the correlation. p anel.ellipse A confidence ellipse and smoothed line are plotted. p anel.pts A scatter plot is plotted. Main diagonal p anel.minmax The minimum and maximum values of the variable are printed. p anel.txt The variable name is printed. Let’s try a second example. The code library(corrgram) corrgram(mtcars, order=TRUE, lower.panel=panel.ellipse, upper.panel=panel.pts, text.panel=panel.txt, diag.panel=panel.minmax, main="Correlogram of mtcars data using scatter plots and ellipses") produces the graph in figure 11.21. Here you’re using smoothed fit lines and confi- dence ellipses in the lower triangle and scatter plots in the upper triangle. Download from Wow! eBook 286 CHAPTER 11 Intermediate graphs Figure 11.21 Correlogram of the correlations among the variables in the mtcars data frame. The lower triangle contains smoothed best fit lines and confidence ellipses, and the upper triangle contains scatter plots. The diagonal panel contains minimum and maximum values. Rows and columns have been reordered using principal components analysis. Why do the scatter plots look odd? Several of the variables that are plotted in figure 11.21 have limited allowable val- ues. For example, the number of gears is 3, 4, or 5. The number of cylinders is 4, 6, or 8. Both am (transmission type) and vs (V/S) are dichotomous. This explains the odd-looking scatter plots in the upper diagonal. Always be careful that the statistical methods you choose are appropriate to the form of the data. Specifying these variables as ordered or unordered factors can serve as a useful check. When R knows that a variable is categorical or ordi- nal, it attempts to apply statistical methods that are appropriate to that level of measurement. Download from Wow! eBook Correlograms 287 We’ll finish with one more example. The code library(corrgram) corrgram(mtcars, lower.panel=panel.shade, upper.panel=NULL, text.panel=panel.txt, main="Car Mileage Data (unsorted)") produces the graph in figure 11.22. Here we’re using shading in the lower triangle, keeping the original variable order, and leaving the upper triangle blank. Before moving on, I should point out that you can control the colors used by the corrgram() function. To do so, specify four colors in the c olorRampPalette() function within the c ol.corrgram() function. Here’s an example: library(corrgram) col.corrgram <- function(ncol){ colorRampPalette(c("darkgoldenrod4", "burlywood1", "darkkhaki", "darkgreen"))(ncol)} corrgram(mtcars, order=TRUE, lower.panel=panel.shade, upper.panel=panel.pie, text.panel=panel.txt, main="A Corrgram (or Horse) of a Different Color") Try it and see what you get. Correlograms can be a useful way to examine large numbers of bivariate relationships among quantitative variables. Because they’re relatively new, the greatest challenge is to educate the recipient on how to interpret them. To learn more, see M ichael Friendly’s article “Corrgrams: Exploratory Displays for Correlation Matrices,” available at http://www.math.yorku.ca/SCS/Papers/corrgram.pdf. Figure 11.22 Correlogram of the correlations among the variables in the mtcars data frame. The lower triangle is shaded to represent the magnitude and direction of the correlations. The variables are plotted in their original order. Car Mileage Data (unsor ted) Download from Wow! eBook 288 CHAPTER 11 Intermediate graphs 11.4 Mosaic plots Up to this point, we’ve been exploring methods of visualizing relationships among quantitative/continuous variables. But what if your variables are categorical? When you’re looking at a single categorical variable, you can use a bar or pie chart. If there are two categorical variables, you can look at a 3D bar chart (which, by the way, is not so easy to do in R). But what do you do if there are more than two categorical variables? One approach is to use mosaic plots. In a mosaic plot, the frequencies in a multidimensional contingency table are represented by nested rectangular regions that are proportional to their cell frequency. Color and or shading can be used to represent residuals from a fitted model. For details, see Meyer, Zeileis and Hornick (2006), or Michael Friendly’s Statistical Graphics page ( http://datavis.ca). S teve Simon has created a good conceptual tutorial on how mosaic plots are created, available at http://www.childrensmercy.org/stats/definitions/mosaic.htm. Mosaic plots can be created with the m osaic() function from the v cd library (there’s a m osaicplot() function in the basic installation of R, but I recommend you use the v cd package for its more extensive features). As an example, consider the Titanic dataset available in the base installation. It describes the number of passengers who survived or died, cross-classified by their class (1st, 2nd, 3rd, Crew), sex (Male, Female), and age (Child, Adult). This is a well-studied dataset. You can see the cross- classification using the following code: > ftable(Titanic) Survived No Yes Class Sex Age 1st Male Child 0 5 Adult 118 57 Female Child 0 1 Adult 4 140 2nd Male Child 0 11 Adult 154 14 Female Child 0 13 Adult 13 80 3rd Male Child 35 13 Adult 387 75 Female Child 17 14 Adult 89 76 Crew Male Child 0 0 Adult 670 192 Female Child 0 0 Adult 3 20 The mosaic() function can be invoked as mosaic(table) where table is a contingency table in array form, or mosaic(formula, data=) where formula is a standard R formula, and data specifies either a data frame or table. Adding the option shade=TRUE will color the figure based on Pearson residuals from Download from Wow! eBook Mosaic plots 289 a fitted model (independence by default) and the option legend=TRUE will display a legend for these residuals. For example, both library(vcd) mosaic(Titanic, shade=TRUE, legend=TRUE) and library(vcd) mosaic(~Class+Sex+Age+Survived, data=Titanic, shade=TRUE, legend=TRUE) will produce the graph shown in figure 11.23. The formula version gives you greater control over the selection and placement of variables in the graph. There’s a great deal of information packed into this one picture. For example, as one moves from crew to first class, the survival rate increases precipitously. Most children were in third and second class. Most females in first class survived, whereas only about half the females in third class survived. There were few females in the crew, causing the Survived labels (No, Yes at the bottom of the chart) to overlap for this group. Keep looking and you’ll see many more interesting facts. Remember to look at the relative widths and heights of the rectangles. What else can you learn about that night? Pearson residuals: p-value = < 2.22e-16 Sex Survived C l a s s A g e C r e w No Yes A d u l t NoYes C h i l d 3 r d A d u l t C h i l d 2 n d A d u l t C h i l d 1 s t Male Female A d u l t C h i l d -10.8 -4.0 -2.0 0.0 2.0 4.0 25.7 Figure 11.23 Mosaic plot describing Titanic survivors by class, sex, and age Download from Wow! eBook 290 CHAPTER 11 Intermediate graphs Extended mosaic plots add color and shading to represent the residuals from a fit- ted model. In this example, the blue shading indicates cross-classifications that occur more often than expected, assuming that survival is unrelated to class, gender, and age. Red shading indicates cross-classifications that occur less often than expected un- der the independence model. Be sure to run the example so that you can see the re- sults in color. The graph indicates that more first-class women survived and more male crew members died than would be expected under an independence model. Fewer third-class men survived than would be expected if survival was independent of class, gender, and age. If you would like to explore mosaic plots in greater detail, try running example(mosaic). 11.5 Summary In this chapter, we considered a wide range of techniques for displaying relationships among two or more variables. This included the use of 2D and 3D scatter plots, scatter plot matrices, bubble plots, line plots, correlograms, and mosaic plots. Some of these methods are standard techniques, while some are relatively new. Taken together with methods that allow you to customize graphs (chapter 3), display univariate distributions (chapter 6), explore regression models (chapter 8), and visualize group differences (chapter 9), you now have a comprehensive toolbox for visualizing and extracting meaning from your data. In later chapters, you’ll expand your skills with additional specialized techniques, including graphics for latent variable models (chapter 14), methods for visualizing missing data patterns (chapter 15), and techniques for creating graphs that are conditioned on one or more variables (chapter 16). In the next chapter, we’ll explore resampling statistics and bootstrapping. These are computer intensive methods that allow you to analyze data in new and unique ways. Download from Wow! eBook 12 291 12Resampling statistics and bootstrapping This chapter covers ■ Understanding the logic of permutation tests ■ Using bootstrapping to obtain confidence intervals Applying permutation tests to linear models ■ In chapters 7, 8, and 9, we reviewed statistical methods that test hypotheses and esti- mate confidence intervals for population parameters by assuming that the observed data is sampled from a normal distribution or some other well-known theoretical distribution. But there will be many cases in which this assumption is unwarranted. Statistical approaches based on randomization and resampling can be used in cases where the data is 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. In this chapter, we’ll explore two broad statistical approaches that use randomization: permutation tests and bootstrapping. Historically, these methods were only available to experienced programmers and expert statisticians. Contributed packages in R now make them readily available to a wider audience of data analysts. Download from Wow! eBook 292 CHAPTER 12 Resampling statistics and bootstrapping We’ll also revisit problems that were initially analyzed using traditional methods (for example, t-tests, chi-square tests, ANOVA, regression) and see how they can be approached using these robust, computer-intensive methods. To get the most out of section 12.2, be sure to read chapter 7 first. Chapters 8 and 9 serve as prerequisites for section 12.3. Other sections can be read on their own. 12.1 Permutation tests Permutation tests, also called randomization or re-randomization tests, have been around for decades, but it took the advent of high-speed computers to make them practically available. To understand the logic of a permutation test, consider the following hypothetical problem. Ten subjects have been randomly assigned to one of two treatment conditions (A or B) and an outcome variable (score) has been recorded. The results of the experiment are presented in table 12.1. The data are also displayed in the strip chart in figure 12.1. Is there enough evidence to conclude that the treatments differ in their impact? In a parametric approach, you might assume that the data are sampled from normal populations with equal variances and apply a two-tailed independent groups t-test. The null hypothesis is that the population mean for treatment A is equal to the population mean for treatment B. You’d calculate a t-statistic from the data and compare it to the theoretical distribution. If the observed t-statistic is sufficiently extreme, say outside the middle 95 percent of values in the theoretical distribution, you’d reject the null hypothesis and declare that the population means for the two groups are unequal at the 0.05 level of significance. score T r e a t m e n t A B 40 45 50 55 60 65 Figure 12.1 Strip chart of the hypothetical treatment data in table 12.1 Table 12.1 Hypothetical two-group problem Treatment ATreatment B 40 57 57 64 45 55 55 62 58 65 Download from Wow! eBook Permutation tests 293 A permutation test takes a different approach. If the two treatments are truly equivalent, the label (Treatment A or Treatment B) assigned to an observed score is arbitrary. To test for differences between the two treatments, we could follow these steps: 1 Calculate the observed t-statistic, as in the parametric approach; call this t0. 2 Place all 10 scores in a single group. 3 Randomly assign five scores to Treatment A and five scores to Treatment B. 4 Calculate and record the new observed t-statistic. 5 Repeat steps 3–4 for every possible way of assigning five scores to Treatment A and five scores to Treatment B. There are 252 such possible arrangements. 6 Arrange the 252 t-statistics in ascending order. This is the empirical distribution, based on (or conditioned on) the sample data. 7 If t0 falls outside the middle 95 percent of the empirical distribution, reject the null hypothesis that the population means for the two treatment groups are equal at the 0.05 level of significance. Notice that the same t-statistic is calculated in both the permutation and parametric approaches. But instead of comparing the statistic to a theoretical distribution in order to determine if it was extreme enough to reject the null hypothesis, it’s compared to an empirical distribution created from permutations of the observed data. This logic can be extended to most classical statistical tests and linear models. In the previous example, the empirical distribution was based on all possible permutations of the data. In such cases, the permutation test is called an “exact” test. As the sample sizes increase, the time required to form all possible permutations can become prohibitive. In such cases, you can use Monte Carlo simulation to sample from all possible permutations. Doing so provides an approximate test. If you’re uncomfortable assuming that the data is normally distributed, concerned about the impact of outliers, or feel that the dataset is too small for standard parametric approaches, a permutation test provides an excellent alternative. R has some of the most comprehensive and sophisticated packages for performing permutation tests currently available. The remainder of this section focuses on two contributed packages: the coin package and the lmPerm package. Be sure to install them before first use: install.packages(c(“coin”,"lmPerm")) The coin package provides a comprehensive framework for permutation tests applied to independence problems, whereas the lmPerm package provides permutation tests for ANOVA and regression designs. We’ll consider each in turn, and end the section with a quick review of other permutation packages available in R. Before moving on, it’s important to remember that permutation tests use pseudo- random numbers to sample from all possible permutations (when performing an approximate test). Therefore, the results will change each time the test is performed. Setting the random number seed in R allows you to fix the random numbers generated. Download from Wow! eBook 294 CHAPTER 12 Resampling statistics and bootstrapping This is particularly useful when you want to share your examples with others, because results will always be the same if the calls are made with the same seed. Setting the random number seed to 1234 (that is, set.seed(1234)) will allow you to replicate the results presented in this chapter. 12.2 Permutation test with the coin package The coin package provides a general framework for applying permutation tests to independence problems. With this package, we can answer such questions as ■ Are responses independent of group assignment? ■ Are two categorical variables independent? Are two numeric variables independent? ■ Using convenience functions provided in the package (see table 12.2), we can per- form permutation test equivalents for most of the traditional statistical tests covered in chapter 7. Table 12.2 coin functions providing permutation test alternatives to traditional tests Test coin function Two- and K-sample permutation test oneway_test(y ~ A) Two- and K-sample permutation test with a stratification (blocking) factor oneway_test(y ~ A | C) Wilcoxon–Mann–Whitney rank sum test wilcox_test(y ~ A ) Kruskal–Wallis test kruskal_test(y ~ A) Person’s chi-square test chisq_test(A ~ B) Cochran–Mantel–Haenszel test cmh_test(A ~ B | C) Linear-by-linear association test lbl_test(D ~ E) Spearman’s test spearman_test(y ~ x) Friedman test friedman_test(y ~ A | C) Wilcoxon–Signed–Rank test wilcoxsign_test(y1 ~ y2) In the coin function column, y and x are numeric variables, A and B are categorical factors, C is a categorical blocking variable, D and E are ordered factors, and y1 and y2 are matched numeric variables. Each of the functions listed in table 12.2 take the form function_name( formula, data, distribution= ) where ■ formula describes the relationship among variables to be tested. Examples are given in the table. ■ data identifies a data frame. ■ distribution specifies how the empirical distribution under the null hypothesis should be derived. Possible values are exact, asymptotic, and approximate. Download from Wow! eBook Permutation test with the coin package 295 If distribution="exact", the distribution under the null hypothesis is computed exactly (that is, from all possible permutations). The distribution can also be approximated by its asymptotic distribution (distribution="asymptotic") or via Monte Carlo resampling (distribution="approximate(B=#)"), where # indicates the number of replications used to approximate the exact distribution. At present, distribution="exact" is only available for two-sample problems. NOTE In the coin package, categorical variables and ordinal variables must be coded as factors and ordered factors, respectively. Additionally, the data must be stored in a data frame. In the remainder of this section, we’ll apply several of the permutation tests described in table 12.2 to problems from previous chapters. This will allow you to compare the results with more traditional parametric and nonparametric approaches. We’ll end this discussion of the coin package by considering advanced extensions. 12.2.1 Independent two-sample and k-sample tests To begin, compare an independent samples t-test with a one-way exact test applied to the hypothetical data in table 12.2. The results are given in the following listing. Listing 12.1 t-test versus one-way permutation test for the hypothetical data > library(coin) > score <- c(40, 57, 45, 55, 58, 57, 64, 55, 62, 65) > treatment <- factor(c(rep("A",5), rep("B",5))) > mydata <- data.frame(treatment, score) > t.test(score~treatment, data=mydata, var.equal=TRUE) Two Sample t-test data: score by treatment t = -2.3, df = 8, p-value = 0.04705 alternative hypothesis: true difference in means is not equal to 0 95 percent confidence interval: -19.04 -0.16 sample estimates: mean in group A mean in group B 51 61 > oneway_test(score~treatment, data=mydata, distribution="exact") Exact 2-Sample Permutation Test data: score by treatment (A, B) Z = -1.9, p-value = 0.07143 alternative hypothesis: true mu is not equal to 0 The traditional t-test indicates a significant group difference (p < .05), whereas the exact test doesn’t (p > 0.072). With only 10 observations, l’d be more inclined to trust the results of the permutation test and attempt to collect more data before reaching a final conclusion. Download from Wow! eBook 296 CHAPTER 12 Resampling statistics and bootstrapping Next, consider the Wilcoxon–Mann–Whitney U test. In chapter 7, we examined the difference in the probability of imprisonment in Southern versus non-Southern US states using the wilcox.test() function. Using an exact Wilcoxon rank sum test, we’d get > library(MASS) > UScrime <- transform(UScrime, So = factor(So)) > wilcox_test(Prob ~ So, data=UScrime, distribution="exact") Exact Wilcoxon Mann-Whitney Rank Sum Test data: Prob by So (0, 1) Z = -3.7, p-value = 8.488e-05 alternative hypothesis: true mu is not equal to 0 suggesting that incarceration is more likely in Southern states. Note that in the previ- ous code, the numeric variable So was transformed into a factor. This is because the coin package requires that all categorical variables be coded as factors. Additionally, the astute reader may have noted that these results agree exactly with the results of the wilcox.test() in chapter 7. This is because the wilcox.test() also computes an exact distribution by default. Finally, consider a k-sample test. In chapter 9, we used a one-way ANOVA to evaluate the impact of five drug regimens on cholesterol reduction in a sample of 50 patients. An approximate k-sample permutation test can be performed instead, using this code: > library(multcomp) > set.seed(1234) > oneway_test(response~trt, data=cholesterol, distribution=approximate(B=9999)) Approximative K-Sample Permutation Test data: response by trt (1time, 2times, 4times, drugD, drugE) maxT = 4.7623, p-value < 2.2e-16 Here, the reference distribution is based on 9,999 permutations of the data. The ran- dom number seed was set so that your results would be the same as mine. There’s clearly a difference in response among patients in the various groups. 12.2.2 Independence in contingency tables We can use permutation tests to assess the independence of two categorical variables using either the chisq_test() or the cmh_test() function. The latter function is used when the data is stratified on a third categorical variable. If both variables are ordinal, we can use the lbl_test() function to test for a linear trend. In chapter 7, we applied a chi-square test to assess the relationship between Arthritis treatment and improvement. Treatment had two levels (Placebo, Treated), and Improved had three levels (None, Some, Marked). The Improved variable was encoded as an ordered factor. Download from Wow! eBook Permutation test with the coin package 297 If you want to perform a permutation version of the chi-square test, you could use the following code: > library(coin) > library(vcd) > Arthritis <- transform(Arthritis, Improved=as.factor(as.numeric(Improved))) > set.seed(1234) > chisq_test(Treatment~Improved, data=Arthritis, distribution=approximate(B=9999)) Approximative Pearson’s Chi-Squared Test data: Treatment by Improved (1, 2, 3) chi-squared = 13.055, p-value = 0.0018 This gives you an approximate chi-square test based on 9,999 replications. You might ask why you transformed the variable Improved from an ordered factor to a categorical factor. (Good question!) If you’d left it an ordered factor, coin() would have gener- ated a linear x linear trend test instead of a chi-square test. Although a trend test would be a good choice in this situation, keeping it a chi-square test allows you to compare the results with those reported in chapter 7. 12.2.3 Independence between numeric variables The spearman_test() function provides a permutation test of the independence of two numeric variables. In chapter 7, we examined the correlation between illiteracy rates and murder rates for US states. You can test the association via permutation, us- ing the following code: > states <- as.data.frame(state.x77) > set.seed(1234) > spearman_test(Illiteracy~Murder, data=states, distribution=approximate(B=9999)) Approximative Spearman Correlation Test data: Illiteracy by Murder Z = 4.7065, p-value < 2.2e-16 alternative hypothesis: true mu is not equal to 0 Based on an approximate permutation test with 9,999 replications, the hypothesis of independence can be rejected. Note that state.x77 is a matrix. It had to be converted into a data frame for use in the coin package. 12.2.4 Dependent two-sample and k-sample tests Dependent sample tests are used when observations in different groups have been matched, or when repeated measures are used. For permutation tests with two paired groups, the wilcoxsign_test() function can be used. For more than two groups, use the friedman_test() function. Download from Wow! eBook 298 CHAPTER 12 Resampling statistics and bootstrapping In chapter 7, we compared the unemployment rate for urban males age 14–24 (U1) with urban males age 35–39 (U2). Because the two variables are reported for each of the 50 US states, you have a two-dependent groups design (state is the matching variable). We can use an exact Wilcoxon Signed Rank Test to see if unemployment rates for the two age groups are equal: > library(coin) > library(MASS) > wilcoxsign_test(U1~U2, data=UScrime, distribution="exact") Exact Wilcoxon-Signed-Rank Test data: y by x (neg, pos) stratified by block Z = 5.9691, p-value = 1.421e-14 alternative hypothesis: true mu is not equal to 0 Based on the results, you’d conclude that the unemployment rates differ. 12.2.5 Going further The coin package provides a general framework for testing that one group of vari- ables is independent of a second group of variables (with optional stratification on a blocking variable) against arbitrary alternatives, via approximate permutation tests. In particular, the independence_test() function allows the user to approach most traditional tests from a permutation perspective, and to create new and novel statisti- cal tests for situations not covered by traditional methods. This flexibility comes at a price: a high level of statistical knowledge is required to use the function appropriately. See the vignettes that accompany the package (accessed via vignette("coin")) for further details. In the next section, you’ll learn about the lmPerm package. This package provides a permutation approach to linear models, including regression and analysis of variance. 12.3 Permutation tests with the lmPerm package The lmPerm package provides support for a permutation approach to linear models. In particular, the lmp() and aovp() functions are the lm() and aov() functions modi- fied to perform permutation tests rather than normal theory tests. The parameters within the lmp() and aovp() functions are similar to those in the lm() and aov()functions, with the addition of a perm= parameter. The perm= option can take on the values "Exact", "Prob", or "SPR". Exact produces an exact test, based on all possible permutations. Prob samples from all possible permutations. Sampling continues until the estimated standard deviation falls below 0.1 of the estimated p-value. The stopping rule is controlled by an optional Ca parameter. Finally, SPR uses a sequential probability ratio test to decide when to stop sampling. Note that if the number of observations is greater than 10, perm="Exact" will automatically default to perm="Prob"; exact tests are only available for small problems. Download from Wow! eBook Permutation tests with the lmPerm package 299 To see how this works, we’ll apply a permutation approach to simple regression, polynomial regression, multiple regression, one-way analysis of variance, one-way analysis of covariance, and a two-way factorial design. 12.3.1 Simple and polynomial regression In chapter 8, we used linear regression to study the relationship between weight and height for a group of 15 women. Using lmp() instead of lm() generates the permuta- tion test results shown in the following listing. Listing 12.2 Permutation tests for simple linear regression > library(lmPerm) > set.seed(1234) > fit <- lmp(weight~height, data=women, perm="Prob") [1] "Settings: unique SS : numeric variables centered" > summary(fit) Call: lmp(formula = weight ~ height, data = women, perm = "Prob") Residuals: Min 1Q Median 3Q Max -1.733 -1.133 -0.383 0.742 3.117 Coefficients: Estimate Iter Pr(Prob) height 3.45 5000 <2e-16 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Residual standard error: 1.5 on 13 degrees of freedom Multiple R-Squared: 0.991, Adjusted R-squared: 0.99 F-statistic: 1.43e+03 on 1 and 13 DF, p-value: 1.09e-14 To fit a quadratic equation, you could use the code in this next listing. Listing 12.3 Permutation tests for polynomial regression > library(lmPerm) > set.seed(1234) > fit <- lmp(weight~height + I(height^2), data=women, perm="Prob") [1] "Settings: unique SS : numeric variables centered" > summary(fit) Call: lmp(formula = weight ~ height + I(height^2), data = women, perm = "Prob") Residuals: Min 1Q Median 3Q Max -0.5094 -0.2961 -0.0094 0.2862 0.5971 Coefficients: Estimate Iter Pr(Prob) Download from Wow! eBook 300 CHAPTER 12 Resampling statistics and bootstrapping height -7.3483 5000 <2e-16 *** I(height^2) 0.0831 5000 <2e-16 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Residual standard error: 0.38 on 12 degrees of freedom Multiple R-Squared: 0.999, Adjusted R-squared: 0.999 F-statistic: 1.14e+04 on 2 and 12 DF, p-value: <2e-16 As you can see, it’s a simple matter to test these regressions using permutation tests and requires little change in the underlying code. The output is also similar to that produced by the lm() function. Note that an Iter column is added indicating how many iterations were required to reach the stopping rule. 12.3.2 Multiple regression In chapter 8, multiple regression was used to predict the murder rate from popula- tion, illiteracy, income, and frost for 50 US states. Applying the lmp() function to this problem, results in the following output. Listing 12.4 Permutation tests for multiple regression > library(lmPerm) > set.seed(1234) > states <- as.data.frame(state.x77) > fit <- lmp(Murder~Population + Illiteracy+Income+Frost, data=states, perm="Prob") [1] "Settings: unique SS : numeric variables centered" > summary(fit) Call: lmp(formula = Murder ~ Population + Illiteracy + Income + Frost, data = states, perm = "Prob") Residuals: Min 1Q Median 3Q Max -4.79597 -1.64946 -0.08112 1.48150 7.62104 Coefficients: Estimate Iter Pr(Prob) Population 2.237e-04 51 1.0000 Illiteracy 4.143e+00 5000 0.0004 *** Income 6.442e-05 51 1.0000 Frost 5.813e-04 51 0.8627 --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '. ' 0.1 ' ' 1 Residual standard error: 2.535 on 45 degrees of freedom Multiple R-Squared: 0.567, Adjusted R-squared: 0.5285 F-statistic: 14.73 on 4 and 45 DF, p-value: 9.133e-08 Looking back to chapter 8, both Population and Illiteracy are significant (p < 0.05) when normal theory is used. Based on the permutation tests, the Population Download from Wow! eBook Permutation tests with the lmPerm package 301 variable is no longer significant. When the two approaches don’t agree, you should look at your data more carefully. It may be that the assumption of normality is unten- able or that outliers are present. 12.3.3 One-way ANOVA and ANCOVA Each of the analysis of variance designs discussed in chapter 9 can be performed via permutation tests. First, let’s look at the one-way ANOVA problem considered in sec- tions 9.1 on the impact of treatment regimens on cholesterol reduction. The code and results are given in the next listing. Listing 12.5 Permutation test for One-Way ANOVA > library(lmPerm) > library(multcomp) > set.seed(1234) > fit <- aovp(response~trt, data=cholesterol, perm="Prob") [1] "Settings: unique SS " > summary(fit) Component 1 : Df R Sum Sq R Mean Sq Iter Pr(Prob) trt 4 1351.37 337.84 5000 < 2.2e-16 *** Residuals 45 468.75 10.42 --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '. ' 0.1 ' ' 1 The results suggest that the treatment effects are not all equal. This second example in this section applies a permutation test to a one-way analysis of covariance. The problem is from chapter 9, where you investigated the impact of four drug doses on the litter weights of rats, controlling for gestation times. The next listing shows the permutation test and results. Listing 12.6 Permutation test for one-way ANCOVA > library(lmPerm) > set.seed(1234) > fit <- aovp(weight ~ gesttime + dose, data=litter, perm="Prob") [1] "Settings: unique SS : numeric variables centered" > summary(fit) Component 1 : Df R Sum Sq R Mean Sq Iter Pr(Prob) gesttime 1 161.49 161.493 5000 0.0006 *** dose 3 137.12 45.708 5000 0.0392 * Residuals 69 1151.27 16.685 --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Based on the p-values, the four drug doses do not equally impact litter weights, control- ling for gestation time. Download from Wow! eBook 302 CHAPTER 12 Resampling statistics and bootstrapping 12.3.4 Two-way ANOVA We’ll end this section by applying permutation tests to a factorial design. In chapter 9, we examined the impact of vitamin C on the tooth growth in guinea pigs. The two manipulated factors were dose (three levels) and delivery method (two levels). Ten guinea pigs were placed in each treatment combination, resulting in a balanced 3 x 2 factorial design. The permutation tests are provided in the next listing. Listing 12.7 Permutation test for two-way ANOVA > library(lmPerm) > set.seed(1234) > fit <- aovp(len~supp*dose, data=ToothGrowth, perm="Prob") [1] "Settings: unique SS : numeric variables centered" > summary(fit) Component 1 : Df R Sum Sq R Mean Sq Iter Pr(Prob) supp 1 205.35 205.35 5000 < 2e-16 *** dose 1 2224.30 2224.30 5000 < 2e-16 *** supp:dose 1 88.92 88.92 2032 0.04724 * Residuals 56 933.63 16.67 --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 At the .05 level of significance, all three effects are statistically different from zero. At the .01 level, only the main effects are significant. It’s important to note that when aovp() is applied to ANOVA designs, it defaults to unique sums of squares (also called SAS Type III sums of squares). Each effect is adjusted for every other effect. The default for parametric ANOVA designs in R is sequential sums of squares (SAS Type I sums of squares). Each effect is adjusted for those that appear earlier in the model. For balanced designs, the two approaches will agree, but for unbalanced designs with unequal numbers of observations per cell, they won’t. The greater the imbalance, the greater the disagreement. If desired, specifying seqs=TRUE in the aovp() function will produce sequential sums of squares. For more on Type I and Type III sums of squares, see chapter 9, section 9.2. 12.4 Additional comments on permutation tests R offers other permutation packages besides coin and lmPerm. The perm package pro- vides some of the same functionality provided by the coin package and can act as an independent validation of that package. The corrperm package provides permutation tests of correlations with repeated measures. The logregperm package offers a per- mutation test for logistic regression. Perhaps most importantly, the glmperm package extends permutation tests to generalized linear models. Generalized linear models are described in the next chapter. Permutation tests provide a powerful alternative to tests that rely on a knowledge of the underlying sampling distribution. In each of the permutation tests described, we were able to test statistical hypotheses without recourse to the normal, t, F, or chi- square distributions. Download from Wow! eBook Bootstrapping 303 You may have noticed how closely the results of the tests based on normal theory agreed with the results of the permutation approach in previous sections. The data in these problems were well behaved and the agreement between methods is a testament to how well normal theory methods work in such cases. Where permutation tests really shine are in cases where the data is clearly non- normal (for example, highly skewed), outliers are present, samples sizes are small, or no parametric tests exist. However, if the original sample is a poor representation of the population of interest, no test, including permutation tests, will improve the inferences generated. Permutation tests are primarily useful for generating p-values that can be used to test null hypotheses. They can help answer the question, “Does an effect exist?” It’s more difficult to use permutation methods to obtain confidence intervals and estimates of measurement precision. Fortunately, this is an area in which bootstrapping excels. 12.5 Bootstrapping Bootstrapping generates an empirical distribution of a test statistic or set of test statis- tics, by repeated random sampling with replacement, from the original sample. It al- lows you to generate confidence intervals and test statistical hypotheses without having to assume a specific underlying theoretical distribution. It’s easiest to demonstrate the logic of bootstrapping with an example. Say that you want to calculate the 95 percent confidence interval for a sample mean. Your sample has 10 observations, a sample mean of 40, and a sample standard deviation of 5. If you’re willing to assume that the sampling distribution of the mean is normally distributed, the (1-α/2 )% confidence interval can be calculated using X t s n X t s n− < < + where t is the upper 1-α/2 critical value for a t distribution with n-1 degrees of free- dom. For a 95 percent confidence interval, you have 40 – 2.262(5/3.163) < µ < 40 + 2.262(5/3.162) or 36.424 < µ < 43.577. You’d expect 95 percent of confidence intervals created in this way to surround the true population mean. But what if you aren’t willing to assume that the sampling distribution of the mean is normally distributed? You could use a bootstrapping approach instead: 1 Randomly select 10 observations from the sample, with replacement after each selection. Some observations may be selected more than once, and some may not be selected at all. 2 Calculate and record the sample mean. 3 Repeat steps 1 and 2 a thousand times. 4 Order the 1,000 sample means from smallest to largest. 5 Find the sample means representing the 2.5th and 97.5th percentiles. In this case, it’s the 25th number from the bottom and top. These are your 95 percent confidence limits. In the present case, where the sample mean is likely to be normally distributed, you gain little from the bootstrap approach. Yet there are many cases where the bootstrap Download from Wow! eBook 304 CHAPTER 12 Resampling statistics and bootstrapping approach is advantageous. What if you wanted confidence intervals for the sample median, or the difference between two sample medians? There are no simple normal theory formulas here, and bootstrapping is the approach of choice. If the underlying distributions are unknown, if outliers are a problem, if sample sizes are small, or if parametric approaches don’t exist, bootstrapping can often provide a useful method of generating confidence intervals and testing hypotheses. 12.6 Bootstrapping with the boot package The boot package provides extensive facilities for bootstrapping and related resam- pling methods. You can bootstrap a single statistic (for example, a median), or a vector of statistics (for example, a set of regression coefficients). Be sure to download and install the boot package before first use: install.packages("boot") The bootstrapping process will seem complicated, but once you review the examples it should make sense. In general, bootstrapping involves three main steps: 1 Write a function that returns the statistic or statistics of interest. If there is a single statistic (for example, a median), the function should return a number. If there is a set of statistics (for example, a set of regression coefficients), the function should return a vector. 2 Process this function through the boot() function in order to generate R bootstrap replications of the statistic(s). 3 Use the boot.ci() function to obtain confidence intervals for the statistic(s) generated in step 2. Now to the specifics. The main bootstrapping function is boot(). The boot() function has the format bootobject <- boot(data=, statistic=, R=, ...) The parameters are described in table 12.3. Table 12.3 Parameters of the boot() function Parameter Description data A vector, matrix, or data frame. statistic A function that produces the k statistics to be bootstrapped (k=1 if bootstrapping a single statistic). The function should include an indices parameter that the boot() function can use to select cases for each replication (see examples in the text). RNumber of bootstrap replicates. ...Additional parameters to be passed to the function that is used to produce statistic(s) of interest. Download from Wow! eBook Bootstrapping with the boot package 305 The boot() function calls the statistic function R times. Each time, it generates a set of random indices, with replacement, from the integers 1:nrow(data). These indices are used within the statistic function to select a sample. The statistics are calculated on the sample and the results are accumulated in the bootobject. The bootobject structure is described in table 12.4. Table 12.4 Elements of the object returned by the boot() function Element Description t0 The observed values of k statistics applied to the original data t An R x k matrix where each row is a bootstrap replicate of the k statistics You can access these elements as bootobject$t0 and bootobject$t. Once you generate the bootstrap samples, you can use print() and plot() to examine the results. If the results look reasonable, you can use the boot.ci() function to obtain confidence intervals for the statistic(s). The format is boot.ci(bootobject, conf=, type= ) The parameters are given in table 12.5. Table 12.5 Parameters of the boot.ci() function Parameter Description bootobject The object returned by the boot() function. conf The desired confidence interval (default: conf=0.95). type The type of confidence interval returned. Possible values are "norm", "basic", "stud", "perc", "bca", and "all" (default: type="all"). The type parameter specifies the method for obtaining the confidence limits. The perc method (percentile) was demonstrated in the sample mean example. The bca provides an interval that makes simple adjustments for bias. I find bca preferable in most circum- stances. See Mooney and Duval (1993) for an introduction to these methods. In the remaining sections, we’ll look at bootstrapping a single statistic and a vector of statistics. 12.6.1 Bootstrapping a single statistic The mtcars dataset contains information on 32 automobiles reported in the 1974 Motor Trend magazine. Suppose you’re using multiple regression to predict miles per gallon from a car’s weight (lb/1,000) and engine displacement (cu. in.). In addition to the standard regression statistics, you’d like to obtain a 95 percent confidence interval for the R-squared value (the percent of variance in the response variable explained by the predictors). The confidence interval can be obtained using nonparametric boot- strapping. Download from Wow! eBook 306 CHAPTER 12 Resampling statistics and bootstrapping The first task is to write a function for obtaining the R-squared value: rsq <- function(formula, data, indices) { d <- data[indices,] fit <- lm(formula, data=d) return(summary(fit)$r.square) } The function returns the R-square value from a regression. The d <- data[indices,] statement is required for boot() to be able to select samples. You can then draw a large number of bootstrap replications (say, 1,000) with the following code: library(boot) set.seed(1234) results <- boot(data=mtcars, statistic=rsq, R=1000, formula=mpg~wt+disp) The boot object can be printed using > print(results) ORDINARY NONPARAMETRIC BOOTSTRAP Call: boot(data = mtcars, statistic = rsq, R = 1000, formula = mpg ~ wt + disp) Bootstrap Statistics : original bias std. error t1* 0.7809306 0.01333670 0.05068926 and plotted using plot(results). The resulting graph is shown in figure 12.2. In figure 12.2, you can see that the distribution of bootstrapped R-squared values isn’t normally distributed. A 95 percent confidence interval for the R-squared values can be obtained using > boot.ci(results, type=c("perc", "bca")) BOOTSTRAP CONFIDENCE INTERVAL CALCULATIONS Based on 1000 bootstrap replicates CALL : boot.ci(boot.out = results, type = c("perc", "bca")) Intervals : Level Percentile BCa 95% ( 0.6838, 0.8833 ) ( 0.6344, 0.8549 ) Calculations and Intervals on Original Scale Some BCa intervals may be unstable You can see from this example that different approaches to generating the confi- dence intervals can lead to different intervals. In this case the bias adjusted interval is Download from Wow! eBook Bootstrapping with the boot package 307 Histogram of t t* D e n s i t y 0.6 0.7 0.8 0.9 0 2 4 6 8 −3 −2 −1 0 1 2 3 0 . 6 0 0 . 6 5 0 . 7 0 0 . 7 5 0 . 8 0 0 . 8 5 0 . 9 0 Quantiles of Standard Normal t * Figure 12.2 Distribution of bootstrapped R-squared values moderately different from the percentile method. In either case, the null hypothesis H0: R-square = 0, would be rejected, because zero is outside the confidence limits. In this section, we estimated the confidence limits of a single statistic. In the next section, we’ll estimate confidence intervals for several statistics. 12.6.2 Bootstrapping several statistics In the previous example, bootstrapping was used to estimate the confidence interval for a single statistic (R-squared). Continuing the example, let’s obtain the 95 percent confidence intervals for a vector of statistics. Specifically, let’s get confidence intervals for the three model regression coefficients (intercept, car weight, and engine displace- ment). First, create a function that returns the vector of regression coefficients: bs <- function(formula, data, indices) { d <- data[indices,] fit <- lm(formula, data=d) return(coef(fit)) } Then use this function to bootstrap 1,000 replications: Download from Wow! eBook 308 CHAPTER 12 Resampling statistics and bootstrapping library(boot) set.seed(1234) results <- boot(data=mtcars, statistic=bs, R=1000, formula=mpg~wt+disp) > print(results) ORDINARY NONPARAMETRIC BOOTSTRAP Call: boot(data = mtcars, statistic = bs, R = 1000, formula = mpg ~ wt + disp) Bootstrap Statistics : original bias std. error t1* 34.9606 0.137873 2.48576 t2* -3.3508 -0.053904 1.17043 t3* -0.0177 -0.000121 0.00879 When bootstrapping multiple statistics, add an index parameter to the plot() and boot.ci() functions to indicate which column of bootobject$t to analyze. In this ex- ample, index 1 refers to the intercept, index 2 is car weight, and index 3 is the engine displacement. To plot the results for car weight, use plot(results, index=2) The graph is given in figure 12.3. To get the 95 percent confidence intervals for car weight and engine displacement, use > boot.ci(results, type="bca", index=2) BOOTSTRAP CONFIDENCE INTERVAL CALCULATIONS Based on 1000 bootstrap replicates CALL : boot.ci(boot.out = results, type = "bca", index = 2) Figure 12.3 Distribution of bootstrapping regression coefficients for car weight Histogram of t t* D e n s i t y −6 −4 −2 0 0 . 0 0 . 1 0 . 2 0 . 3 0 . 4 −3 −2 −1 0 1 2 3 − 6 − 5 − 4 − 3 − 2 − 1 0 Quantiles of Standard Normal t * Download from Wow! eBook Summary 309 Intervals : Level BCa 95% (-5.66, -1.19 ) Calculations and Intervals on Original Scale > boot.ci(results, type="bca", index=3) BOOTSTRAP CONFIDENCE INTERVAL CALCULATIONS Based on 1000 bootstrap replicates CALL : boot.ci(boot.out = results, type = "bca", index = 3) Intervals : Level BCa 95% (-0.0331, 0.0010 ) Calculations and Intervals on Original Scale NOTE In the previous example, we resampled the entire sample of data each time. If we assume that the predictor variables have fixed levels (typical in planned experiments), we’d do better to only resample residual terms. See Mooney and Duval (1993, pp. 16–17) for a simple explanation and algorithm. Before we leave bootstrapping, it’s worth addressing two questions that come up often: ■ How many replications are needed? How large does the original sample need to be? ■ There’s no simple answer to the first question. Some say that an original sample size of 20–30 is sufficient for good results, as long as the sample is representative of the popu- lation. Random sampling from the population of interest is the most trusted method for assuring the original sample’s representativeness. With regard to the second ques- tion, I find that 1,000 replications are more than adequate in most cases. Computer power is cheap and you can always increase the number of replications if desired. There are many helpful sources of information on permutation tests and bootstrapping. An excellent starting place is an online article by Yu (2003). Good (2006) provides a comprehensive overview of resampling in general and includes R code. A good, accessible introduction to the bootstrap is provided by Mooney and Duval (1993). The definitive source on bootstrapping is Efron and Tibshirani (1998). Finally, there are a number of great online resources, including Simon (1997), Canty (2002), Shah (2005), and Fox (2002). 12.7 Summary In this chapter, we introduced a set of computer-intensive methods based on random- ization and resampling that allow you to test hypotheses and form confidence intervals without reference to a known theoretical distribution. They’re particularly valuable when your data comes from unknown population distributions, when there are serious Download from Wow! eBook 310 CHAPTER 12 Resampling statistics and bootstrapping outliers, when your sample sizes are small, and when there are no existing parametric methods to answer the hypotheses of interest. The methods in this chapter are particularly exciting because they provide an avenue for answering questions when your standard data assumptions are clearly untenable, or when you have no other idea how to approach the problem. Permutation tests and bootstrapping aren’t panaceas, though. They can’t turn bad data into good data. If your original samples aren’t representative of the population of interest, or are too small to accurately reflect it, then these techniques won’t help. In the next chapter, we’ll consider data models for variables that follow known, but not necessarily normal, distributions. Download from Wow! eBook Part 4 Advanced methods In this final section, we consider advanced methods of statistical and graphi- cal analysis to round out your data analysis toolkit. Chapter 13 expands on the regression methods in chapter 8 to cover parametric approaches to data that aren’t normally distributed. The chapter starts with a discussion of the general- ized linear model, and then focuses on cases where we’re trying to predict an outcome variable that’s either categorical (logistic regression) or a count (pois- son regression). Dealing with a large number of variables can be challenging, due to the complexity inherent in multivariate data. Chapter 14 describes two popular methods for exploring and simplifying multivariate data. Principal components analysis can be used to transform a large number of correlated variables into a smaller set of composite variables. Factor analysis consists of a set of techniques for uncovering the latent structure underlying a given set of variables. Chapter 14 provides step-by-step instructions for carrying out each. More often than not, researchers must deal with incomplete datasets. 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 approaches are described here, along with guidance around which ones to use, and which ones to avoid. Chapter 16 completes our discussion of graphics with presentations of some of R’s most advanced and useful approaches to visualizing data. This includes visual representations of complex data using the lattice package, and an introduction to the new, and increasingly popular, ggplot2 package. The chapter ends with a review of packages that provide functions for interacting with graphs in real-time. Download from Wow! eBook After completing part 4, you will have the tools to manage a wide range of complex data analysis problems. This includes modeling non-normal outcome variables, dealing with large numbers of correlated variables, and handling messy and incomplete data. Additionally, you will have the tools to visualize complex data in useful, innovative and creative ways. Download from Wow! eBook 313 13Generalized linear models This chapter covers .n Formulating a generalized linear model .n Predicting categorical outcomes .n Modeling count data In chapters 8 (regression) and 9 (ANOVA), we explored linear models that can be used to predict a normally distributed response variable from a set of continuous and/or categorical predictor variables. But there are many situations in which it’s unreasonable to assume that the dependent variable is normally distributed (or even continuous). For example: .n The outcome variable may be categorical. Binary variables (for example, yes/ no, passed/failed, lived/died) and polytomous variables (for example, poor/ good/excellent, republican/democrat/independent) are clearly not normal- ly distributed. .n The outcome variable may be a count (for example, number of traffic acci- dents in a week, number of drinks per day). Such variables take on a limited number of values and are never negative. Additionally, their mean and vari- ance are often related (which isn’t true for normally distributed variables). Download from Wow! eBook 14 Chapter 13 Generalized linear models Generalized linear models extend the linear model framework to include dependent vari- ables that are decidedly non-normal. In this chapter, we’ll start with a brief overview of generalized linear models and the glm() function used to estimate them. Then we’ll focus on two popular models within this framework: logistic regression (where the dependent variable is categorical) and Poisson regression (where the dependent variable is a count variable). To motivate the discussion, we’ll apply generalized linear models to two research questions that aren’t easily addressed with standard linear models: .n What personal, demographic, and relationship variables predict marital infidel- ity? In this case, the outcome variable is binary (affair/no affair). .n What impact does a drug treatment for seizures have on the number of seizures experienced over an eight-week period? In this case, the outcome variable is a count (number of seizures). We’ll apply logistic regression to address the first question and Poisson regression to address the second. Along the way, we’ll consider extensions of each technique. 13.1 Generalized linear models and the glm() function A wide range of popular data analytic methods are subsumed within the framework of the generalized linear model. In this section we’ll briefly explore some of the theory behind this approach. You can safely skip over this section if you like and come back to it later. Let’s say that you want to model the relationship between a response variable Y and a set of p predictor variables X1 ...Xp . In the standard linear model, you assume that Y is normally distributed and that the form of the relationship is This equation states that the conditional mean of the response variable is a linear com- bination of the predictor variables. The bj are the parameters specifying the expected change in Y for a unit change in Xj and b0 is the expected value of Y when all the pre- dictor variables are 0. You’re saying that you can predict the mean of the Y distribution for observations with a given set of X values by applying the proper weights to the X variables and adding them up. Note that you’ve made no distributional assumptions about the predictor variables, Xj. Unlike Y, there’s no requirement that they be normally distributed. In fact, they’re often categorical (for example, ANOVA designs). Additionally, nonlinear functions of the predictors are allowed. You often include such predictors as X 2 or X1 × X2. What is important is that the equation is linear in the parameters (b0, b1,... bp ). In generalized linear models, you fit models of the form where g(µY) is a function of the conditional mean (called the link function). Addition- ally, you relax the assumption that Y is normally distributed. Instead, you assume that Download from Wow! eBook eneralized linear models and the glm() function 315 Y follows a distribution that’s a member of the exponential family. You specify the link function and the probability distribution, and the parameters are derived through an iterative maximum likelihood estimation procedure. 13.1.1 The glm() function Generalized linear models are typically fit in R through the glm() function (although other specialized functions are available). The form of the function is similar to lm() but includes additional parameters. The basic format of the function is glm(formula, family=family(link=function), data=) where the probability distribution (family) and corresponding default link function (function) are given in table 13.1. Table 13.1 glm() parameters Family Default link function binomial (link = "logit") gaussian (link = "identity") gamma (link = "inverse") inverse.gaussian (link = "1/mu^2") poisson (link = "log") quasi (link = "identity", variance = "constant") quasibinomial (link = "logit") quasipoisson (link = "log") The glm() function allows you to fit a number of popular models, including logistic regression, Poisson regression, and survival analysis (not considered here). You can demonstrate this for the first two models as follows. Assume that you have a single response variable (Y), three predictor variables (X1, X2, X3), and a data frame (my- data) containing the data. Logistic regression is applied to situations in which the response variable is dichotomous (0,1). The model assumes that Y follows a binomial distribution, and that you can fit a linear model of the form where p = mY is the conditional mean of Y (that is, the probability that Y = 1 given a set of X values), (p/1 – p) is the odds that Y = 1, and log(p/1 – p) is the log odds, or logit. In this case, log(p/1 – p) is the link function, the probability distribution is binomial, and the logistic regression model can be fit using glm(Y~X1+X2+X3, family=binomial(link="logit"), data=mydata) Logistic regression is described more fully in section 13.2. Download from Wow! eBook 16 Chapter 13 Generalized linear models Poisson regression is applied to situations in which the response variable is the number of events to occur in a given period of time. The Poisson regression model assumes that Y follows a Poisson distribution, and that you can fit a linear model of the form where l is the mean (and variance) of Y. In this case, the link function is log(l), the probability distribution is Poisson, and the Poisson regression model can be fit using glm(Y~X1+X2+X3, family=poisson(link="log"), data=mydata) Poisson regression is described in section 13.3. It is worth noting that the standard linear model is also a special case of the generalized linear model. If you let the link function g(mY ) = mY or the identity function and specify that the probability distribution is normal (Gaussian), then glm(Y~X1+X2+X3, family=gaussian(link="identity"), data=mydata) would produce the same results as lm(Y~X1+X2+X3, data=mydata) To summarize, generalized linear models extend the standard linear model by fitting a function of the conditional mean response (rather than the conditional mean re- sponse), and assuming that the response variable follows a member of the exponential family of distributions (rather than being limited to the normal distribution). The parameter estimates are derived via maximum likelihood rather than least squares. 13.1.2 Supporting functions Many of the functions that you used in conjunction with lm() when analyzing standard linear models have corresponding versions for glm(). Some commonly used functions are given in table 13.2. We’ll explore examples of these functions in later sections. In the next section, we’ll briefly consider the assessment of model adequacy. Table 13.2 Functions that support glm() Function Description summary()Displays detailed results for the fitted model coefficients(), coef()Lists the model parameters (intercept and slopes) for the fitted model confint()Provides confidence intervals for the model parameters (95 percent by default) residuals()Lists the residual values for a fitted model anova()Generates an ANOVA table comparing two fitted models plot()Generates diagnostic plots for evaluating the fit of a model predict()Uses a fitted model to predict response values for a new dataset Download from Wow! eBook ogistic regression 317 13.1.3 Model fit and regression diagnostics The assessment of model adequacy is as important for generalized linear models as it is for standard (OLS) linear models. Unfortunately, there’s less agreement in the statisti- cal community regarding appropriate assessment procedures. In general, you can use the techniques described in chapter 8, with the following caveats. When assessing model adequacy, you’ll typically want to plot predicted values expressed in the metric of the original response variable against residuals of the deviance type. For example, a common diagnostic plot would be plot(predict(model, type="response"), residuals(model, type= "deviance")) where model is the object returned by the glm() function. The hat values, studentized residuals, and Cook’s D statistics that R provides will be approximate values. Additionally, there’s no general consensus on cutoff values for identifying problematic observations. Values have to be judged relative to each other. One approach is to create index plots for each statistic and look for unusually large values. For example, you could use the following code to create three diagnostic plots: plot(hatvalues(model)) plot(rstudent(model)) plot(cooks.distance(model)) Alternatively, you could use the code library(car) influencePlot(model) to create one omnibus plot. In the latter graph, the horizontal axis is the leverage, the vertical axis is the studentized residual, and the plotted symbol is proportional to the Cook’s distance. Diagnostic plots tend to be most helpful when the response variable takes on many values. When the response variable can only take on a limited number of values (for example, logistic regression), their utility is decreased. For more on regression diagnostics for generalized linear models, see Fox (2008) and Faraway (2006). In the remaining portion of this chapter, we’ll consider two of the most popular forms of the generalized linear model in detail: logistic regression and Poisson regression. 13.2 Logistic regression Logistic regression is useful when predicting a binary outcome from a set of continu- ous and/or categorical predictor variables. To demonstrate this, we’ll explore the data on infidelity contained in the data frame Affairs, provided with the AER package. Be sure to download and install the package (using install.packages("AER")) before first use. The infidelity data, known as Fair’s Affairs, is based on a cross-sectional survey conducted by Psychology Today in 1969, and is described in Greene (2003) and Fair Download from Wow! eBook 18 Chapter 13 Generalized linear models (1978). It contains nine variables collected on 601 participants and includes how often the respondent engaged in extramarital sexual intercourse during the past year, as well as their gender, age, years married, whether or not they had children, their religiousness (on a 5-point scale from 1=anti to 5=very), education, occupation (Hollingshead 7-point classification with reverse numbering), and a numeric self- rating of their marriage (from 1=very unhappy to 5=very happy). Let’s look at some descriptive statistics: > data(Affairs, package="AER") > summary(Affairs) affairs gender age yearsmarried children Min. : 0.000 female:315 Min. :17.50 Min. : 0.125 no :171 1st Qu.: 0.000 male :286 1st Qu.:27.00 1st Qu.: 4.000 yes:430 Median : 0.000 Median :32.00 Median : 7.000 Mean : 1.456 Mean :32.49 Mean : 8.178 3rd Qu.: 0.000 3rd Qu.:37.00 3rd Qu.:15.000 Max. :12.000 Max. :57.00 Max. :15.000 religiousness education occupation rating Min. :1.000 Min. : 9.00 Min. :1.000 Min. :1.000 1st Qu.:2.000 1st Qu.:14.00 1st Qu.:3.000 1st Qu.:3.000 Median :3.000 Median :16.00 Median :5.000 Median :4.000 Mean :3.116 Mean :16.17 Mean :4.195 Mean :3.932 3rd Qu.:4.000 3rd Qu.:18.00 3rd Qu.:6.000 3rd Qu.:5.000 Max. :5.000 Max. :20.00 Max. :7.000 Max. :5.000 > table(Affairs$affairs) 0 1 2 3 7 12 451 34 17 19 42 38 From these statistics, you can see that that 52 percent of respondents were female, that 72 percent had children, and that the median age for the sample was 32 years. With regard to the response variable, 75 percent of respondents reported not engaging in an infidelity in the past year (451/601). The largest number of encounters reported was 12 (6 percent). Although the number of indiscretions was recorded, our interest here is in the binary outcome (had an affair/didn’t have an affair). You can transform affairs into a dichotomous factor called ynaffair with the following code. > Affairs$ynaffair[Affairs$affairs > 0] <- 1 > Affairs$ynaffair[Affairs$affairs == 0] <- 0 > Affairs$ynaffair <- factor(Affairs$ynaffair, levels=c(0,1), labels=c("No","Yes")) > table(Affairs$ynaffair) No Yes 451 150 This dichotomous factor can now be used as the outcome variable in a logistic regres- sion model: > fit.full <- glm(ynaffair ~ gender + age + yearsmarried + children + religiousness + education + occupation +rating, data=Affairs,family=binomial()) Download from Wow! eBook ogistic regression 319 > summary(fit.full) Call: glm(formula = ynaffair ~ gender + age + yearsmarried + children + religiousness + education + occupation + rating, family = binomial(), data = Affairs) Deviance Residuals: Min 1Q Median 3Q Max -1.571 -0.750 -0.569 -0.254 2.519 Coefficients: Estimate Std. Error z value Pr(>|z|) (Intercept) 1.3773 0.8878 1.55 0.12081 gendermale 0.2803 0.2391 1.17 0.24108 age -0.0443 0.0182 -2.43 0.01530 * yearsmarried 0.0948 0.0322 2.94 0.00326 ** childrenyes 0.3977 0.2915 1.36 0.17251 religiousness -0.3247 0.0898 -3.62 0.00030 *** education 0.0211 0.0505 0.42 0.67685 occupation 0.0309 0.0718 0.43 0.66663 rating -0.4685 0.0909 -5.15 2.6e-07 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 (Dispersion parameter for binomial family taken to be 1) Null deviance: 675.38 on 600 degrees of freedom Residual deviance: 609.51 on 592 degrees of freedom AIC: 627.5 Number of Fisher Scoring iterations: 4 From the p-values for the regression coefficients (last column), you can see that gen- der, presence of children, education, and occupation may not make a significant con- tribution to the equation (you can’t reject the hypothesis that the parameters are 0). Let’s fit a second equation without them, and test whether this reduced model fits the data as well: > fit.reduced <- glm(ynaffair ~ age + yearsmarried + religiousness + rating, data=Affairs, family=binomial()) > summary(fit.reduced) Call: glm(formula = ynaffair ~ age + yearsmarried + religiousness + rating, family = binomial(), data = Affairs) Deviance Residuals: Min 1Q Median 3Q Max -1.628 -0.755 -0.570 -0.262 2.400 Coefficients: Estimate Std. Error z value Pr(>|z|) (Intercept) 1.9308 0.6103 3.16 0.00156 ** age -0.0353 0.0174 -2.03 0.04213 * Download from Wow! eBook 20 Chapter 13 Generalized linear models yearsmarried 0.1006 0.0292 3.44 0.00057 *** religiousness -0.3290 0.0895 -3.68 0.00023 *** rating -0.4614 0.0888 -5.19 2.1e-07 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 (Dispersion parameter for binomial family taken to be 1) Null deviance: 675.38 on 600 degrees of freedom Residual deviance: 615.36 on 596 degrees of freedom AIC: 625.4 Number of Fisher Scoring iterations: 4 Each regression coefficient in the reduced model is statistically significant (p<.05). Because the two models are nested (fit.reduced is a subset of fit.full), you can use the anova() function to compare them. For generalized linear models, you’ll want a chi-square version of this test. > anova(fit.reduced, fit.full, test="Chisq") Analysis of Deviance Table Model 1: ynaffair ~ age + yearsmarried + religiousness + rating Model 2: ynaffair ~ gender + age + yearsmarried + children + religiousness + education + occupation + rating Resid. Df Resid. Dev Df Deviance P(>|Chi|) 1 596 615 2 592 610 4 5.85 0.21 The nonsignificant chi-square value (p=0.21) suggests that the reduced model with four predictors fits as well as the full model with nine predictors, reinforcing your belief that gender, children, education, and occupation don’t add significantly to the prediction above and beyond the other variables in the equation. Therefore, you can base your interpretations on the simpler model. 13.2.1 Interpreting the model parameters Let’s take a look at the regression coefficients: > coef(fit.reduced) (Intercept) age yearsmarried religiousness rating 1.931 -0.035 0.101 -0.329 -0.461 In a logistic regression, the response being modeled is the log(odds) that Y=1. The regression coefficients give the change in log(odds) in the response for a unit change in the predictor variable, holding all other predictor variables constant. Because log(odds) are difficult to interpret, you can exponentiate them to put the results on an odds scale: > exp(coef(fit.reduced)) (Intercept) age yearsmarried religiousness rating 6.895 0.965 1.106 0.720 0.630 Download from Wow! eBook ogistic regression 321 Now you can see that the odds of an extramarital encounter are increased by a factor of 1.106 for a one-year increase in years married (holding age, religiousness, and marital rating constant). Conversely, the odds of an extramarital affair are multiplied by a fac- tor of 0.965 for every year increase in age. The odds of an extramarital affair increase with years married, and decrease with age, religiousness, and marital rating. Because the predictor variables can’t equal 0, the intercept isn’t meaningful in this case. If desired, you can use the confint() function to obtain confidence intervals for the coefficients. For example, exp(confint(fit.reduced)) would print 95 percent confidence intervals for each of the coefficients on an odds scale. Finally, a one-unit change in a predictor variable may not be inherently interesting. For binary logistic regression, the change in the odds of the higher value on the response variable for an n unit change in a predictor variable is exp(bj)^n. If a one-year increase in years married multiplies the odds of an affair by 1.106, a 10-year increase would increase the odds by a factor of 1.106^10, or 2.7, holding the other predictor variables constant. 13.2.2 Assessing the impact of predictors on the probability of an outcome For many of us, it’s easier to think in terms of probabilities than odds. You can use the predict() function to observe the impact of varying the levels of a predictor variable on the probability of the outcome. The first step is to create an artificial dataset con- taining the values of the predictor variables that you’re interested in. Then you can use this artificial dataset with the predict() function to predict the probabilities of the outcome event occurring for these values. Let’s apply this strategy to assess the impact of marital ratings on the probability of having an extramarital affair. First, create an artificial dataset, where age, years married, and religiousness are set to their means, and marital rating varies from 1 to 5. > testdata <- data.frame(rating=c(1, 2, 3, 4, 5), age=mean(Affairs$age), yearsmarried=mean(Affairs$yearsmarried), religiousness=mean(Affairs$religiousness)) > testdata rating age yearsmarried religiousness 1 1 32.5 8.18 3.12 2 2 32.5 8.18 3.12 3 3 32.5 8.18 3.12 4 4 32.5 8.18 3.12 5 5 32.5 8.18 3.12 Next, use the test dataset and prediction equation to obtain probabilities: > testdata$prob <- predict(fit.reduced, newdata=testdata, type="response") testdata rating age yearsmarried religiousness prob 1 1 32.5 8.18 3.12 0.530 2 2 32.5 8.18 3.12 0.416 3 3 32.5 8.18 3.12 0.310 4 4 32.5 8.18 3.12 0.220 5 5 32.5 8.18 3.12 0.151 Download from Wow! eBook 22 Chapter 13 Generalized linear models From these results you see that the probability of an extramarital affair decreases from 0.53 when the marriage is rated 1=very unhappy to 0.15 when the marriage is rated 5=very happy (holding age, years married, and religiousness constant). Now look at the impact of age: > testdata <- data.frame(rating=mean(Affairs$rating), age=seq(17, 57, 10), yearsmarried=mean(Affairs$yearsmarried), religiousness=mean(Affairs$religiousness)) > testdata rating age yearsmarried religiousness 1 3.93 17 8.18 3.12 2 3.93 27 8.18 3.12 3 3.93 37 8.18 3.12 4 3.93 47 8.18 3.12 5 3.93 57 8.18 3.12 > testdata$prob <- predict(fit.reduced, newdata=testdata, type="response") > testdata rating age yearsmarried religiousness prob 1 3.93 17 8.18 3.12 0.335 2 3.93 27 8.18 3.12 0.262 3 3.93 37 8.18 3.12 0.199 4 3.93 47 8.18 3.12 0.149 5 3.93 57 8.18 3.12 0.109 Here, you see that as age increases from 17 to 57, the probability of an extramarital encounter decreases from 0.34 to 0.11, holding the other variables constant. Using this approach, you can explore the impact of each predictor variable on the outcome. 13.2.3 Overdispersion The expected variance for data drawn from a binomial distribution is s2 = np(1 - p), where n is the number of observations and p is the probability of belonging to the Y=1 group. Overdispersion occurs when the observed variance of the response variable is larger than what would be expected from a binomial distribution. Overdispersion can lead to distorted test standard errors and inaccurate tests of significance. When overdispersion is present, you can still fit a logistic regression using the glm() function, but in this case, you should use the quasibinomial distribution rather than the binomial distribution. One way to detect overdispersion is to compare the residual deviance with the residual degrees of freedom in your binomial model. If the ratio f = Residual deviance Residual df is considerably larger than 1, you have evidence of overdispersion. Applying this to the Affairs example, you have f = Residual deviance Residual df = 615.36 596 = 1.03 Download from Wow! eBook ogistic regression 323 which is close to 1, suggesting no overdispersion. You can also test for overdispersion. To do this, you fit the model twice, but in the first instance you use family="binomial" and in the second instance you use family="quasibinomial". If the glm() object returned in the first case is called fit and the object returned in the second case is called fit.od, then pchisq(summary(fit.od)$dispersion * fit$df.residual, fit$df.residual, lower = F) provides the p-value for testing the null hypothesis H0: f = 1 versus the alternative hy- pothesis H1: f ≠ 1. If p is small (say, less than 0.05), you’d reject the null hypothesis. Applying this to the Affairs dataset, you have > fit <- glm(ynaffair ~ age + yearsmarried + religiousness + rating, family = binomial(), data = Affairs) > fit.od <- glm(ynaffair ~ age + yearsmarried + religiousness + rating, family = quasibinomial(), data = Affairs) > pchisq(summary(fit.od)$dispersion * fit$df.residual, fit$df.residual, lower = F) [1] 0.34 The resulting p-value (0.34) is clearly not significant (p>0.05), strengthening our be- lief that overdispersion isn’t a problem. We’ll return to the issue of overdispersion when we discuss Poisson regression. 13.2.4 Extensions Several logistic regression extensions and variations are available in R: .n Robust logistic regression —The glmRob() function in the robust package can be used to fit a robust generalized linear model, including robust logistic regres- sion. Robust logistic regression can be helpful when fitting logistic regression models to data containing outliers and influential observations. .n Multinomial logistic regression —If the response variable has more than two unor- dered categories (for example, married/widowed/divorced), you can fit a polyto- mous logistic regression using the mlogit() function in the mlogit package. .n Ordinal logistic regression —If the response variable is a set of ordered categories (for example, credit risk as poor/good/excellent), you can fit an ordinal logis- tic regression using the lrm() function in the rms package. The ability to model a response variable with multiple categories (both ordered and unordered) is an important extension, but it comes at the expense of greater interpre- tive complexity. Assessing model fit and regression diagnostics in these cases will also be more complex. In the Affairs example, the number of extramarital contacts was dichotomized into a yes/no response variable because our interest centered on whether respondents had an affair in the past year. If our interest had been centered on magnitude—the number of encounters in the past year—we would have analyzed the count data directly. One popular approach to analyzing count data is Poisson regression, the next topic we’ll address. Download from Wow! eBook 24 Chapter 13 Generalized linear models 13.3 Poisson regression Poisson regression is useful when you’re predicting an outcome variable representing counts from a set of continuous and/or categorical predictor variables. A comprehen- sive yet accessible introduction to Poisson regression is provided by Coxe, West, and Aiken (2009). To illustrate the fitting of a Poisson regression model, along with some issues that can come up in the analysis, we’ll use the Breslow seizure data (Breslow, 1993) provided in the robust package. Specifically, we’ll consider the impact of an antiepileptic drug treatment on the number of seizures occurring over an eight-week period following the initiation of therapy. Be sure to install the robust package before continuing. Data were collected on the age and number of seizures reported by patients suffering from simple or complex partial seizures during an eight-week period before, and eight- week period after, randomization into a drug or placebo condition. sumY (the number of seizures in the eight-week period post-randomization) is the response variable. Treatment condition (Trt), age in years (Age), and number of seizures reported in the baseline eight-week period (Base) are the predictor variables. The baseline number of seizures and age are included because of their potential effect on the response variable. We are interested in whether or not evidence exists that the drug treatment decreases the number of seizures after accounting for these covariates. First, let’s look at summary statistics for the dataset: > data(breslow.dat, package="robust") > names(breslow.dat) [1] "ID" "Y1" "Y2" "Y3" "Y4" "Base" "Age" "Trt" "Ysum" [10] "sumY" "Age10" "Base4" > summary(breslow.dat[c(6,7,8,10)]) Base Age Trt sumY Min. : 6.0 Min. :18.0 placebo :28 Min. : 0.0 1st Qu.: 12.0 1st Qu.:23.0 progabide:31 1st Qu.: 11.5 Median : 22.0 Median :28.0 Median : 16.0 Mean : 31.2 Mean :28.3 Mean : 33.1 3rd Qu.: 41.0 3rd Qu.:32.0 3rd Qu.: 36.0 Max. :151.0 Max. :42.0 Max. :302.0 Note that although there are 12 variables in the dataset, we’re limiting our attention to the four described earlier. Both the baseline and post-randomization number of sei- zures is highly skewed. Let’s look at the response variable in more detail. The following code produces the graphs in figure 13.1. opar <- par(no.readonly=TRUE) par(mfrow=c(1,2)) attach(breslow.dat) hist(sumY, breaks=20, xlab=”Seizure Count”, main=”Distribution of Seizures”) boxplot(sumY ~ Trt, xlab=”Treatment”, main=”Group Comparisons”) par(opar) Download from Wow! eBook oisson regression 325 Distribution of Seizures Seizure Count F r e q u e n c y 0 50 150 250 05 1 0 1 5 2 0 2 5 3 0 placebo progabide 0 5 0 1 0 0 1 5 0 2 0 0 2 5 0 3 0 0 Group Comparisons Treatment Figure 13.1 Distribution of post-treatment seizure counts (Source: Breslow seizure data) You can clearly see the skewed nature of the dependent variable and the possible pres- ence of outliers. At first glance, the number of seizures in the drug condition appears to be smaller and have a smaller variance. (You’d expect a smaller variance to accom- pany a smaller mean with Poisson distributed data.) Unlike standard OLS regression, this heterogeneity of variance isn’t a problem in Poisson regression. The next step is to fit the Poisson regression: > fit <- glm(sumY ~ Base + Age + Trt, data=breslow.dat, family=poisson()) > summary(fit) Call: glm(formula = sumY ~ Base + Age + Trt, family = poisson(), data = breslow. dat) Deviance Residuals: Min 1Q Median 3Q Max -6.057 -2.043 -0.940 0.793 11.006 Coefficients: Estimate Std. Error z value Pr(>|z|) (Intercept) 1.948826 0.135619 14.37 < 2e-16 *** Base 0.022652 0.000509 44.48 < 2e-16 *** Download from Wow! eBook 26 Chapter 13 Generalized linear models Age 0.022740 0.004024 5.65 1.6e-08 *** Trtprogabide -0.152701 0.047805 -3.19 0.0014 ** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 (Dispersion parameter for poisson family taken to be 1) Null deviance: 2122.73 on 58 degrees of freedom Residual deviance: 559.44 on 55 degrees of freedom AIC: 850.7 Number of Fisher Scoring iterations: 5 The output provides the deviances, regression parameters, standard errors, and tests that these parameters are 0. Note that each of the predictor variables is significant at the p<0.05 level. 13.3.1 Interpreting the model parameters The model coefficients are obtained using the coef() function, or by examining the Coefficients table in the summary() function output: > coef(fit) (Intercept) Base Age Trtprogabide 1.9488 0.0227 0.0227 -0.1527 In a Poisson regression, the dependent variable being modeled is the log of the con- ditional mean loge(l) . The regression parameter 0.0227 for Age indicates that a one- year increase in age is associated with a 0.03 increase in the log mean number of sei- zures, holding baseline seizures and treatment condition constant. The intercept is the log mean number of seizures when each of the predictors equals 0. Because you can’t have a zero age and none of the participants had a zero number of baseline seizures, the intercept isn’t meaningful in this case. It’s usually much easier to interpret the regression coefficients in the original scale of the dependent variable (number of seizures, rather than log number of seizures). To accomplish this, exponentiate the coefficients: > exp(coef(fit)) (Intercept) Base Age Trtprogabide 7.020 1.023 1.023 0.858 Now you see that a one-year increase in age multiplies the expected number of sei- zures by 1.023, holding the other variables constant. This means that increased age is associated with higher numbers of seizures. More importantly, a one-unit change in Trt (that is, moving from placebo to progabide) multiplies the expected number of seizures by 0.86. You’d expect a 20 percent decrease in the number of seizures for the drug group compared with the placebo group, holding baseline number of seizures and age constant. It’s important to remember that, like the exponeniated parameters in logistic Download from Wow! eBook oisson regression 327 regression, the exponeniated parameters in the Poisson model have a multiplicative rather than an additive effect on the response variable. Also, as with logistic regression, you must evaluate your model for overdispersion. 13.3.2 Overdispersion In a Poisson distribution, the variance and mean are equal. Overdispersion occurs in Poisson regression when the observed variance of the response variable is larger than would be predicted by the Poisson distribution. Because overdispersion is often encountered when dealing with count data, and can have a negative impact on the interpretation of the results, we’ll spend some time discussing it. There are several reasons why overdispersion may occur (Coxe et al., 2009): .n The omission of an important predictor variable can lead to overdispersion. .n Overdispersion can also be caused by a phenomenon known as state depen- dence. Within observations, each event in a count is assumed to be independent. For the seizure data, this would imply that for any patient, the probability of a seizure is independent of each other seizure. But this assumption is often unten- able. For a given individual, the probability of having a first seizure is unlikely to be the same as the probability of having a 40th seizure, given that they’ve already had 39. .n In longitudinal studies, overdispersion can be caused by the clustering inherent in repeated measures data. We won’t discuss longitudinal Poisson models here. If overdispersion is present and you don’t account for it in your model, you’ll get stan- dard errors and confidence intervals that are too small, and significance tests that are too liberal (that is, you’ll find effects that aren’t really there). As with logistic regression, overdispersion is suggested if the ratio of the residual deviance to the residual degrees of freedom is much larger than 1. For your seizure data, the ratio is Residual deviance Residual df = 559.44 55 = 10.17 which is clearly much larger than 1. The qcc package provides a test for overdispersion in the Poisson case. (Be sure to download and install this package before first use.) You can test for overdispersion in the seizure data using the following code: > library(qcc) > qcc.overdispersion.test(breslow.dat$sumY, type="poisson") Overdispersion test Obs.Var/Theor.Var Statistic p-value poisson data 62.9 3646 0 Not surprisingly, the significance test has a p-value less than 0.05, strongly suggesting the presence of overdispersion. You can still fit a model to your data using the glm() function, by replacing Download from Wow! eBook 28 Chapter 13 Generalized linear models family="poisson" with family="quasipoisson". Doing so is analogous to our approach to logistic regression when overdispersion is present. > fit.od <- glm(sumY ~ Base + Age + Trt, data=breslow.dat, family=quasipoisson()) > summary(fit.od) Call: glm(formula = sumY ~ Base + Age + Trt, family = quasipoisson(), data = breslow.dat) Deviance Residuals: Min 1Q Median 3Q Max -6.057 -2.043 -0.940 0.793 11.006 Coefficients: Estimate Std. Error t value Pr(>|t|) (Intercept) 1.94883 0.46509 4.19 0.00010 *** Base 0.02265 0.00175 12.97 < 2e-16 *** Age 0.02274 0.01380 1.65 0.10509 Trtprogabide -0.15270 0.16394 -0.93 0.35570 --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 (Dispersion parameter for quasipoisson family taken to be 11.8) Null deviance: 2122.73 on 58 degrees of freedom Residual deviance: 559.44 on 55 degrees of freedom AIC: NA Number of Fisher Scoring iterations: 5 Notice that the parameter estimates in the quasi-Poisson approach are identical to those produced by the Poisson approach. The standard errors are much larger, though. In this case, the larger standard errors have led to p-values for Trt (and Age) that are greater than 0.05. When you take overdispersion into account, there’s insufficient evi- dence to declare that the drug regimen reduces seizure counts more than receiving a placebo, after controlling for baseline seizure rate and age. Please remember that this example is used for demonstration purposes only. The results shouldn’t be taken to imply anything about the efficacy of progabide in the real world. I’m not a doctor—at least not a medical doctor—and I don’t even play one on TV. We’ll finish this exploration of Poisson regression with a discussion of some important variants and extensions. 13.3.3 Extensions R provides several useful extensions to the basic Poisson regression model, including models that allow varying time periods, models that correct for too many zeros, and robust models that are useful when data includes outliers and influential observations. I’ll describe each separately. Download from Wow! eBook oisson regression 329 POISSON REGRESSION WITH VARYING TIME PERIODS Our discussion of Poisson regression has been limited to response variables that measure a count over a fixed length of time (for example, number of seizures in an eight-week period, number of traffic accidents in the past year, number of pro-social behaviors in a day). The length of time is constant across observations. But you can fit Poisson regression models that allow the time period to vary for each observation. In this case, the outcome variable is a rate. To analyze rates, you must include a variable (for example, time) that records the length of time over which the count occurs for each observation. You then change your model from to or equivalently to To fit this new model, you use the offset option in the glm() function. For example, assume that the length of time that patients participated post-randomization in the Breslow study varied from 14 days to 60 days. You could use the rate of seizures as the dependent variable (assuming you had recorded time for each patient in days), and fit the model fit <- glm(sumY ~ Base + Age + Trt, data=breslow.dat, offset= log(time), family=poisson()) where sumY is the number of seizures that occurred post-randomization for a patient dur- ing the time the patient was studied. In this case you’re assuming that rate doesn’t vary over time (for example, 2 seizures in 4 days is equivalent to 10 seizures in 20 days). ZERO-INFLATED POISSON REGRESSION There are times when the number of zero counts in a dataset is larger than would be predicted by the Poisson model. This can occur when there’s a subgroup of the population that would never engage in the behavior being counted. For example, in the Affairs dataset described in the section on logistic regression, the original outcome variable (affairs) counted the number of extramarital sexual intercourse experience participants had in the past year. It’s likely that there’s a subgroup of faithful marital partners who would never have an affair, no matter how long the period of time stud- ied. These are called structural zeros (primarily by the swingers in the group). In such cases, you can analyze the data using an approach called zero-inflated Poisson regression. The approach fits two models simultaneously—one that predicts who would or would not have an affair, and the second that predicts how many affairs a participant Download from Wow! eBook 30 Chapter 13 Generalized linear models would have if you excluded the permanently faithful. Think of this as a model that combines a logistic regression (for predicting structural zeros) and a Poisson regression model (that predicts counts for observations that aren’t structural zeros). Zero-inflated Poisson regression can be fit using the zeroinfl() function in the pscl package. ROBUST POISSON REGRESSION Finally, the glmRob() function in the robust package can be used to fit a robust gener- alized linear model, including robust Poisson regression. As mentioned previously, this can be helpful in the presence of outliers and influential observations. Going further Generalized linear models are a complex and mathematically sophisticated subject, but many fine resources are available for learning about them. A good, short introduction to the topic is Dunteman and Ho (2006). The classic (and advanced) text on generalized linear models is provided by McCullagh and Nelder (1989). Comprehensive and accessible presentations are provided by Dobson and Barnett (2008) and Fox (2008). Faraway (2006) and Fox (2002) provide excellent introductions within the context of R. 13.4 Summary In this chapter, we used generalized linear models to expand the range of approaches available for helping you to understand your data. In particular, the framework allows you to analyze response variables that are decidedly non-normal, including categori- cal outcomes and discrete counts. After briefly describing the general approach, we focused on logistic regression (for analyzing a dichotomous outcome) and Poisson regression (for analyzing outcomes measured as counts or rates). We also discussed the important topic of overdispersion, including how to detect it and how to adjust for it. Finally, we looked at some of the extensions and variations that are available in R. Each of the statistical approaches covered so far has dealt with directly observed and recorded variables. In the next chapter, we’ll look at statistical models that deal with latent variables—unobserved, theoretical variables that you believe underlie and account for the behavior of the variables you do observe. In particular, you’ll see how you can use factor analytic methods to detect and test hypotheses about these unobserved variables. Download from Wow! eBook 331 14Principal components and factor analysis This chapter covers ■ Principal components analysis ■ Other latent variable models Exploratory factor analysis ■ One of the most challenging aspects of multivariate data is the sheer complexity of the information. If you have a dataset with 100 variables, how do you make sense of all the interrelationships present? Even with 20 variables, there are 190 pairwise cor- relations to consider when you’re trying to understand how the individual variables relate to one another. Two related but distinct methodologies for exploring and simplifying complex multivariate data are principal components and exploratory factor analysis. P rincipal components analysis (PCA) is a data reduction technique that transforms a larger number of correlated variables into a much smaller set of uncorrelated variables called principal components. For example, you might use PCA to transform 30 correlated (and possibly redundant) environmental variables into five uncorrelated composite variables that retain as much information from the original set of variables as possible. Download from Wow! eBook 332 CHAPTER 14 Principal components and factor analysis In contrast, e xploratory factor analysis (EFA) is a collection of methods designed to uncover the latent structure in a given set of variables. It looks for a smaller set of underlying or latent constructs that can explain the relationships among the observed or manifest variables. For example, the dataset Harman74.cor contains the correlations among 24 psychological tests given to 145 seventh- and eighth-grade children. If you apply EFA to this data, the results suggest that the 276 test intercorrelations can be explained by the children’s abilities on four underlying factors (verbal ability, processing speed, deduction, and memory). The differences between the PCA and EFA models can be seen in figure 14.1. Principal components (PC1 and PC2) are linear combinations of the observed variables (X1 to X5). The weights used to form the linear composites are chosen to maximize the variance each principal component accounts for, while keeping the components uncorrelated. In contrast, factors (F1 and F2) are assumed to underlie or “cause” the observed variables, rather than being linear combinations of them. The errors (e1 to e5) represent the variance in the observed variables unexplained by the factors. The circles indicate that the factors and errors aren’t directly observable but are inferred from the correlations among the variables. In this example, the curved arrow between the factors indicates that they’re correlated. Correlated factors are common, but not required, in the EFA model. The methods described in this chapter require large samples to derive stable solutions. What constitutes an adequate sample size is somewhat complicated. Until recently, analysts used rules of thumb like “factor analysis requires 5–10 times as many subjects as variables.” Recent studies suggest that the required sample size depends on the number of factors, the number of variables associated with each factor, and how well the set of factors explains the variance in the variables (Bandalos and Boehm-Kaufman, 2009). I’ll go out on a limb and say that if you have several hundred observations, you’re probably safe. In this chapter, we’ll look at artificially small problems in order to keep the output (and page count) manageable. Figure 14.1 Comparing principal components and factor analysis models. The diagrams show the observed variables (X1 to X5), the principal components (PC1, PC2), factors (F1, F2), and errors (e1 to e5). Download from Wow! eBook Principal components and factor analysis in R 333 We’ll start by reviewing the functions in R that can be used to perform PCA or EFA and give a brief overview of the steps involved. Then we’ll work carefully through two PCA examples, followed by an extended EFA example. A brief overview of other packages in R that can be used for fitting latent variable models is provided at the end of the chapter. This discussion includes packages for confirmatory factor analysis, structural equation modeling, correspondence analysis, and latent class analysis. 14.1 Principal components and factor analysis in R In the base installation of R, the functions for PCA and EFA are p rincomp() and f ac- tanal(), respectively. In this chapter, in this chapter, we’ll focus on functions provided in the psych package. They offer many more useful options than their base counter- parts. Additionally, the results are reported in a metric that will be more familiar to social scientists and more likely to match the output provided by corresponding pro- grams in other statistical packages such as SAS and SPSS. The p sych package functions that are most relevant here are listed in table 14.1. Be sure to install the package before trying the examples in this chapter. Table 14.1 Useful factor analytic functions in the psych package Function Description p rincipal()Principal components analysis with optional rotation f a()Factor analysis by principal axis, minimum residual, weighted least squares, or maximum likelihood f a.parallel()Scree plots with parallel analyses f actor.plot()Plot the results of a factor or principal components analysis f a.diagram()Graph factor or principal components loading matrices s cree()Scree plot for factor and principal components analysis EFA (and to a lesser degree PCA) are often confusing to new users. The reason is that they describe a wide range of approaches, and each approach requires several steps (and decisions) to achieve a final result. The most common steps are as follows: 1 Prepare the data. Both PCA and EFA derive their solutions from the correlations among the observed variables. Users can input either the raw data matrix or the correlation matrix to the p rincipal() and f a() functions. If raw data is input, the correlation matrix will automatically be calculated. Be sure to screen the data for missing values before proceeding. 2 Select a factor model. Decide whether PCA (data reduction) or EFA (uncovering latent structure) is a better fit for your research goals. If you select an EFA approach, you’ll also need to choose a specific factoring method (for example, maximum likelihood). Download from Wow! eBook 334 CHAPTER 14 Principal components and factor analysis 3 Decide how many components/factors to extract. 4 Extract the components/factors. 5 Rotate the components/factors. 6 Interpret the results. 7 Compute component or factor scores. In the remainder of this chapter, we’ll carefully consider each of the steps, starting with PCA. At the end of the chapter, you’ll find a detailed flow chart of the possible steps in PCA/EFA (figure 14.7). The chart will make more sense once you’ve read through the intervening material. 14.2 Principal components The goal of PCA is to replace a large number of correlated variables with a smaller number of uncorrelated variables while capturing as much information in the origi- nal variables as possible. These derived variables, called principal components, are linear combinations of the observed variables. Specifically, the first principal component PC1 = a1X1 + a2X2 + … + akX k is the weighted combination of the k observed variables that accounts for the most variance in the original set of variables. The second principal component is the linear combination that accounts for the most variance in the original variables, under the constraint that it’s orthogonal (uncorrelated) to the first principal component. Each subsequent component maximizes the variance accounted for, while at the same time remaining uncorrelated with all previous components. Theoretically, you can extract as many principal components as there are variables. But from a practical viewpoint, you hope that you can approximate the full set of variables with a much smaller set of components. Let’s look at a simple example. The dataset USJudgeRatings contains lawyers’ ratings of state judges in the US Superior Court. The data frame contains 43 observations on 12 numeric variables. The variables are listed in table 14.2. Table 14.2 Variables in the USJudgeRatings dataset Variable Description Variable Description C ONTNumber of contacts of lawyer with judge P REPPreparation for trial I NTGJudicial integrity F AMIFamiliarity with law DMNRDemeanor O RALSound oral rulings D ILGDiligence W RITSound written rulings C FMGCase flow managing P HYSPhysical ability D ECIPrompt decisions R TENWorthy of retention Download from Wow! eBook Principal components 335 From a practical point of view, can you summarize the 11 evaluative ratings (INTG to RTEN) with a smaller number of composite variables? If so, how many will you need and how will they be defined? Because our goal is to simplify the data, we’ll approach this problem using PCA. The data are in raw score format and there are no missing values. Therefore, your next decision is deciding how many principal components you’ll need. 14.2.1 Selecting the number of components to extract Several criteria are available for deciding how many components to retain in a PCA. They include: ■ Basing the number of components on prior experience and theory ■ Selecting the number of components needed to account for some threshold cumulative amount of variance in the variables (for example, 80 percent) ■ Selecting the number of components to retain by examining the eigenvalues of the k x k correlation matrix among the variables The most common approach is based on the eigenvalues. Each component is associ- ated with an eigenvalue of the correlation matrix. The first PC is associated with the largest eigenvalue, the second PC with the second-largest eigenvalue, and so on. The Kaiser–Harris criterion suggests retaining components with eigenvalues greater than 1. Components with eigenvalues less than 1 explain less variance than contained in a single variable. In the Cattell Scree test, the eigenvalues are plotted against their component numbers. Such plots will typically demonstrate a bend or elbow, and the components above this sharp break are retained. Finally, you can run simulations, ex- tracting eigenvalues from random data matrices of the same size as the original matrix. If an eigenvalue based on real data is larger than the average corresponding eigenval- ues from a set of random data matrices, that component is retained. The approach is called p arallel analysis (see Hayton, Allen, and Scarpello, 2004 for more details). You can assess all three eigenvalue criteria at the same time via the f a.parallel() function. For the 11 ratings (dropping the CONT variable), the necessary code is as follows: library(psych) fa.parallel(USJudgeRatings[,-1], fa="PC", ntrials=100, show.legend=FALSE, main="Scree plot with parallel analysis") This code produces the graph shown in figure 14.2. The plot displays the scree test based on the observed eigenvalues (as straight-line segments and x’s), the mean eigen- values derived from 100 random data matrices (as dashed lines), and the eigenvalues greater than 1 criteria (as a horizontal line at y=1). All three criteria suggest that a single component is appropriate for summarizing this dataset. Your next step is to extract the principal component using the principal() function. Download from Wow! eBook 336 CHAPTER 14 Principal components and factor analysis 2 4 6 8 10 0246810 Scree plot with parallel analysis Factor Number e i g e n v a l u e s o f p r i n c i p a l c o m p o n e n t s Figure 14.2 Assessing the number of principal components to retain for the US Judge Rating example. A scree plot (the line with x’s), eigenvalues greater than 1 criteria (horizontal line), and parallel analysis with 100 simulations (dashed line) suggest retaining a single component. 14.2.2 Extracting principal components As indicated earlier, the p rincipal() function will perform a principal components analysis starting with either a raw data matrix or a correlation matrix. The format is principal(r, nfactors=, rotate=, scores=) where ■ r is a correlation matrix or a raw data matrix ■ nfactors specifies the number of principal components to extract (1 by default) ■ rotate indicates the rotation to be applied (varimax by default; see section 14.2.3) ■ scores specifies whether or not to calculate principal component scores (false by default) To extract the first principal component, you can use the code in the following listing. Listing 14.1 Principal components analysis of US Judge Ratings > library(psych) > pc <- principal(USJudgeRatings[,-1], nfactors=1) > pc Download from Wow! eBook Principal components 337 Principal Components Analysis Call: principal(r = USJudgeRatings[, -1], nfactors=1) Standardized loadings based upon correlation matrix PC1 h2 u2 INTG 0.92 0.84 0.157 DMNR 0.91 0.83 0.166 DILG 0.97 0.94 0.061 CFMG 0.96 0.93 0.072 DECI 0.96 0.92 0.076 PREP 0.98 0.97 0.030 FAMI 0.98 0.95 0.047 ORAL 1.00 0.99 0.009 WRIT 0.99 0.98 0.020 PHYS 0.89 0.80 0.201 RTEN 0.99 0.97 0.028 PC1 SS loadings 10.13 Proportion Var 0.92 [… additional output omitted …] Here, you’re inputting the raw data without the C ONT variable and specifying that one unrotated component should be extracted. (Rotation will be explained in section 14.3.3.) Because PCA is performed on a correlation matrix, the raw data is automati- cally converted to a correlation matrix before extracting the components. The column labeled PC1 contains the component loadings, which are the correlations of the observed variables with the principal component(s). If you had extracted more than one principal component, there would be columns for PC2, PC3, and so on. Component loadings are used to interpret the meaning of components. You can see that each variable correlates highly with the first component (PC1). It therefore appears to be a general evaluative dimension. The column labeled h2 contains the component communalities—the amount of variance in each variable explained by the components. The u 2 column contains the component uniquenesses, the amount of variance not accounted for by the components (or 1–h2). For example, 80 percent of the variance in physical ability (PHYS) ratings is accounted for by the first PC, and 20 percent is not. PHYS is the variable least well represented by a one-component solution. The row labeled SS loadings contains the eigenvalues associated with the components. The eigenvalues are the standardized variance associated with a particular component (in this case, the value for the first component is 10.). Finally, the row labeled P roportion Var represents the amount of variance accounted for by each component. Here you see that the first principal component accounts for 92 percent of the variance in the 11 variables. Let’s consider a second example, one that results in a solution with more than one principal component. The dataset Harman23.cor contains data on 8 body measurements for 305 girls. In this case, the dataset consists of the correlations among the variables rather than the original data (see table 14.3). Download from Wow! eBook 338 CHAPTER 14 Principal components and factor analysis Table 14.3 Correlations among body measurements for 305 girls (Harman23.cor) height arm span forearm lower leg weight bitro diameter chest girth chest width height 1.00 0.85 0.80 0.86 0.47 0.40 0.30 0.38 arm span 0.85 1.00 0.88 0.83 0.38 0.33 0.28 0.41 forearm 0.80 0.88 1.00 0.80 0.38 0.32 0.24 0.34 lower.leg 0.86 0.83 0.8 1.00 0.44 0.33 0.33 0.36 weight 0.47 0.38 0.38 0.44 1.00 0.76 0.73 0.63 bitro diameter 0.40 0.33 0.32 0.33 0.76 1.00 0.58 0.58 chest girth 0.30 0.28 0.24 0.33 0.73 0.58 1.00 0.54 chest width 0.38 0.41 0.34 0.36 0.63 0.58 0.54 1.00 Source: Harman, H. H. (1976) Modern Factor Analysis, Third Edition Revised, University of Chicago Press, Table 2.3. Again, you wish to replace the original physical measurements with a smaller number of derived variables. You can determine the number of components to extract using the following code. In this case, you need to identify the correlation matrix (the cov component of the Harman23.cor object) and specify the sample size (n.obs): library(psych) fa.parallel(Harman23.cor$cov, n.obs=302, fa="pc", ntrials=100, show.legend=FALSE, main="Scree plot with parallel analysis") The resulting graph is displayed in figure 14.3. 1 2 3 4 5 6 7 8 01234 Scree plot with parallel analysis Factor Number e i g e n v a l u e s o f p r i n c i p a l c o m p o n e n t s Figure 14.3 Assessing the number of principal components to retain for the Body Measurements example. The scree plot (line with x’s), eigenvalues greater than 1 criteria (horizontal line), and parallel analysis with 100 simulations (dashed line) suggest retaining two components. Download from Wow! eBook Principal components 339 You can see from the plot that a two-component solution is suggested. As in the first example, the Kaiser–Harris criteria, scree test, and parallel analysis agree. This won’t always be the case, and you may need to extract different numbers of components and select the solution that appears most useful. The next listing extracts the first two prin- cipal components from the correlation matrix. Listing 14.2 Principal components analysis of body measurements > library(psych) > PC <- principal(Harman23.cor$cov, nfactors=2, rotate="none") > PC Principal Components Analysis Call: principal(r = Harman23.cor$cov, nfactors = 2, rotate = "none") Standardized loadings based upon correlation matrix PC1 PC2 h2 u2 height 0.86 -0.37 0.88 0.123 arm.span 0.84 -0.44 0.90 0.097 forearm 0.81 -0.46 0.87 0.128 lower.leg 0.84 -0.40 0.86 0.139 weight 0.76 0.52 0.85 0.150 bitro.diameter 0.67 0.53 0.74 0.261 chest.girth 0.62 0.58 0.72 0.283 chest.width 0.67 0.42 0.62 0.375 PC1 PC2 SS loadings 4.67 1.77 Proportion Var 0.58 0.22 Cumulative Var 0.58 0.81 [… additional output omitted …] If you examine the PC1 and PC2 columns in listing 14.2, you see that the first compo- nent accounts for 58 percent of the variance in the physical measurements, while the second component accounts for 22 percent. Together, the two components account for 81 percent of the variance. The two components together account for 88 percent of the variance in the height variable. Components and factors are interpreted by examining their loadings. The first component correlates positively with each physical measure and appears to be a general size factor. The second component contrasts the first four variables (h eight, a rm.span, f orearm, and l ower.leg), with the second four variables (w eight, b itro. diameter, c hest.girth, and c hest.width). It therefore appears to be a length- versus-volume factor. Conceptually, this isn’t an easy construct to work with. Whenever two or more components have been extracted, you can rotate the solution to make it more interpretable. This is the topic we’ll turn to next. 14.2.3 Rotating principal components Rotations are a set of mathematical techniques for transforming the component loading matrix into one that’s more interpretable. They do this by “purifying” the Download from Wow! eBook 340 CHAPTER 14 Principal components and factor analysis components as much as possible. Rotation methods differ with regard to whether the resulting components remain uncorrelated (o rthogonal rotation) or are allowed to correlate (o blique rotation). They also differ in their definition of purifying. The most popular orthogonal rotation is the v arimax rotation, which attempts to purify the columns of the loading matrix, so that each component is defined by a limited set of variables (that is, each column has a few large loadings and many very small loadings). Applying a varimax rotation to the body measurement data, you get the results provided in the next listing. You’ll see an example of an oblique rotation in section 14.4. Listing 14.3 Principal components analysis with varimax rotation > rc <- principal(Harman23.cor$cov, nfactors=2, rotate="varimax") > rc Principal Components Analysis Call: principal(r = Harman23.cor$cov, nfactors = 2, rotate = "varimax") Standardized loadings based upon correlation matrix RC1 RC2 h2 u2 height 0.90 0.25 0.88 0.123 arm.span 0.93 0.19 0.90 0.097 forearm 0.92 0.16 0.87 0.128 lower.leg 0.90 0.22 0.86 0.139 weight 0.26 0.88 0.85 0.150 bitro.diameter 0.19 0.84 0.74 0.261 chest.girth 0.11 0.84 0.72 0.283 chest.width 0.26 0.75 0.62 0.375 RC1 RC2 SS loadings 3.52 2.92 Proportion Var 0.44 0.37 Cumulative Var 0.44 0.81 [… additional output omitted …] The column names change from PC to RC to denote rotated components. Looking at the loadings in column R C1, you see that the first component is primarily defined by the first four variables (length variables). The loadings in the column R C2 indicate that the second component is primarily defined by variables 5 through 8 (volume vari- ables). Note that the two components are still uncorrelated and that together, they still explain the variables equally well. You can see that the rotated solution explains the variables equally well because the variable communalities haven’t changed. Addi- tionally, the cumulative variance accounted for by the two-component rotated solution (81 percent) hasn’t changed. But the proportion of variance accounted for by each in- dividual component has changed (from 58 percent to 44 percent for component 1 and from 22 percent to 37 percent for component 2). This spreading out of the variance across components is common, and technically you should now call them components rather than principal components (because the variance maximizing properties of indi- vidual components has not been retained). Download from Wow! eBook Principal components 341 Our ultimate goal is to replace a larger set of correlated variables with a smaller set of derived variables. To do this, you need to obtain scores for each observation on the components. 14.2.4 Obtaining principal components scores In the US Judge Rating example, you extracted a single principal component from the raw data describing lawyers’ ratings on 11 variables. The principal() func- tion makes it easy to obtain scores for each participant on this derived variable (see the next listing). Listing 14.4 Obtaining component scores from raw data > library(psych) > pc <- principal(USJudgeRatings[,-1], nfactors=1, score=TRUE) > head(pc$scores) PC1 AARONSON,L.H. -0.1857981 ALEXANDER,J.M. 0.7469865 ARMENTANO,A.J. 0.0704772 BERDON,R.I. 1.1358765 BRACKEN,J.J. -2.1586211 BURNS,E.B. 0.7669406 The principal component scores are saved in the s cores element of the object re- turned by the p rincipal() function when the option s cores=TRUE. If you wanted, you could now get the correlation between the number of contacts occurring between a lawyer and a judge and their evaluation of the judge using > cor(USJudgeRatings$CONT, PC$score) PC1 [1,] -0.008815895 Apparently, there’s no relationship between the lawyer’s familiarity and his or her opinions! When the principal components analysis is based on a correlation matrix and the raw data aren’t available, getting principal component scores for each observation is clearly not possible. But you can get the coefficients used to calculate the principal components. In the body measurement data, you have correlations among body measurements, but you don’t have the individual measurements for these 305 girls. You can get the scoring coefficients using the code in the following listing. Listing 14.5 Obtaining principal component scoring coefficients > library(psych) > rc <- principal(Harman23.cor$cov, nfactors=2, rotate="varimax") > round(unclass(rc$weights), 2) RC1 RC2 height 0.28 -0.05 arm.span 0.30 -0.08 Download from Wow! eBook 342 CHAPTER 14 Principal components and factor analysis forearm 0.30 -0.09 lower.leg 0.28 -0.06 weight -0.06 0.33 bitro.diameter -0.08 0.32 chest.girth -0.10 0.34 chest.width -0.04 0.27 The component scores are obtained using the formulas PC1 = 0.28*height + 0.30*arm.span + 0.30*forearm + 0.29*lower.leg - 0.06*weight - 0.08*bitro.diameter - 0.10*chest.girth - 0.04*chest.width and PC2 = -0.05*height - 0.08*arm.span - 0.09*forearm - 0.06*lower.leg + 0.33*weight + 0.32*bitro.diameter + 0.34*chest.girth + 0.27*chest.width These equations assume that the physical measurements have been standardized (mean=0, sd=1). Note that the weights for PC1 tend to be around 0.3 or 0. The same is true for PC2. As a practical matter, you could simplify your approach further by taking the first composite variable as the mean of the standardized scores for the first four variables. Similarly, you could define the second composite variable as the mean of the standardized scores for the second four variables. This is typically what I’d do in practice. Little Jiffy conquers the world There’s quite a bit of confusion among data analysts regarding PCA and EFA. One reason for this is historical and can be traced back to a program called Little Jiffy (no kidding). Little Jiffy was one of the most popular early programs for factor analysis, and defaulted to a principal components analysis, extracting components with eigen- values greater than 1 and rotating them to a varimax solution. The program was so widely used that many social scientists came to think of this defaults as synonymous with EFA. Many later statistical packages also incorporated these defaults in their EFA programs. As I hope you’ll see in the next section, there are important and fundamental dif- ferences between PCA and EFA. To learn more about the PCA/EFA confusion, see Hayton, Allen, and Scarpello, 2004. If your goal is to look for latent underlying variables that explain your observed vari- ables, you can turn to factor analysis. This is the topic of the next section. 14.3 Exploratory factor analysis The goal of EFA is to explain the correlations among a set of observed variables by un- covering a smaller set of more fundamental unobserved variables underlying the data. These hypothetical, unobserved variables are called factors. (Each factor is assumed to explain the variance shared among two or more observed variables, so technically, they are called c ommon factors.) Download from Wow! eBook Exploratory factor analysis 343 The model can be represented as Xi = a1F1 + a2F2 + … + apFp + Ui where Xi is the ith observed variable (i = 1…k), Fj are the common factors (j =1…p), and p options(digits=2) > covariances <- ability.cov$cov > correlations <- cov2cor(covariances) > correlations general picture blocks maze reading vocab general 1.00 0.47 0.55 0.34 0.58 0.51 picture 0.47 1.00 0.57 0.19 0.26 0.24 blocks 0.55 0.57 1.00 0.45 0.35 0.36 maze 0.34 0.19 0.45 1.00 0.18 0.22 reading 0.58 0.26 0.35 0.18 1.00 0.79 vocab 0.51 0.24 0.36 0.22 0.79 1.00 Because you’re looking for hypothetical constructs that explain the data, you’ll use an EFA approach. As in PCA, the next task is to decide how many factors to extract. 14.3.1 Deciding how many common factors to extract To decide on the number of factors to extract, turn to the f a.parallel() function: > library(psych) > covariances <- ability.cov$cov > correlations <- cov2cor(covariances) > fa.parallel(correlations, n.obs=112, fa="both", ntrials=100, main="Scree plots with parallel analysis") The resulting plot is shown in figure 14.4. Notice you’ve requested that the function display results for both a principal components and common factor approach, so that you can compare them (fa="both"). Download from Wow! eBook 344 CHAPTER 14 Principal components and factor analysis 1 2 3 4 5 6 0 . 0 0 . 5 1 . 0 1 . 5 2 . 0 2 . 5 3 . 0 Scree plots with parallel analysis Factor Number e i g e n v a l u e s o f p r i n c i p a l c o m p o n e n t s a n d f a c t o r a n a l y s i s PC Actual Data PC Simulated Data FA Actual Data FA Simulated Data Figure 14.4 Assessing the number of factors to retain for the psychological tests example. Results for both PCA and EFA are present. The PCA results suggest one or two components. The EFA results suggest two factors. There are several things to notice in this graph. If you’d taken a PCA approach, you might have chosen one component (scree test, parallel analysis) or two components (eigenvalues greater than 1). When in doubt, it’s usually a better idea to overfactor than to underfactor. Overfactoring tends to lead to less distortion of the “true” solution. Looking at the EFA results, a two-factor solution is clearly indicated. The first two eigenvalues (triangles) are above the bend in the scree test and also above the mean eigenvalues based on 100 simulated data matrices. For EFA, the Kaiser–Harris criterion is number of eigenvalues above 0, rather than 1. (Most people don’t realize this, so it’s a good way to win bets at parties.) In the present case the Kaiser–Harris criteria also suggest two factors. 14.3.2 Extracting common factors Now that you’ve decided to extract two factors, you can use the f a() function to obtain your solution. The format of the fa() function is fa(r, nfactors=, n.obs=, rotate=, scores=, fm=) where ■ r is a correlation matrix or a raw data matrix ■ nfactors specifies the number of factors to extract (1 by default) ■ n.obs is the number of observations (if a correlation matrix is input) ■ rotate indicates the rotation to be applied (oblimin by default) ■ scores specifies whether or not to calculate factor scores (false by default) ■ fm specifies the factoring method (minres by default) Unlike PCA, there are many methods of extracting common factors. They include maximum likelihood (ml), iterated principal axis (pa), weighted least square (wls), Download from Wow! eBook Exploratory factor analysis 345 generalized weighted least squares (gls), and minimum residual (minres). Statisti- cians tend to prefer the maximum likelihood approach because of its well-defined statistical model. Sometimes, this approach fails to converge, in which case the iterated principal axis option often works well. To learn more about the different approaches, see Mulaik (2009) and Gorsuch (1983). For this example, you’ll extract the unrotated factors using the iterated principal axis (fm="pa") approach. The results are given in the next listing. Listing 14.6 Principal axis factoring without rotation > fa <- fa(correlations, nfactors=2, rotate="none", fm="pa") > fa Factor Analysis using method = pa Call: fa(r = correlations, nfactors = 2, rotate = "none", fm = "pa") Standardized loadings based upon correlation matrix PA1 PA2 h2 u2 general 0.75 0.07 0.57 0.43 picture 0.52 0.32 0.38 0.62 blocks 0.75 0.52 0.83 0.17 maze 0.39 0.22 0.20 0.80 reading 0.81 -0.51 0.91 0.09 vocab 0.73 -0.39 0.69 0.31 PA1 PA2 SS loadings 2.75 0.83 Proportion Var 0.46 0.14 Cumulative Var 0.46 0.60 [… additional output deleted …] You can see that the two factors account for 60 percent of the variance in the six psy- chological tests. When you examine the loadings, though, they aren’t easy to interpret. Rotating them should help. 14.3.3 Rotating factors You can rotate the two-factor solution from section 14.3.4 using either an o rthogonal rotation or an o blique rotation. Let’s try both so you can see how they differ. First try an orthogonal rotation (in the next listing). Listing 14.7 Factor extraction with orthogonal rotation > fa.varimax <- fa(correlations, nfactors=2, rotate="varimax", fm="pa") > fa.varimax Factor Analysis using method = pa Call: fa(r = correlations, nfactors = 2, rotate = "varimax", fm = "pa") Standardized loadings based upon correlation matrix PA1 PA2 h2 u2 general 0.49 0.57 0.57 0.43 picture 0.16 0.59 0.38 0.62 blocks 0.18 0.89 0.83 0.17 maze 0.13 0.43 0.20 0.80 reading 0.93 0.20 0.91 0.09 Download from Wow! eBook 346 CHAPTER 14 Principal components and factor analysis vocab 0.80 0.23 0.69 0.31 PA1 PA2 SS loadings 1.83 1.75 Proportion Var 0.30 0.29 Cumulative Var 0.30 0.60 [… additional output omitted …] Looking at the factor loadings, the factors are certainly easier to interpret. Reading and vocabulary load on the first factor, and picture completion, block design, and mazes loads on the second factor. The general nonverbal intelligence measure loads on both factors. This may indicate a verbal intelligence factor and a nonverbal intel- ligence factor. By using an orthogonal rotation, you’ve artificially forced the two factors to be uncorrelated. What would you find if you allowed the two factors to correlate? You can try an oblique rotation such as promax (see the next listing). Listing 14.8 Factor extraction with oblique rotation > fa.promax <- fa(correlations, nfactors=2, rotate="promax", fm="pa") > fa.promax Factor Analysis using method = pa Call: fa(r = correlations, nfactors = 2, rotate = "promax", fm = "pa") Standardized loadings based upon correlation matrix PA1 PA2 h2 u2 general 0.36 0.49 0.57 0.43 picture -0.04 0.64 0.38 0.62 blocks -0.12 0.98 0.83 0.17 maze -0.01 0.45 0.20 0.80 reading 1.01 -0.11 0.91 0.09 vocab 0.84 -0.02 0.69 0.31 PA1 PA2 SS loadings 1.82 1.76 Proportion Var 0.30 0.29 Cumulative Var 0.30 0.60 With factor correlations of PA1 PA2 PA1 1.00 0.57 PA2 0.57 1.00 [… additional output omitted …] Several differences exist between the orthogonal and oblique solutions. In an orthogonal solution, attention focuses on the f actor structure matrix (the correlations of the variables with the factors). In an oblique solution, there are three matrices to consider: the factor structure matrix, the f actor pattern matrix, and the f actor intercorrelation matrix. The factor pattern matrix is a matrix of standardized regression coefficients. They give the weights for predicting the variables from the factors. The factor intercorrelation matrix gives the correlations among the factors. Download from Wow! eBook Exploratory factor analysis 347 In listing 14.8, the values in the P A1 and P A2 columns constitute the factor pattern matrix. They’re standardized regression coefficients rather than correlations. Examination of the columns of this matrix is still used to name the factors (although there’s some controversy here). Again you’d find a verbal and nonverbal factor. The factor intercorrelation matrix indicates that the correlation between the two factors is 0.57. This is a hefty correlation. If the factor intercorrelations had been low, you might have gone back to an orthogonal solution to keep things simple. The factor structure matrix (or factor loading matrix) isn’t provided. But you can easily calculate it using the formula F = P*Phi, where F is the factor loading matrix, P is the factor pattern matrix, and Phi is the factor intercorrelation matrix. A simple function for carrying out the multiplication is as follows: fsm <- function(oblique) { if (class(oblique)[2]=="fa" & is.null(oblique$Phi)) { warning("Object doesn't look like oblique EFA") } else { P <- unclass(oblique$loading) F <- P %*% oblique$Phi colnames(F) <- c("PA1", "PA2") return(F) } } Applying this to the example, you get > fsm(fa.promax) PA1 PA2 general 0.64 0.69 picture 0.33 0.61 blocks 0.44 0.91 maze 0.25 0.45 reading 0.95 0.47 vocab 0.83 0.46 Now you can review the correlations between the variables and the factors. Compar- ing them to the factor loading matrix in the orthogonal solution, you see that these columns aren’t as pure. This is because you’ve allowed the underlying factors to be cor- related. Although the oblique approach is more complicated, it’s often a more realistic model of the data. You can graph an orthogonal or oblique solution using the f actor.plot() or f a. diagram() function. The code factor.plot(fa.promax, labels=rownames(fa.promax$loadings)) produces the graph in figure 14.5. The code fa.diagram(fa.promax, simple=FALSE) produces the diagram in figure 14.6. If you let simple=TRUE, only the largest loading per item would be displayed. It shows the largest loadings for each factor, as well as the correlations between the factors. This type of diagram is helpful when there are several factors. Download from Wow! eBook 348 CHAPTER 14 Principal components and factor analysis 0.0 0.2 0.4 0.6 0.8 1.0 0 . 0 0 . 2 0 . 4 0 . 6 0 . 8 1 . 0 Factor Analysis PA1 P A 2 general picture blocks maze reading vocab Figure 14.5 Two factor plot for the psychological tests in ability.cov. Vocab and reading load on the first factor (PA1). while blocks, picture, and maze load on the second factor (PA2). The general intelligence test loads on both. When you’re dealing with data in real life, it’s unlikely that you’d apply factor analysis to a dataset with so few variables. You’ve done it here to keep things manageable. If you’d like to test your skills, try factor-analyzing the 24 psychological tests contained in Harman74.cor. The code library(psych) fa.24tests <- fa(Harman74.cor$cov, nfactors=4, rotate="promax") should get you started! Factor Analysis reading vocab blocks picture general maze PA1 1 0.8 0.4 PA2 1 0.6 0.5 0.5 0.6 Figure 14.6 Diagram of the oblique two factor solution for the psychological test data in ability.cov Download from Wow! eBook Other latent variable models 349 14.3.4 Factor scores Compared with PCA, the goal of EFA is much less likely to be the calculation of factor scores. But these scores are easily obtained from the f a() function by including the score=TRUE option (when raw data is available). Additionally, the scoring coefficients (standardized regression weights) are available in the weights element of the object returned. For the ability.cov dataset, you can obtain the beta weights for calculating the factor score estimates for the two-factor oblique solution using > fa.promax$weights [,1] [,2] general 0.080 0.210 picture 0.021 0.090 blocks 0.044 0.695 maze 0.027 0.035 reading 0.739 0.044 vocab 0.176 0.039 Unlike component scores, which are calculated exactly, factor scores can only be es- timated. Several methods exist. The f a() function uses the regression approach. To learn more about factor scores, see DiStefano, Zhu, and Mîndrila˘, (2009). Before moving on, let’s briefly review other R packages that are useful for exploratory factor analysis. 14.3.5 Other EFA-related packages R contains a number of other contributed packages that are useful for conducting factor analyses. The F actoMineR package provides methods for PCA and EFA, as well as other latent variable models. It provides many options that we haven’t considered here, including the use of both numeric and categorical variables. The F AiR package estimates factor analysis models using a genetic algorithm that permits the ability to impose inequality restrictions on model parameters. The G PArotation package offers many additional factor rotation methods. Finally, the n Factors package offers sophis- ticated techniques for determining the number of factors underlying data. 14.4 Other latent variable models EFA is only one of a wide range of latent variable models used in statistics. We’ll end this chapter with a brief description of other models that can be fit within R. These include models that test a priori theories, that can handle mixed data types (numeric and categorical), or that are based solely on categorical multiway tables. In EFA, you allow the data to determine the number of factors to be extracted and their meaning. But you could start with a theory about how many factors underlie a set of variables, how the variables load on those factors, and how the factors correlate with one another. You could then test this theory against a set of collected data. The approach is called c onfirmatory factor analysis (CFA). CFA is a subset of a methodology called s tructural equation modeling (SEM). SEM not only allows you to posit the number and composition of underlying factors but Download from Wow! eBook 350 CHAPTER 14 Principal components and factor analysis how these factors impact one another as well. You can think of SEM as a combination of confirmatory factor analyses (for the variables) and regression analyses (for the factors). The resulting output includes statistical tests and fit indices. There are several excellent packages for CFA and SEM in R. They include s em, o penMx, and l avaan. The ltm package can be used to fit latent models to the items contained in tests and questionnaires. The methodology is often used to create large scale standardized tests. Examples include the S cholastic Aptitude Test (SAT) and the G raduate Record Exam (GRE). Latent class models (where the underlying factors are assumed to be categorical rather than continuous) can be fit with the F lexMix, l cmm, r andomLCA, and p oLC packages. The l cda package performs latent class discriminant analysis, and the l sa package performs latent semantic analysis, a methodology used in natural language processing. The ca package provides functions for simple and multiple correspondence analysis. These methods allow you to explore the structure of categorical variables in two-way and multiway tables, respectively. Finally, R contains numerous methods for m ultidimensional scaling (MDS). MDS is designed to detect underlying dimensions that explain the similarities and distances between a set of measured objects (for example, countries). The c mdscale() function in the base installation performs a classical MDS, while the i soMDS() function in the M ASS package performs a nonmetric MDS. The vegan package also contains functions for classical and nonmetric MDS. 14.5 Summary In this chapter, we reviewed methods for principal components (PCA) analysis and exploratory factor analysis (EFA). PCA is a useful data reduction method that can re- place a large number of correlated variables with a smaller number of uncorrelated variables, simplifying the analyses. EFA contains a broad range of methods for identify- ing latent or unobserved constructs (factors) that may underlie a set of observed or manifest variables. Whereas the goal of PCA is typically to summarize the data and reduce its dimensionality, EFA can be used as a hypothesis generating tool, useful when you’re trying to understand the relationships between a large number of variables. It’s often used in the social sciences for theory development. Although there are many superficial similarities between the two approaches, important differences exist as well. In this chapter, we considered the models underlying each, methods for selecting the number of components/factors to extract, methods for extracting components/factors and rotating (transforming) them to enhance interpretability, and techniques for obtaining component or factor scores. The steps in a PCA or EFA are summarized in figure 14.7. We ended the chapter with a brief discussion of other latent variable methods available in R. Download from Wow! eBook Summary 351 Select Factor Model Components Common Factor Principal Axis Maximum Likelihood Weighted Least Squares Minimum Residual Select Number of Components/Factors Kaiser/Harris Scree Test Parallel Analysis TheoryInterpretabilityVariance Accounted Rotate Components/Factors Orthogonal Oblique Interpret Components/Factors Principal Components Varimax Other Orthogonal Rotaon Promax Other Oblique Rotaon Calculate Factor Scores Figure 14.7 A principal components/exploratory factor analysis decision chart Because PCA and EFA are based on correlation matrices, it’s important that any missing data be eliminated before proceeding with the analyses. Section 4.5 briefly mentioned simple methods for dealing with missing data. In the next chapter, we’ll consider more sophisticated methods for both understanding and handling missing values. Download from Wow! eBook 352 15Advanced methods for missing data This chapter covers ■ Visualization of missing data patterns Identification of missing data ■ Complete-case analysis■ ■ Multiple imputation of missing data In previous chapters, we focused on the analysis of complete datasets (that is, data- sets without missing values). Although doing so has helped simplify the presentation of statistical and graphical methods, in the real world, missing data are ubiquitous. In some ways, the impact of missing data is a subject that most of us want to avoid. Statistics books may not mention it or may limit discussion to a few paragraphs. Statistical packages offer automatic handling of missing data using methods that may not be optimal. Even though most data analyses (at least in social sciences) involve missing data, this topic is rarely mentioned in the methods and results sections of journal articles. Given how often missing values occur, and the degree to which their presence can invalidate study results, it’s fair to say that the subject has received insufficient attention outside of specialized books and courses. Download from Wow! eBook Steps in dealing with missing data 353 Data can be missing for many reasons. Survey participants may forget to answer one or more questions, refuse to answer sensitive questions, or grow fatigued and fail to complete a long questionnaire. Study participants may miss appointments or drop out of a study prematurely. Recording equipment may fail, internet connections may be lost, and data may be miscoded. The presence of missing data may even be planned. For example, to increase study efficiency or reduce costs, you may choose not to collect all data from all participants. Finally, data may be lost for reasons that you’re never able to ascertain. Unfortunately, most statistical methods assume that you’re working with complete matrices, vectors, and data frames. In most cases, you have to eliminate missing data before you address the substantive questions that led you to collect the data. You can eliminate missing data by (1) removing cases with missing data, or (2) replacing missing data with reasonable substitute values. In either case, the end result is a dataset without missing values. In this chapter, we’ll look at both traditional and modern approaches for dealing with missing data. We’ll primarily use the V IM and m ice packages. The command install.packages(c("VIM", "mice")) will download and install both. To motivate the discussion, we’ll look at the mammal sleep dataset (sleep) provided in the VIM package (not to be confused with the sleep dataset describing the impact of drugs on sleep provided in the base installation). The data come from a study by Allison and Chichetti (1976) that examined the relationship between sleep, ecological, and constitutional variables for 62 mammal species. The authors were interested in why animals’ sleep requirements vary from species to species. The sleep variables served as the dependent variables, whereas the ecological and constitutional variables served as the independent or predictor variables. Sleep variables included length of dreaming sleep (Dream), nondreaming sleep (NonD), and their sum (Sleep). The constitutional variables included body weight in kilograms (BodyWgt), brain weight in grams (BrainWgt), life span in years (Span), and gestation time in days (Gest). The ecological variables included degree to which species were preyed upon (Pred), degree of their exposure while sleeping (Exp), and overall danger (Danger) faced. The ecological variables were measured on 5-point rating scales that ranged from 1 (low) to 5 (high). In their original article, Allison and Chichetti limited their analyses to the species that had complete data. We’ll go further, analyzing all 62 cases using a multiple imputation approach. 15.1 Steps in dealing with missing data Readers new to the study of missing data will find a bewildering array of approaches, critiques, and methodologies. The classic text in this area is Little and Rubin (2002). Excellent, accessible reviews can be found in Allison (2001), Schafer and Graham (2002) and Schlomer, Bauman, and Card (2010). A comprehensive approach will usu- ally include the following steps: Download from Wow! eBook 354 CHAPTER 15 Advanced methods for missing data 1 Identify the missing data. 2 Examine the causes of the missing data. 3 Delete the cases containing missing data or replace (impute) the missing values with reasonable alternative data values. Unfortunately, identifying missing data is usually the only unambiguous step. Learning why data are missing depends on your understanding of the processes that generated the data. Deciding how to treat missing values will depend on your estimation of which procedures will produce the most reliable and accurate results. A classification system for missing data Statisticians typically classify missing data into one of three types. These types are usually described in probabilistic terms, but the underlying ideas are straightforward. We’ll use the measurement of dreaming in the sleep study (where 12 animals have missing values) to illustrate each type in turn. (1) Missing completely at random—If the presence of missing data on a variable is unrelated to any other observed or unobserved variable, then the data are m issing completely at random (MCAR). If there’s no systematic reason why dream sleep is missing for these 12 animals, the data is said to be MCAR. Note that if every vari- able with missing data is MCAR, you can consider the complete cases to be a simple random sample from the larger dataset. (2) Missing at random—If the presence of missing data on a variable is related to other observed variables but not to its own unobserved value, the data is m issing at random (MAR). For example, if animals with smaller body weights are more likely to have missing values for dream sleep (perhaps because it’s harder to observe smaller animals), and the “missingness” is unrelated to an animal’s time spent dreaming, the data would be considered MAR. In this case, the presence or absence of dream sleep data would be random, once you controlled for body weight. (3) Not missing at random—If the missing data for a variable is neither MCAR nor MAR, it is n ot missing at random (NMAR). For example, if animals that spend less time dreaming are also more likely to have a missing dream value (perhaps because it’s harder to measure shorter events), the data would be considered NMAR. Most approaches to missing data assume that the data is either MCAR or MAR. In this case, you can ignore the mechanism producing the missing data and (after replacing or deleting the missing data) model the relationships of interest directly. Data that’s NMAR can be difficult to analyze properly. When data is NMAR, you have to model the mechanisms that produced the missing values, as well as the relation- ships of interest. (Current approaches to analyzing NMAR data include the use of selection models and pattern mixtures. The analysis of NMAR data can be quite complex and is beyond the scope of this book.) Download from Wow! eBook Identifying missing values 355 Identify Missing Values is.na() !complete.cases() VIM package Delete Missing Values Maximum Likelihood Estimation mvmle package Impute Missing Values Casewise (Listwise) omit.na() Available Case (Pairwise) Option available for some functions Single (simple) Imputation Hmisc Package Multiple Imputation mi package mice package amelia package mitools package Figure 15.1 Methods for handling incomplete data, along with the R packages that support them There are many methods for dealing with missing data—and no guarantee that they’ll produce the same results. Figure 15.1 describes an array of methods used for handling incomplete data and the R packages that support them. A complete review of missing data methodologies would require a book in itself. In this chapter, we’ll review methods for exploring missing values patterns and focus on the three most popular methods for dealing with incomplete data (a rational approach, listwise deletion, and multiple imputation). We’ll end the chapter with a brief discussion of other methods, including those that are useful in special circumstances. 15.2 Identifying missing values To begin, let’s review the material introduced in chapter 4, section 4.5, and expand on it. R represents missing values using the symbol N A (not available) and impossible values by the symbol N aN (not a number). In addition, the symbols Inf and -Inf represent posi- tive infinity and negative infinity, respectively. The functions i s.na(), i s.nan(), and i s.infinite() can be used to identify missing, impossible, and infinite values respec- tively. Each returns either TRUE or FALSE. Examples are given in table 15.1. Table 15.1 Examples of return values for the is.na(), is.nan(), and is.infinite() functions x is.na(x) is.nan(x) is.infinite(x) x <- NATRUEFALSEFALSE x <- 0 / 0 TRUETRUEFALSE x <- 1 / 0 FALSEFALSETRUE Download from Wow! eBook 356 CHAPTER 15 Advanced methods for missing data These functions return an object that’s the same size as its argument, with each ele- ment replaced by TRUE if the element is of the type being tested, and FALSE otherwise. For example, let y <- c(1, 2, 3, NA). Then is.na(y) will return the vector c(FALSE, FALSE, FALSE, TRUE). The function c omplete.cases() can be used to identify the rows in a matrix or data frame that don’t contain missing data. It returns a logical vector with TRUE for every row that contains complete cases and FALSE for every row that has one or more missing values. Let’s apply this to the sleep dataset: # load the dataset data(sleep, package="VIM") # list the rows that do not have missing values sleep[complete.cases(sleep),] # list the rows that have one or more missing values sleep[!complete.cases(sleep),] Examining the output reveals that 42 cases have complete data and 20 cases have one or more missing values. Because the logical values TRUE and FALSE are equivalent to the numeric values 1 and 0, the s um() and m ean() functions can be used to obtain useful information about missing data. Consider the following: > sum(is.na(sleep$Dream)) [1] 12 > mean(is.na(sleep$Dream)) [1] 0.19 > mean(!complete.cases(sleep)) [1] 0.32 The results indicate that there are 12 missing values for the variable D ream. Nineteen percent of the cases have a missing value on this variable. In addition, 32 percent of the cases in the dataset contain one or more missing values. There are two things to keep in mind when identifying missing values. First, the c omplete.cases() function only identifies NA and NaN as missing. Infinite values (Inf and –Inf) are treated as valid values. Second, you must use missing values functions, like those in this section, to identify the missing values in R data objects. Logical comparisons such as myvar == NA are never true. Now that you know how to identify missing values programmatically, let’s look at tools that help you explore possible patterns in the occurrence of missing data. 15.3 Exploring missing values patterns Before deciding how to deal with missing data, you’ll find it useful to determine which variables have missing values, in what amounts, and in what combinations. In this sec- tion, we’ll review tabular, graphical, and correlational methods for exploring missing values patterns. Ultimately, you want to understand why the data is missing. The answer will have implications for how you proceed with further analyses. Download from Wow! eBook Exploring missing values patterns 357 15.3.1 Tabulating missing values You’ve already seen a rudimentary approach to identifying missing values. You can use the c omplete.cases() function from section 15.2 to list cases that are complete, or conversely, list cases that have one or more missing values. As the size of a dataset grows, though, it becomes a less attractive approach. In this case, you can turn to other R functions. The m d.pattern() function in the m ice package will produce a tabulation of the missing data patterns in a matrix or data frame. Applying this function to the sleep dataset, you get the following: > library(mice) > data(sleep, package="VIM") > md.pattern(sleep) BodyWgt BrainWgt Pred Exp Danger Sleep Span Gest Dream NonD 42 1 1 1 1 1 1 1 1 1 1 0 2 1 1 1 1 1 1 0 1 1 1 1 3 1 1 1 1 1 1 1 0 1 1 1 9 1 1 1 1 1 1 1 1 0 0 2 2 1 1 1 1 1 0 1 1 1 0 2 1 1 1 1 1 1 1 0 0 1 1 2 2 1 1 1 1 1 0 1 1 0 0 3 1 1 1 1 1 1 1 0 1 0 0 3 0 0 0 0 0 4 4 4 12 14 38 The 1’s and 0’s in the body of the table indicate the missing values patterns, with a 0 indicating a missing value for a given column variable and a 1 indicating a nonmissing value. The first row describes the pattern of “no missing values” (all elements are 1). The second row describes the pattern “no missing values except for Span.” The first column indicates the number of cases in each missing data pattern, and the last col- umn indicates the number of variables with missing values present in each pattern. Here you can see that there are 42 cases without missing data and 2 cases that are missing Span alone. Nine cases are missing both NonD and Dream values. The dataset contains a total of (42 x 0) + (2 x 1) + … + (1 x 3) = 38 missing values. The last row gives the total number of missing values present on each variable. 15.3.2 Exploring missing data visually Although the tabular output from the md.pattern() function is compact, I often find it easier to discern patterns visually. Luckily, the VIM package provides numerous func- tions for visualizing missing values patterns in datasets. In this section, we’ll review several, including aggr(), matrixplot(), and scattMiss(). The a ggr() function plots the number of missing values for each variable alone and for each combination of variables. For example, the code library("VIM") aggr(sleep, prop=FALSE, numbers=TRUE) Download from Wow! eBook 358 CHAPTER 15 Advanced methods for missing data N u m b e r o f M i s s i n g s 02468 1 0 1 2 1 4 B o d y W g t B r a i n W g t N o n D D r e a m S l e e p S p a n G e s t P r e d E x p D a n g e r C o m b i n a t i o n s B o d y W g t B r a i n W g t N o n D D r e a m S l e e p S p a n G e s t P r e d E x p D a n g e r 42 9 3 2 2 2 1 1 Figure 15.2 aggr() produced plot of missing values patterns for the sleep dataset. produces the graph in figure 15.2. (The VIM package opens up a GUI interface. You can close it; we’ll be using code to accomplish the tasks in this chapter.) You can see that the variable NonD has the largest number of missing values (14), and that 2 mammals are missing NonD, Dream, and Sleep scores. Forty-two mammals have no missing data. The statement aggr(sleep, prop=TRUE, numbers=TRUE)produces the same plot, but proportions are displayed instead of counts. The option numbers=FALSE (the default) suppresses the numeric labels. The m atrixplot() function produces a plot displaying the data for each case. A graph created using matrixplot(sleep) is displayed in figure 15.3. Here, the numeric data is rescaled to the interval [0, 1] and represented by grayscale colors, with lighter colors representing lower values and darker colors representing larger values. By default, missing values are represented in red. Note that in figure 15.3, red has been replaced with crosshatching by hand, so that the missing values are viewable in grayscale. It will look different when you create the graph yourself. The graph is interactive: clicking on a column will re-sort the matrix by that variable. The rows in figure 15.3 are sorted in descending order by BodyWgt. A matrix plot allows you to see if the presence of missing values on one or more variables is related to the actual values of other variables. Here, you can see that there are no missing values on sleep variables (Dream, NonD, Sleep) for low values of body or brain weight (BodyWgt, BrainWgt). Download from Wow! eBook Exploring missing values patterns 359 Figure 15.3 Matrix plot of actual and missing values by case (row) for the sleep dataset. The matrix is sorted by BodyWgt. The m arginplot() function produces a scatter plot between two variables with infor- mation about missing values shown in the plot’s margins. Consider the relationship be- tween amount of dream sleep and the length of a mammal’s gestation. The statement marginplot(sleep[c("Gest","Dream")], pch=c(20), col=c("darkgray", "red", "blue")) produces the graph in figure 15.4. The p ch and c ol parameters are optional and pro- vide control over the plotting symbols and colors used. The body of the graph displays the scatter plot between Gest and Dream (based on complete cases for the two variables). In the left margin, box plots display the distribution of Dream for mammals with (dark gray) and without (red) Gest values. Note that in grayscale, red is the darker shade. Four red dots represent the values of Dream for mammals missing Gest scores. In the bottom margin, the roles of Gest and Dream are reversed. You can see that a negative relationship exists between length of gestation and dream sleep and that dream sleep tends to be higher for mammals that are missing a gestation score. The number of observations with missing values on both variables at the same time is printed in blue at the intersection of both margins (bottom left). The V IM package has many graphs that can help you understand the role of missing data in a dataset and is well worth exploring. There are functions to produce scatter plots, box plots, histograms, scatter plot matrices, parallel plots, rug plots, and bubble plots that incorporate information about missing values. Download from Wow! eBook 360 CHAPTER 15 Advanced methods for missing data 12 40 0 100 200 300 400 500 600 0123456 Gest D r e a m Figure 15.4 Scatter plot between amount of dream sleep and length of gestation, with information about missing data in the margins 15.3.3 Using correlations to explore missing values Before moving on, there’s one more approach worth noting. You can replace the data in a dataset with indicator variables, coded 1 for missing and 0 for present. The result- ing matrix is sometimes called a s hadow matrix. Correlating these indicator variables with each other and with the original (observed) variables can help you to see which variables tend to be missing together, as well as relationships between a variable’s “miss- ingness” and the values of the other variables. Consider the following code: x <- as.data.frame(abs(is.na(sleep))) The elements of data frame x are 1 if the corresponding element of sleep is missing and 0 otherwise. You can see this by viewing the first few rows of each: > head(sleep, n=5) BodyWgt BrainWgt NonD Dream Sleep Span Gest Pred Exp Danger 1 6654.000 5712.0 NA NA 3.3 38.6 645 3 5 3 2 1.000 6.6 6.3 2.0 8.3 4.5 42 3 1 3 3 3.385 44.5 NA NA 12.5 14.0 60 1 1 1 4 0.920 5.7 NA NA 16.5 NA 25 5 2 3 5 2547.000 4603.0 2.1 1.8 3.9 69.0 624 3 5 4 > head(x, n=5) BodyWgt BrainWgt NonD Dream Sleep Span Gest Pred Exp Danger 1 0 0 1 1 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 3 0 0 1 1 0 0 0 0 0 0 4 0 0 1 1 0 1 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 Download from Wow! eBook Exploring missing values patterns 361 The statement y <- x[which(sd(x) > 0)] extracts the variables that have some (but not all) missing values, and cor(y) gives you the correlations among these indicator variables: NonD Dream Sleep Span Gest NonD 1.000 0.907 0.486 0.015 -0.142 Dream 0.907 1.000 0.204 0.038 -0.129 Sleep 0.486 0.204 1.000 -0.069 -0.069 Span 0.015 0.038 -0.069 1.000 0.198 Gest -0.142 -0.129 -0.069 0.198 1.000 Here, you can see that Dream and NonD tend to be missing together (r=0.91). To a lesser extent, Sleep and NonD tend to be missing together (r=0.49) and Sleep and Dream tend to be missing together (r=0.20). Finally, you can look at the relationship between the presence of missing values in a variable and the observed values on other variables: > cor(sleep, y, use="pairwise.complete.obs") NonD Dream Sleep Span Gest BodyWgt 0.227 0.223 0.0017 -0.058 -0.054 BrainWgt 0.179 0.163 0.0079 -0.079 -0.073 NonD NA NA NA -0.043 -0.046 Dream -0.189 NA -0.1890 0.117 0.228 Sleep -0.080 -0.080 NA 0.096 0.040 Span 0.083 0.060 0.0052 NA -0.065 Gest 0.202 0.051 0.1597 -0.175 NA Pred 0.048 -0.068 0.2025 0.023 -0.201 Exp 0.245 0.127 0.2608 -0.193 -0.193 Danger 0.065 -0.067 0.2089 -0.067 -0.204 Warning message: In cor(sleep, y, use = "pairwise.complete.obs") : the standard deviation is zero In this correlation matrix, the rows are observed variables, and the columns are indica- tor variables representing missingness. You can ignore the warning message and NA values in the correlation matrix; they’re artifacts of our approach. From the first column of the correlation matrix, you can see that nondreaming sleep scores are more likely to be missing for mammals with higher body weight (r=0.227), gestation period (r=0.202), and sleeping exposure (0.245). Other columns are read in a similar fashion. None of the correlations in this table are particularly large or striking, which suggests that the data deviates minimally from MCAR and may be MAR. Note that you can never rule out the possibility that the data are NMAR because you don’t know what the actual values would have been for data that are missing. For example, you don’t know if there’s a relationship between the amount of dreaming a mammal engages in and the probability of obtaining a missing value on this variable. In the absence of strong external evidence to the contrary, we typically assume that data is either MCAR or MAR. Download from Wow! eBook 362 CHAPTER 15 Advanced methods for missing data 15.4 Understanding the sources and impact of missing data We identify the amount, distribution, and pattern of missing data in order to evaluate (1) the potential mechanisms producing the missing data and (2) the impact of the missing data on our ability to answer substantive questions. In particular, we want to answer the following questions: ■ What percentage of the data is missing? ■ Is it concentrated in a few variables, or widely distributed? ■ Does it appear to be random? ■ Does the covariation of missing data with each other or with observed data sug- gest a possible mechanism that’s producing the missing values? Answers to these questions will help determine which statistical methods are most ap- propriate for analyzing your data. For example, if the missing data are concentrated in a few relatively unimportant variables, you may be able to delete these variables and continue your analyses normally. If there’s a small amount of data (say less than 10 percent) that’s randomly distributed throughout the dataset (MCAR), you may be able to limit your analyses to cases with complete data and still get reliable and valid results. If you can assume that the data are either MCAR or MAR, you may be able to apply multiple imputation methods to arrive at valid conclusions. If the data are NMAR, you can turn to specialized methods, collect new data, or go into an easier and more rewarding profession. Here are some examples: ■ In a recent survey employing paper questionnaires, I found that several items tend- ed to be missing together. It became apparent that these items clustered together because participants didn’t realize that the third page of the questionnaire had a reverse side containing them. In this case, the data could be considered MCAR. ■ In another study, an education variable was frequently missing in a global sur- vey of leadership styles. Investigation revealed that European participants were more likely to leave this item blank. It turned out that the categories didn’t make sense for participants in certain countries. In this case, the data was most likely MAR. ■ Finally, I was involved in a study of depression in which older patients were more likely to omit items describing depressed mood when compared with young- er patients. Interviews revealed that older patients were loath to admit to such symptoms because doing so violated their values about keeping a “stiff upper lip.” Unfortunately, it was also determined that severely depressed patients were more likely to omit these items due to a sense of hopelessness and difficulties with concentration. In this case, the data had to be considered NMAR. As you can see, the identification of patterns is only the first step. You need to bring your understanding of the research subject matter and the data collection process to bear in order to determine the source of the missing values. Download from Wow! eBook Rational approaches for dealing with incomplete data 363 Now that we’ve considered the source and impact of missing data, let’s see how standard statistical approaches can be altered to accommodate them. We’ll focus on three approaches that are very popular: a rational approach for recovering data, a traditional approach that involves deleting missing data, and a modern approach that involves the use of simulation. Along the way, we’ll briefly look at methods for specialized situations, and methods that have become obsolete and should be retired. Our goal will remain constant: to answer, as accurately as possible, the substantive questions that led us to collect the data, given the absence of complete information. 15.5 Rational approaches for dealing with incomplete data In a rational approach, you use mathematical or logical relationships among variables to attempt to fill in or recover the missing values. A few examples will help clarify this approach. In the sleep dataset, the variable S leep is the sum of the D ream and N onD variables. If you know a mammal’s scores on any two, you can derive the third. Thus, if there were some observations that were missing only one of the three variables, you could recover the missing information through addition or subtraction. As a second example, consider research that focuses on work/ life balance differences between generational cohorts (for example, Silents, Early Boomers, Late Boomers, Xers, Millennials), where cohorts are defined by their birth year. Participants are asked both their date of birth and their age. If date of birth is missing, you can recover their birth year (and therefore their generational cohort) by knowing their age and the date they completed the survey. An example that uses logical relationships to recover missing data comes from a set of leadership studies in which participants were asked if they were a manager (yes/ no) and the number of their direct reports (integer). If they left the manager question blank but indicated that they had one or more direct reports, it would be reasonable to infer that they were a manager. As a final example, I frequently engage in gender research that compares the leadership styles and effectiveness of men and women. Participants complete surveys that include their name (first and last), gender, and a detailed assessment of their leadership approach and impact. If participants leave the gender question blank, I have to impute the value in order to include them in the research. In one recent study of 66,000 managers, 11,000 (17 percent) had a missing value for gender. To remedy the situation, I employed the following rational process. First, I cross- tabulated first name with gender. Some first names were associated with males, some with females, and some with both. For example, “William” appeared 417 times and was always a male. Conversely, the name “Chris” appeared 237 times but was sometimes a male (86 percent) and sometimes a female (14 percent). If a first name appeared more than 20 times in the dataset and was always associated with males or with females (but never both), I assumed that the name represented a single gender. I used this assumption to create a gender lookup table for gender-specific first names. Using this lookup table for participants with missing gender values, I was able to recover 7,000 cases (63 percent of the missing responses). Download from Wow! eBook 364 CHAPTER 15 Advanced methods for missing data A rational approach typically requires creativity and thoughtfulness, along with a degree of data management skill. Data recovery may be exact (as in the sleep example) or approximate (as in the gender example). In the next section, we’ll explore an approach that creates complete datasets by removing observations. 15.6 Complete-case analysis (listwise deletion) In complete-case analysis, only observations containing valid data values on every vari- able are retained for further analysis. Practically, this involves deleting any row contain- ing one or more missing values, and is also known as listwise, or case-wise, deletion. Most popular statistical packages employ listwise deletion as the default approach for handling missing data. In fact, it’s so common that many analysts carrying out analyses like regression or ANOVA may not even realize that there’s a “missing values problem” to be dealt with! The function c omplete.cases() can be used to save the cases (rows) of a matrix or data frame without missing data: newdata <- mydata[complete.cases(mydata),] The same result can be accomplished with the n a.omit function: newdata <- na.omit(mydata) In both statements, any rows containing missing data are deleted from mydata before the results are saved to newdata. Suppose you’re interested in the correlations among the variables in the sleep study. Applying listwise deletion, you’d delete all mammals with missing data prior to calculating the correlations: > options(digits=1) > cor(na.omit(sleep)) BodyWgt BrainWgt NonD Dream Sleep Span Gest Pred Exp Danger BodyWgt 1.00 0.96 -0.4 -0.07 -0.3 0.47 0.71 0.10 0.4 0.26 BrainWgt 0.96 1.00 -0.4 -0.07 -0.3 0.63 0.73 -0.02 0.3 0.15 NonD -0.39 -0.39 1.0 0.52 1.0 -0.37 -0.61 -0.35 -0.6 -0.53 Dream -0.07 -0.07 0.5 1.00 0.7 -0.27 -0.41 -0.40 -0.5 -0.57 Sleep -0.34 -0.34 1.0 0.72 1.0 -0.38 -0.61 -0.40 -0.6 -0.60 Span 0.47 0.63 -0.4 -0.27 -0.4 1.00 0.65 -0.17 0.3 0.01 Gest 0.71 0.73 -0.6 -0.41 -0.6 0.65 1.00 0.09 0.6 0.31 Pred 0.10 -0.02 -0.4 -0.40 -0.4 -0.17 0.09 1.00 0.6 0.93 Exp 0.41 0.32 -0.6 -0.50 -0.6 0.32 0.57 0.63 1.0 0.79 Danger 0.26 0.15 -0.5 -0.57 -0.6 0.01 0.31 0.93 0.8 1.00 The correlations in this table are based solely on the 42 mammals that have complete data on all variables. (Note that the statement cor(sleep, use="complete.obs") would have produced the same results.) If you wanted to study the impact of life span and length of gestation on the amount of dream sleep, you could employ linear regression with listwise deletion: > fit <- lm(Dream ~ Span + Gest, data=na.omit(sleep)) > summary(fit) Download from Wow! eBook Multiple imputation 365 Call: lm(formula = Dream ~ Span + Gest, data = na.omit(sleep)) Residuals: Min 1Q Median 3Q Max -2.333 -0.915 -0.221 0.382 4.183 Coefficients: Estimate Std. Error t value Pr(>|t|) (Intercept) 2.480122 0.298476 8.31 3.7e-10 *** Span -0.000472 0.013130 -0.04 0.971 Gest -0.004394 0.002081 -2.11 0.041 * --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ‘ 1 Residual standard error: 1 on 39 degrees of freedom Multiple R-squared: 0.167, Adjusted R-squared: 0.125 F-statistic: 3.92 on 2 and 39 DF, p-value: 0.0282 Here you see that mammals with shorter gestation periods have more dream sleep (controlling for life span) and that life span is unrelated to dream sleep when control- ling for gestation period. The analysis is based on 42 cases with complete data. In the previous example, what would have happened if data=na.omit(sleep) had been replaced with data=sleep? Like many R function, l m() uses a limited definition of listwise deletion. Cases with any missing data on the variables fitted by the function (Dream, Span, and Gest in this case) would have been deleted. The analysis would have been based on 44 cases. Listwise deletion assumes that the data are MCAR (that is, the complete observations are a random subsample of the full dataset). In the current example, we’ve assumed that the 42 mammals used are a random subsample of the 62 mammals collected. To the degree that the MCAR assumption is violated, the resulting regression parameters will be biased. Deleting all observations with missing data can also reduce statistical power by reducing the available sample size. In the current example, listwise deletion reduced the sample size by 32 percent. Next, we’ll consider an approach that employs the entire dataset (including cases with missing data). 15.7 Multiple imputation M ultiple imputation (MI) provides an approach to missing values that’s based on re- peated simulations. MI is frequently the method of choice for complex missing values problems. In MI, a set of complete datasets (typically 3 to 10) is generated from an existing dataset containing missing values. Monte Carlo methods are used to fill in the missing data in each of the simulated datasets. Standard statistical methods are applied to each of the simulated datasets, and the outcomes are combined to provide estimated results and confidence intervals that take into account the uncertainty in- troduced by the missing values. Good implementations are available in R through the A melia, m ice, and m i packages. In this section we’ll focus on the approach provided by the mice (multivariate imputation by chained equations) package. Download from Wow! eBook 366 CHAPTER 15 Advanced methods for missing data with() pool() Final result Imputed datasets Analysis results Data frame mice() Figure 15.5 Steps in applying multiple imputation to missing data via the mice approach. To understand how the mice package operates, consider the diagram in figure 15.5. The function m ice() starts with a data frame containing missing data and returns an object containing several complete datasets (the default is 5). Each complete dataset is created by imputing values for the missing data in the original data frame. There’s a random component to the imputations, so each complete dataset is slightly different. The w ith() function is then used to apply a statistical model (for example, linear or generalized linear model) to each complete dataset in turn. Finally, the p ool() function combines the results of these separate analyses into a single set of results. The standard errors and p-values in this final model correctly reflect the uncertainty produced by both the missing values and the multiple imputations. How does the m ice() function impute missing values? Missing values are imputed by G ibbs sampling. By default, each variable containing missing values is predicted from all other variables in the dataset. These prediction equations are used to impute plausible values for the missing data. The process iterates until convergence over the missing values is achieved. For each variable, the user can choose the form of the prediction model (called an elementary imputation method), and the variables entered into it. By default, predictive mean matching is used to replace missing data on con- tinuous variables, while logistic or polytomous logistic regression is used for target variables that are dichotomous (factors with two levels) or polytomous (factors with more than two levels) respectively. Other elementary imputation methods include Bayesian linear regression, discriminant function analysis, two-level normal impu- tation, and random sampling from observed values. Users can supply their own methods as well. Download from Wow! eBook Multiple imputation 367 An analysis based on the mice package will typically conform to the following structure: library(mice) imp <- mice(mydata, m) fit <- with(imp, analysis) pooled <- pool(fit) summary(pooled) where ■ mydata is a matrix or data frame containing missing values. ■ imp is a list object containing the m imputed datasets, along with information on how the imputations were accomplished. By default, m=5. ■ analysis is a formula object specifying the statistical analysis to be applied to each of the m imputed datasets. Examples include lm() for linear regression models, glm() for generalized linear models, gam() for generalized additive models, and nbrm() for negative binomial models. Formulas within the paren- theses give the response variables on the left of the ~ and the predictor variables (separated by + signs) on the right. ■ fit is a list object containing the results of the m separate statistical analyses. ■ pooled is a list object containing the averaged results of these m statistical analyses. Let’s apply multiple imputation to our sleep dataset. We’ll repeat the analysis from sec- tion 15.6, but this time, use all 62 mammals. Set the seed value for the random number generator to 1234 so that your results will match mine. > library(mice) > data(sleep, package="VIM") > imp <- mice(sleep, seed=1234) […output deleted to save space…] > fit <- with(imp, lm(Dream ~ Span + Gest)) > pooled <- pool(fit) > summary(pooled) est se t df Pr(>|t|) lo 95 (Intercept) 2.58858 0.27552 9.395 52.1 8.34e-13 2.03576 Span -0.00276 0.01295 -0.213 52.9 8.32e-01 -0.02874 Gest -0.00421 0.00157 -2.671 55.6 9.91e-03 -0.00736 hi 95 nmis fmi (Intercept) 3.14141 NA 0.0870 Span 0.02322 4 0.0806 Gest -0.00105 4 0.0537 Here, you see that the regression coefficient for Span isn’t significant (p ≅ 0.08), and the coefficient for Gest is significant at the p<0.01 level. If you compare these results with those produced by a complete case analysis (section 15.6), you see that you’d come to the same conclusions in this instance. Length of gestation has a (statistically) significant, negative relationship with amount of dream sleep, controlling for life span. Although the complete-case analysis was based on the 42 mammals with complete data, Download from Wow! eBook 368 CHAPTER 15 Advanced methods for missing data the current analysis is based on information gathered from the full set of 62 mammals. By the way, the f mi column reports the fraction of missing information (that is, the proportion of variability that is attributable to the uncertainty introduced by the miss- ing data). You can access more information about the imputation by examining the objects created in the analysis. For example, let’s view a summary of the imp object: > imp Multiply imputed data set Call: mice(data = sleep, seed = 1234) Number of multiple imputations: 5 Missing cells per column: BodyWgt BrainWgt NonD Dream Sleep Span Gest Pred 0 0 14 12 4 4 4 0 Exp Danger 0 0 Imputation methods: BodyWgt BrainWgt NonD Dream Sleep Span Gest Pred "" "" "pmm" "pmm" "pmm" "pmm" "pmm" "" Exp Danger "" "" VisitSequence: NonD Dream Sleep Span Gest 3 4 5 6 7 PredictorMatrix: BodyWgt BrainWgt NonD Dream Sleep Span Gest Pred Exp Danger BodyWgt 0 0 0 0 0 0 0 0 0 0 BrainWgt 0 0 0 0 0 0 0 0 0 0 NonD 1 1 0 1 1 1 1 1 1 1 Dream 1 1 1 0 1 1 1 1 1 1 Sleep 1 1 1 1 0 1 1 1 1 1 Span 1 1 1 1 1 0 1 1 1 1 Gest 1 1 1 1 1 1 0 1 1 1 Pred 0 0 0 0 0 0 0 0 0 0 Exp 0 0 0 0 0 0 0 0 0 0 Danger 0 0 0 0 0 0 0 0 0 0 Random generator seed value: 1234 From the resulting output, you can see that five synthetic datasets were created, and that the predictive mean matching (pmm) method was used for each variable with miss- ing data. No imputation ("") was needed for BodyWgt, BrainWgt, Pred, Exp, or Dan- ger, because they had no missing values. The Visit Sequence tells you that variables were imputed from right to left, starting with NonD and ending with Gest. Finally, the Predictor Matrix indicates that each variable with missing data was imputed using all the other variables in the dataset. (In this matrix, the rows represent the variables be- ing imputed, the columns represent the variables used for the imputation, and 1’s/0’s indicate used/not used). You can view the actual imputations by looking at subcomponents of the imp object. For example, Download from Wow! eBook Multiple imputation 369 > imp$imp$Dream 1 2 3 4 5 1 0.5 0.5 0.5 0.5 0.0 3 2.3 2.4 1.9 1.5 2.4 4 1.2 1.3 5.6 2.3 1.3 14 0.6 1.0 0.0 0.3 0.5 24 1.2 1.0 5.6 1.0 6.6 26 1.9 6.6 0.9 2.2 2.0 30 1.0 1.2 2.6 2.3 1.4 31 5.6 0.5 1.2 0.5 1.4 47 0.7 0.6 1.4 1.8 3.6 53 0.7 0.5 0.7 0.5 0.5 55 0.5 2.4 0.7 2.6 2.6 62 1.9 1.4 3.6 5.6 6.6 displays the five imputed values for each of the 12 mammals with missing data on the Dream variable. A review of these matrices helps you determine if the imputed values are reasonable. A negative value for length of sleep might give you pause (or nightmares). You can view each of the m imputed datasets via the c omplete() function. The format is complete(imp, action=#) where # specifies one of the m synthetically complete datasets. For example, > dataset3 <- complete(imp, action=3) > dataset3 BodyWgt BrainWgt NonD Dream Sleep Span Gest Pred Exp Danger 1 6654.00 5712.0 2.1 0.5 3.3 38.6 645 3 5 3 2 1.00 6.6 6.3 2.0 8.3 4.5 42 3 1 3 3 3.38 44.5 10.6 1.9 12.5 14.0 60 1 1 1 4 0.92 5.7 11.0 5.6 16.5 4.7 25 5 2 3 5 2547.00 4603.0 2.1 1.8 3.9 69.0 624 3 5 4 6 10.55 179.5 9.1 0.7 9.8 27.0 180 4 4 4 […output deleted to save space…] displays the third (out of five) complete datasets created by the multiple imputation process. Due to space limitations, we’ve only briefly considered the MI implementation provided in the m ice package. The m i and A melia packages also contain valuable approaches. If you are interested in the multiple imputation approach to missing data, I recommend the following resources: ■ The multiple imputation FAQ page (www.stat.psu.edu/~jls/mifaq.html) ■ Articles by Van Buuren and Groothuis-Oudshoorn (2010) and Yu-Sung, Gelman, Hill, and Yajima (2010) ■ Amelia II: A Program for Missing Data (http://gking.harvard.edu/amelia/) Each can help to reinforce and extend your understanding of this important, but un- derutilized, methodology. Download from Wow! eBook 370 CHAPTER 15 Advanced methods for missing data 15.8 Other approaches to missing data R supports several other approaches for dealing with missing data. Although not as broadly applicable as the methods described thus far, the packages described in table 15.2 offer functions that can be quite useful in specialized circumstances. Table 15.2 Specialized methods for dealing with missing data Package Description H misc Contains numerous functions supporting simple imputation, multiple imputation, and imputation using canonical variates m vnmle Maximum likelihood estimation for multivariate normal data with missing values c at Multiple imputation of multivariate categorical data under log-linear models a rrayImpute, a rrayMissPattern, S eqKnn Useful functions for dealing with missing microarray data l ongitudinalData Contains utility functions, including interpolation routines for imputing missing time series values k mi Kaplan–Meier multiple imputation for survival analysis with missing data m ix Multiple imputation for mixed categorical and continuous data under the general location model p an Multiple imputation for multivariate panel or clustered data Finally, there are two methods for dealing with missing data that are still in use, but should now be considered obsolete. They are pairwise deletion and simple imputation. 15.8.1 Pairwise deletion Pairwise deletion is often considered an alternative to listwise deletion when working with datasets containing missing values. In pairwise deletion, observations are only deleted if they’re missing data for the variables involved in a specific analysis. Consider the following code: > cor(sleep, use="pairwise.complete.obs") BodyWgt BrainWgt NonD Dream Sleep Span Gest Pred Exp Danger BodyWgt 1.00 0.93 -0.4 -0.1 -0.3 0.30 0.7 0.06 0.3 0.13 BrainWgt 0.93 1.00 -0.4 -0.1 -0.4 0.51 0.7 0.03 0.4 0.15 NonD -0.38 -0.37 1.0 0.5 1.0 -0.38 -0.6 -0.32 -0.5 -0.48 Dream -0.11 -0.11 0.5 1.0 0.7 -0.30 -0.5 -0.45 -0.5 -0.58 Sleep -0.31 -0.36 1.0 0.7 1.0 -0.41 -0.6 -0.40 -0.6 -0.59 Span 0.30 0.51 -0.4 -0.3 -0.4 1.00 0.6 -0.10 0.4 0.06 Gest 0.65 0.75 -0.6 -0.5 -0.6 0.61 1.0 0.20 0.6 0.38 Pred 0.06 0.03 -0.3 -0.4 -0.4 -0.10 0.2 1.00 0.6 0.92 Exp 0.34 0.37 -0.5 -0.5 -0.6 0.36 0.6 0.62 1.0 0.79 Danger 0.13 0.15 -0.5 -0.6 -0.6 0.06 0.4 0.92 0.8 1.00 Download from Wow! eBook Summary 371 In this example, correlations between any two variables use all available observations for those two variables (ignoring the other variables). The correlation between Body- Wgt and BrainWgt is based on all 62 mammals (the number of mammals with data on both variables). The correlation between BodyWgt and NonD is based on the 42 mam- mals, and the correlation between Dream and NonDream is based on 46 mammals. Although pairwise deletion appears to use all available data, in fact each calculation is based on a different subset of the data. This can lead to distorted and difficult-to- interpret results. I recommend staying away from this approach. 15.8.2 Simple (nonstochastic) imputation In simple imputation, the missing values in a variable are replaced with a single value (for example, mean, median, or mode). Using m ean substitution you could replace miss- ing values on Dream with the value 1.97 and missing values on NonD with the value 8.67 (the means on Dream and NonD, respectively). Note that the substitution is nonstochas- tic, meaning that random error isn’t introduced (unlike multiple imputation). An advantage to simple imputation is that it solves the “missing values problem” without reducing the sample size available for the analyses. Simple imputation is, well, simple, but it produces biased results for data that aren’t MCAR. If there are moderate to large amounts of missing data, simple imputation is likely to underestimate standard errors, distort correlations among variables, and produce incorrect p-values in statistical tests. Like pairwise deletion, I recommend avoiding this approach for most missing data problems. 15.9 Summary Most statistical methods assume that the input data is complete and doesn’t include missing values (for example, NA, NaN, Inf). But most datasets in real-world settings contain missing values. Therefore, you must either delete the missing values or replace them with reasonable substitute values before continuing with the desired analyses. Often, statistical packages will provide default methods for handling missing data, but these approaches may not be optimal. Therefore, it’s important that you understand the various approaches available, and the ramifications of using each. In this chapter, we examined methods for identifying missing values and exploring patterns of missing data. Our goal was to understand the mechanisms that led to the missing data and their possible impact on subsequent analyses. We then reviewed three popular methods for dealing with missing data: a rational approach, listwise deletion, and the use of multiple imputation. Rational approaches can be used to recover missing values when there are redundancies in the data, or external information that can be brought to bear on the problem. The listwise deletion of missing data is useful if the data are MCAR and the subsequent sample size reduction doesn’t seriously impact the power of statistical tests. Multiple imputation is rapidly becoming the method of choice for complex Download from Wow! eBook 372 CHAPTER 15 Advanced methods for missing data missing data problems when you can assume that the data are MCAR or MAR. Although many analysts may be unfamiliar with multiple imputation strategies, user-contributed packages (mice, mi, Amelia) make them readily accessible. I believe that we’ll see a rapid growth in their use over the next few years. We ended the chapter by briefly mentioning R packages that provide specialized approaches for dealing with missing data, and singled out general approaches for handling missing data (pairwise deletion, simple imputation) that should be avoided. In the next chapter, we’ll explore advanced graphical methods, including the use of lattice graphs, the ggplot2 system, and interactive graphical methods. Download from Wow! eBook 373 16Advanced graphics This chapter covers ■ The grammar of graphs via ggplot2 Trellis graphs and the lattice package ■ Interactive graphics■ In previous chapters, we created a wide variety of both general and specialized graphs (and had lots of fun in the process). Most were produced using R’s base graphics sys- tem. Given the diversity of methods available in R, it may not surprise you to learn that there are actually four separate and complete graphics systems currently available. In addition to base graphics, we have graphics systems provided by the grid, lattice, and ggplot2 packages. Each is designed to expand on the capabilities of, and correct for deficiencies in, R’s base graphics system. The grid graphics system provides low-level access to graphic primitives, giving programmers a great deal of flexibility in the creation of graphic output. The lattice package provides an intuitive approach for examining multivariate relationships through conditional 1-, 2-, or 3-dimensional graphs called trellis graphs. The ggplot2 package provides a method of creating innovative graphs based on a comprehensive graphical “grammar.” In this chapter, we’ll start with an overview of the four graphic systems. Then we’ll focus on graphs that can be generated with the lattice and ggplot2 packages. These packages greatly expand the range and quality of the graphs you can produce in R. Download from Wow! eBook 374 CHAPTER 16 Advanced graphics We’ll end the chapter by considering interactive graphics. Interacting with graphs in real time can help you understand your data more thoroughly and develop greater insights into the relationships among variables. Here, we’ll focus on the functionality offered by the iplots, playwith, latticist, and rggobi packages. 16.1 The four graphic systems in R As stated earlier, four primary graphical systems are available in R. The base graphic system in R, written by Ross Ihaka, is included in every R installation. Most of the graphs produced in previous chapters rely on base graphics functions. The grid graphics system, written by Paul Murrell (2006), is implemented through the grid package. Grid graphics offer a lower-level alternative to the standard graphics system. The user can create arbitrary rectangular regions on graphics devices, define coordinate systems for each region, and use a rich set of drawing primitives to control the arrangement and appearance of graphic elements. This flexibility makes grid graphics a valuable tool for software developers. But the grid package doesn’t provide functions for producing statistical graphics or complete plots. Because of this, the package is rarely used directly by data analysts. The lattice package , written by Deepayan Sarkar (2008), implements trellis graphics as outlined by Cleveland (1985, 1993) and described on the Trellis website (http:// netlib.bell-labs.com/cm/ms/departments/sia/project/trellis/). Built using the grid package, the lattice package has grown beyond Cleveland’s original approach to visualizing multivariate data, and now provides a comprehensive alternative system for creating statistical graphics in R. The ggplot2 package , written by Hadley Wickham (2009a), provides a system for creating graphs based on the grammar of graphics described by Wilkinson (2005) and expanded by Wickham (2009b). The intention of the ggplot2 package is to provide a comprehensive, grammar-based system for generating graphs in a unified and coherent manner, allowing users to create new and innovative data visualizations. Access to the four systems differs, as outlined in table 16.1. Base graphic functions are automatically available. To access grid and lattice function s, you must load the package explicitly (for example, library(lattice)) . To access ggplot2 functions , you have to download and install the package (install.packages("ggplot2")) before first use, and then load it (library(ggplot2)) . Table 16.1 Access to graphic systems System Included in base installation?Must be explicitly loaded? base Yes No grid Yes Yes lattice Yes Yes ggplot2 No Yes Download from Wow! eBook The lattice package 375 Because our attention is primarily focused on practical data analyses, we won’t elabo- rate on the grid package in this chapter. (If you’re interested, refer to Dr. Murrell’s Grid website [www.stat.auckland.ac.nz/~paul/grid/grid.html] for details on this pack- age.) Instead, we’ll explore the lattice and ggplot2 packages in some detail. Each allows you to create unique and useful graphs that aren’t easily created in other ways. 16.2 The lattice package The lattice package provides a comprehensive graphical system for visualizing uni- variate and multivariate data. In particular, many users turn to the lattice package because of its ability to easily generate trellis graphs. A trellis graph displays the distribution of a variable or the relationship between variables, separately for each level of one or more other variables. Consider the following question: How do the heights of singers in the New York Choral Society vary by their vocal parts? Data on the heights and voice parts of choral members is provided in the singer dataset contained in the lattice package. In the following code library(lattice) histogram(~height | voice.part, data = singer, main="Distribution of Heights by Voice Pitch", xlab="Height (inches)") height is the dependent variable, voice.part is called the conditioning variable, and a histogram is created for each of the eight voice parts. The graph is shown in figure 16.1. It appears that tenors and basses tend to be taller than altos and sopranos. In trellis graphs, a separate panel is created for each level of the conditioning variable. If more than one conditioning variable is specified, a panel is created for each combination of factor levels. The panels are arranged into an array to facilitate comparisons. A label is provided for each panel in an area called the strip. As you’ll see, the user has control over the graph displayed in each panel, the format and placement of the strip, the arrangement of the panels, the placement and content of legends, and many other graphic features. The lattice package provides a wide variety of functions for producing univariate (dot plots, kernel density plots, histograms, bar charts, box plots), bivariate (scatter plots, strip plots, parallel box plots), and multivariate (3D plots, scatter plot matrices) graphs. Each high-level graphing function follows the format graph_function(formula, data=, options) where: ■ graph_function is one of the functions listed in the second column of table 16.2. ■ formula specifies the variable(s) to display and any conditioning variables. ■ data specifies a data frame. ■ options are comma-separated parameters used to modify the content, arrange- ment, and annotation of the graph. See table 16.3 for a description of common options. Download from Wow! eBook 376 CHAPTER 16 Advanced graphics Distribution of Heights by Voice Pitch Height (inches) P e r c e n t o f T o t a l 0 10 20 30 40 60 65 70 75 Bass 2 Bass 1 60 65 70 75 Tenor 2 Tenor 1 Alto 2 0 10 20 30 40 Alto 1 0 10 20 30 40 Soprano 2 60 65 70 75 Soprano 1 Figure 16.1 Trellis graph of singer heights by voice pitch Let lowercase letters represent numeric variables and uppercase letters represent categorical variables (factors). The formula in a high-level graphing function typically takes the form y ~ x | A * B where variables on the left side of the vertical bar are called the primary variables and variables on the right are the conditioning variables. Primary variables map variables to the axes in each panel. Here, y~x describes the variables to place on the vertical and horizontal axes, respectively. For single-variable plots, replace y~x with ~x. For 3D plots, replace y~x with z~x*y. Finally, for multivariate plots (scatter plot matrix or par- allel coordinates plot) replace y~x with a data frame. Note that conditioning variables are always optional. Following this logic, ~x|A displays numeric variable x for each level of factor A. y~x|A*B displays the relationship between numeric variables y and x separately for every combination of factor A and B levels. A~x displays categorical variable A on the vertical axis and numeric variable x on the horizontal axis. ~x displays numeric variable x alone. Other examples are shown in table 16.2. To gain a quick overview of lattice graphs, try running the code in listing 16.1. The graphs are based on the automotive data (mileage, weight, number of gears, number Download from Wow! eBook The lattice package 377 Table 16.2 Graph types and corresponding functions in the lattice package Graph type Function Formula examples 3D contour plot contourplot() z~x*y 3D level plot levelplot() z~y*x 3D scatter plot cloud() z~x*y|A 3D wireframe graph wireframe() z~y*x Bar chart barchart() x~A or A~x Box plot bwplot() x~A or A~x Dot plot dotplot() ~x|A Histogram histogram() ~x Kernel density plot densityplot() ~x|A*B Parallel coordinates plot parallel() dataframe Scatter plot xyplot() y~x|A Scatter plot matrix splom() dataframe Strip plots stripplot()A~x or x~A Note: In these formulas, lowercase letters represent numeric variables and uppercase letters represent categorical variables. of cylinders, and so on) included in the mtcars data frame . You may want to vary the formulas and view the results. (The resulting output has been omitted to save space.) Listing 16.1 lattice plot examples library(lattice) attach(mtcars) gear <- factor(gear, levels=c(3, 4, 5), labels=c("3 gears", "4 gears", "5 gears")) cyl <- factor(cyl, levels=c(4, 6, 8), labels=c("4 cylinders", "6 cylinders", "8 cylinders")) densityplot(~mpg, main="Density Plot", xlab="Miles per Gallon") densityplot(~mpg | cyl, main="Density Plot by Number of Cylinders", xlab="Miles per Gallon") bwplot(cyl ~ mpg | gear, Create factors with value labels Download from Wow! eBook 378 CHAPTER 16 Advanced graphics main="Box Plots by Cylinders and Gears", xlab="Miles per Gallon", ylab="Cylinders") xyplot(mpg ~ wt | cyl * gear, main="Scatter Plots by Cylinders and Gears", xlab="Car Weight", ylab="Miles per Gallon") cloud(mpg ~ wt * qsec | cyl, main="3D Scatter Plots by Cylinders") dotplot(cyl ~ mpg | gear, main="Dot Plots by Number of Gears and Cylinders", xlab="Miles Per Gallon") splom(mtcars[c(1, 3, 4, 5, 6)], main="Scatter Plot Matrix for mtcars Data") detach(mtcars) High-level plotting functions in the lattice package produce graphic objects that can be saved and manipulated. For example, library(lattice) mygraph <- densityplot(~height|voice.part, data=singer) creates a trellis density plot and saves it as object mygraph. But no graph is displayed. Issuing the statement plot(mygraph) (or simply mygraph) will display the graph. It’s easy to modify lattice graphs through the use of options. Common options are given in table 16.3. You’ll see examples of many of these later in the chapter. Table 16.3 Common options for lattice high-level graphing functions Options Description aspect A number specifying the aspect ratio (height/width) for the graph in each panel. col , pch , lty , lwd Vectors specifying the colors, symbols, line types, and line widths to be used in plotting, respectively. groups Grouping variable (factor). index.cond List specifying the display order of the panels. key (or auto.key) Function used to supply legend(s) for grouping variable(s). layout Two-element numeric vector specifying the arrangement of the panels (number of columns, number of rows). If desired, a third element can be added to indicate the number of pages. main, sub Character vectors specifying the main title and subtitle. panel Function used to generate the graph in each panel. Download from Wow! eBook The lattice package 379 Table 16.3 Common options for lattice high-level graphing functions (continued) Options Description scales List providing axis annotation information. strip Function used to customize panel strips. split , position Numeric vectors used to place more than one graph on a page. type Character vector specifying one or more plotting options for scatter plots (p=points, l=lines, r=regression line, smooth=loess fit, g=grid, and so on). xlab, ylab Character vectors specifying horizontal and vertical axis labels. xlim , ylim Two-element numeric vectors giving the minimum and maximum values for the horizontal and vertical axes, respectively. You can issue these options in the high-level function calls or within the panel func- tions discussed in section 16.2.2. You can also use the update() function to modify a lattice graphic object. Continuing the singer example, the following update(mygraph, col=”red”, pch=16, cex=.8, jitter=.05, lwd=2) would redraw the graph using red curves and symbols (color="red"), filled dots (pch=16), smaller (cex=.8) and more highly jittered points (jitter=.05), and curves of double thickness (lwd=2). Now that we’ve reviewed the general structure of a high- level lattice function, let’s look at conditioning variables in more detail. 16.2.1 Conditioning variables As you’ve seen, one of the most powerful features of lattice graphs is the ability to add conditioning variables. If one conditioning variable is present, a separate panel is created for each level. If two conditioning variables are present, a separate panel is created for each combination of levels for the two variables. It’s rarely useful to include more than two conditioning variables. Typically, conditioning variables are factors. But what if you want to condition on a continuous variable? One approach would be to transform the continuous variable into a discrete variable using R’s cut() function . Alternatively, the lattice package provides functions for transforming a continuous variable into a data structure called a shingle. Specifically, the continuous variable is divided up into a series of (possibly) overlapping ranges. For example, the function myshingle <- equal.count(x, number=#, overlap=proportion) will take continuous variable x and divide it up into # intervals, with proportion overlap, and equal numbers of observations in each range, and return it as the vari- able myshingle (of class shingle). Printing or plotting this object (for example, plot(myshingle)) will display the shingle’s intervals. Download from Wow! eBook 380 CHAPTER 16 Advanced graphics Once a continuous variable has been converted to a shingle, you can use it as a conditioning variable. For example, let’s use the mtcars dataset to explore the relationship between miles per gallon and car weight conditioned on engine displacement. Because engine displacement is a continuous variable, first let’s convert it to a shingle variable with three levels: displacement <- equal.count(mtcars$disp, number=3, overlap=0) Next, use this variable in the xyplot() function: xyplot(mpg~wt|displacement, data=mtcars, main = "Miles per Gallon vs. Weight by Engine Displacement", xlab = "Weight", ylab = "Miles per Gallon", layout=c(3, 1), aspect=1.5) The results are shown in figure 16.2. Note that we’ve also used options to modify the layout of the panels (three columns and one row) and the aspect ratio (height/width) in order to make comparisons among the three groups easier. You can see that the labels in the panel strips of figure 16.1 and figure 16.2 differ. The representation in figure 16.2 indicates the continuous nature of the conditioning variable, with the darker color indicating the range of values for the conditioning variable in the given panel. In the next section, we’ll use panel functions to customize the output further. Miles per Gallon vs. Weight by Engine Displacement Weight M i l e p e r G a l l o n 10 15 20 25 30 35 2 3 4 5 displacement 2 3 4 5 displacement 2 3 4 5 displacement Figure 16.2 Trellis plot of mpg versus car weight conditioned on engine displacement. Because engine displacement is a continuous variable, it has been converted to three nonoverlapping shingles with equal numbers of observations. Download from Wow! eBook The lattice package 381 16.2.2 Panel functions Each of the high-level plotting functions in table 16.2 employs a default function to draw the panels. These default functions follow the naming convention panel. graph_function, where graph_function is the high-level function. For example, xyplot(mpg~wt|displacement, data=mtcars) could have also be written as xyplot(mpg~wt|displacement, data=mtcars, panel=panel.xyplot) This is a powerful feature because it allows you to replace the default panel function with a customized function of your own design. You can incorporate one or more of the 50+ default panel functions in the lattice package into your customized function as well. Customized panel functions give you a great deal of flexibility in designing an output that meets your needs. Let’s look at some examples. In the previous section, you plotted gas mileage by automobile weight, conditioned on engine displacement. What if you wanted to include regression lines, rug plots, and grid lines? You can do this by creating your own panel function (see the following listing). The resulting graph is provided in figure 16.3. Listing 16.2 xyplot with custom panel function displacement <- equal.count(mtcars$disp, number=3, overlap=0) mypanel <- function(x, y) { panel.xyplot(x, y, pch=19) panel.rug(x, y) panel.grid(h=-1, v=-1) q panel.lmline(x, y, col="red", lwd=1, lty=2) } xyplot(mpg~wt|displacement, data=mtcars, layout=c(3, 1), aspect=1.5, main = "Miles per Gallon vs. Weight by Engine Displacement", xlab = "Weight", ylab = "Miles per Gallon", panel = mypanel) Here, we’ve wrapped four separate building block functions into our own mypanel() function and applied it within xyplot() through the panel= option q. The panel. xyplot() function generates the scatter plot using a filled circle (pch=19). The panel. rug() function adds rug plots to both the x and y axes of each panel. panel.rug(x, FALSE) or panel.rug(FALSE, y) would have added rugs to just the horizontal or ver- tical axis, respectively. The panel.grid() function adds horizontal and vertical grid lines (using negative numbers forces them to line up with the axis labels). Finally, the panel.lmline() function adds a regression line that’s rendered as red (col="red"), dashed (lty=2) lines, of standard thickness (lwd=1). Each default panel function has its own structure and options. See the help page on each (for example, help(panel. abline)) for further details. Customized panel function Download from Wow! eBook 382 CHAPTER 16 Advanced graphics Miles per Gallon vs. Weight by Engine Displacement Weight M i l e p e r G a l l o n 10 15 20 25 30 35 2 3 4 5 displacement 2 3 4 5 displacement 2 3 4 5 displacement Figure 16.3 Trellis plot of mpg versus car weight conditioned on engine displacement. A custom panel function has been used to add regression lines, rug plots, and grid lines. As a second example, we’ll graph the relationship between gas mileage and engine dis- placement (considered as a continuous variable), conditioned on type of automobile transmission. In addition to creating separate panels for automatic and manual trans- mission engines, we’ll add smoothed fit lines and horizontal mean lines. The code is given in the following listing. Listing 16.3 xyplot with custom panel function and additional options library(lattice) mtcars$transmission <- factor(mtcars$am, levels=c(0,1), labels=c("Automatic", "Manual")) panel.smoother <- function(x, y) { panel.grid(h=-1, v=-1) panel.xyplot(x, y) panel.loess(x, y) panel.abline(h=mean(y), lwd=2, lty=2, col="green") } xyplot(mpg~disp|transmission,data=mtcars, scales=list(cex=.8, col="red"), panel=panel.smoother, xlab="Displacement", ylab="Miles per Gallon", main="MGP vs Displacement by Transmission Type", sub = "Dotted lines are Group Means", aspect=1) The graph produced by this code is provided in figure 16.4. Download from Wow! eBook The lattice package 383 MGP vs Displacement by Transmission Type Dotted lines are Group Means Displacement M i l e s p e r G a l l o n 10 15 20 25 30 35 100 200 300 400 Automatic 100 200 300 400 Manual Figure 16.4 Trellis graph of mpg versus engine displacement conditioned on transmission type. Smoothed lines (loess), grids, and group mean levels have been added. There are several things to note in this new code. The panel.xyplot() function plots the individual points, and the panel.loess() function plots nonparametric fit lines in each panel. The panel.abline() function adds horizontal reference lines at the mean mpg value for each level of the conditioning variable. (If we had replaced h=mean(y) with h=mean(mtcars$mpg), a single reference line would have been drawn at the mean mpg value for the entire sample.) The scales= option renders scale an- notations in red and at 80 percent of their default size. In the previous example, we could have used scales=list(x=list() , y=list()) to specify separate options for the horizontal and vertical axes. See help(xyplot) for details on the many scale options available. In the next section, you’ll learn how to superimpose data from groups of observations, rather than presenting them in separate panels. 16.2.3 Grouping variables When you include a conditioning variable in a lattice graph formula, a separate panel is produced for each level of that variable. If you want to superimpose the results for each level instead, you can specify the variable as a group variable. Let’s say that you want to display the distribution of gas mileage for cars with manual and automatic transmissions using kernel density plots. You can superimpose these plots using this code: Download from Wow! eBook 384 CHAPTER 16 Advanced graphics library(lattice) mtcars$transmission <- factor(mtcars$am, levels=c(0, 1), labels=c("Automatic", "Manual")) densityplot(~mpg, data=mtcars, group=transmission, main="MPG Distribution by Transmission Type", xlab="Miles per Gallon", auto.key=TRUE) The resulting graph is presented in figure 16.5. By default, the group=option super- imposes the plots from each level of the grouping variable. Points are plotted as open circles, lines are solid, and level information is distinguished by color. As you can see, the colors are difficult to differentiate when printed in grayscale. Later you’ll see how to change these defaults. Note that legends or keys aren’t produced by default. The option auto.key=TRUE will create a rudimentary legend and place it above the graph. You can make limited changes to this automated key by specifying options in a list. For example, auto.key=list(space=”right”, columns=1, title=”Transmission”) would move the legend to the right of the graph, present the key values in a single column, and add a legend title. If you want to exert greater control over the legend, you can use the key= option. An example is given in listing 16.4. The resulting graph is provided in figure 16.6. MPG Distribution by Transmission Type Miles per Gallon D e n s i t y 0.00 0.02 0.04 0.06 0.08 0.10 10 20 30 40 Automatic Manual Figure 16.5 Kernel density plots for miles per gallon grouped by transmission type. Jittered points are provided on the horizontal axis. Download from Wow! eBook The lattice package 385 Listing 16.4 Kernel density plot with a group variable and customized legend library(lattice) mtcars$transmission <- factor(mtcars$am, levels=c(0, 1), labels=c("Automatic", "Manual")) colors = c("red", "blue") lines = c(1,2) qpoints = c(16,17) key.trans <- list(title="Trasmission", space="bottom", columns=2, w text=list(levels(mtcars$transmission)), points=list(pch=points, col=colors), lines=list(col=colors, lty=lines), cex.title=1, cex=.9) densityplot(~mpg, data=mtcars, group=transmission, main="MPG Distribution by Transmission Type", xlab="Miles per Gallon", pch=points, lty=lines, col=colors, lwd=2, jitter=.005, e key=key.trans) Here, the plotting symbols, line types, and colors are specified as vectors q. The first element of each vector will be applied to the first level of the group variable, the sec- ond element to the second level, and so forth. A list object is created to hold the legend options w. These options place the legend below the graph in two columns, and include the level names, point symbols, line types, and colors. The legend title is rendered slightly larger than the text for the symbols. MPG Distribution by Transmission Type Miles per Gallon D e n s i t y 0.00 0.02 0.04 0.06 0.08 0.10 10 20 30 40 Trasmission Automatic Manual Figure 16.6 Kernel density plots for miles per gallon grouped by transmission type. Graphical parameters have been modified and a customized legend has been added. The custom legend specifies color, shape, line type, character size, and title. Color, line, point specifications Legend customization Density plot customization Download from Wow! eBook 386 CHAPTER 16 Advanced graphics The same plot symbols, line types, and colors are specified within the densityplot() function e. Additionally, the line width and jitter are increased to improve the ap- pearance of the graph. Finally, the key is set to use the previously defined list. This ap- proach to specifying a legend for the grouping variable allows a great deal of flexibility. In fact, you can create more than one legend and place them in different areas of the graph (not shown here). Before completing this section, let’s consider an example that includes group and conditioning variables in a single plot. The CO2 data frame, included with the base R installation, describes a study of cold tolerance of the grass species Echinocholoa crus-galli. The data describe carbon dioxide uptake rates (uptake) for 12 plants (Plant), at seven ambient carbon dioxide concentrations (conc). Six plants were from Quebec and six plants were from Mississippi. Three plants from each location were studied under chilled conditions and three plants were studied under nonchilled conditions. In this example, Plant is the group variable and both Type (Quebec/Mississippi) and Treatment (chilled/nonchilled) are conditioning variables. The following code produces the plot in figure 16.7. Listing 16.5 xyplot with group and conditioning variables and customized legend library(lattice) colors <- "darkgreen" symbols <- c(1:12) linetype <- c(1:3) key.species <- list(title="Plant", space="right", text=list(levels(CO2$Plant)), points=list(pch=symbols, col=colors)) xyplot(uptake~conc|Type*Treatment, data=CO2, group=Plant, type="o", pch=symbols, col=colors, lty=linetype, main="Carbon Dioxide Uptake\nin Grass Plants", ylab=expression(paste("Uptake ", bgroup("(", italic(frac("umol","m"^2)), ")"))), xlab=expression(paste("Concentration ", bgroup("(", italic(frac(mL,L)), ")"))), sub = "Grass Species: Echinochloa crus-galli", key=key.species) Note the use of \n to give you a two-line title and the use of the expression() func- tion to add mathematical notation to the axis labels. Here, color is suppressed as a group differentiator by specifying a single color in the col= option. In this case, add- ing 12 different colors is overkill and distracts from the goal of easily visualizing the relationships in each panel. Clearly, there’s something different about the Mississippi grasses in the chilled condition. Download from Wow! eBook The lattice package 387 Carbon Dioxide Uptake in Grass Plants Concentration mL L U p t a k e u m o l m 2 10 20 30 40 200 400 600 800 1000 Quebec nonchilled Mississippi nonchilled Quebec chilled 200 400 600 800 1000 10 20 30 40 Mississippi chilled Plant Qn1 Qn2 Qn3 Qc1 Qc3 Qc2 Mn3 Mn2 Mn1 Mc2 Mc3 Mc1 Figure 16.7 xyplot showing the impact of ambient carbon dioxide concentrations on carbon dioxide uptake for 12 plants in two treatment conditions and two types. Plant is the group variable and Treatment and Type are the conditioning variables. Up to this point, you’ve been modifying graphic elements in your charts through op- tions passed to either the high-level graph function (for example, xyplot(pch=17)) or within the panel functions that they use (for example, panel.xyplot(pch=17)). But such changes are in effect only for the duration of the function call. In the next section, we’ll review a method for changing graphical parameters that persists for the duration of the interactive session or batch execution. 16.2.4 Graphic parameters In chapter 3, you learned how to view and set default graphics parameters using the par() function . Although this works for graphs produced with R’s native graphic sys- tem, lattice graphs are unaffected by these settings. Instead, the graphic defaults used by lattice functions are contained in a large list object that can be accessed with the trellis.par.get() function and modified through the trellis.par.set() func- tion . The show.settings() function can be used to display the current graphic set- tings visually. Download from Wow! eBook 388 CHAPTER 16 Advanced graphics As an example, let’s change the default symbol used for superimposed points (that is, points in a graph that includes a group variable). The default is an open circle. We’ll give each group their own symbol instead. First, view the current defaults and save them into a list called mysettings: > show.settings() > mysettings <- trellis.par.get() Next, look at the defaults that are specific to superimposed symbols: > mysettings$superpose.symbol$alpha [1] 1 1 1 1 1 1 1 $cex [1] 0.8 0.8 0.8 0.8 0.8 0.8 0.8$col [1] "#0080ff" "#ff00ff" "darkgreen" "#ff0000" "orange" "#00ff00" [7] "brown" $fill [1] "#CCFFFF" "#FFCCFF" "#CCFFCC" "#FFE5CC" "#CCE6FF" "#FFFFCC" "#FFCCCC"$font [1] 1 1 1 1 1 1 1 $pch [1] 1 1 1 1 1 1 1 Here you see that the symbol used for each level of a group variable is an open circle (pch=1). Seven levels are defined, after which symbols recycle. Finally, issue the following statements: mysettings$superpose.symbol$pch <- c(1:10) trellis.par.set(mysettings) show.settings() Lattice graphs now use symbol 1 (open circle) for the first level of a group variable, symbol 2 (open triangle) for the second, and so on. Additionally, symbols have been defined for 10 levels of a grouping variable, rather than 7. The changes will remain in effect until all graphic devices are closed. You can change any graphic setting in this manner. 16.2.5 Page arrangement In chapter 3 you learned how to place more than one graph on a page using the par() function. Because lattice functions don’t recognize par() settings, you’ll need a dif- ferent approach. The easiest method involves saving your lattice graphs as objects, and using the plot() function with either the split= or position= option specified. The split option divides a page up into a specified number of rows and columns and places graphs into designated cells of the resulting matrix. The format for the split option is Download from Wow! eBook The lattice package 389 split=c(placement row, placement column, total number of rows, total number of columns) For example, the following code library(lattice) graph1 <- histogram(~height|voice.part, data=singer, main="Heights of Choral Singers by Voice Part") graph2 <- densityplot(~height, data=singer, group=voice.part, plot.points=FALSE, auto.key=list(columns=4)) plot(graph1, split=c(1, 1, 1, 2)) plot(graph2, split=c(1, 2, 1, 2), newpage=FALSE) places the first graph directly above the second graph. Specifically, the first plot() state- ment divides the page up into one column and two rows and places the graph in the first column and first row (counting top-down and left-right). The second plot() statement divides the page up in the same way, but places the graph in the first column and second row. Because the plot() function starts a new page by default, you suppress this action by including the newpage=FALSE option. (I’ve omitted the graph to save space.) You can gain more control of sizing and placement by using the position= option. Consider the following code: library(lattice) graph1 <- histogram(~height|voice.part, data=singer, main="Heights of Choral Singers by Voice Part") graph2 <- densityplot(~height, data=singer, group=voice.part, plot.points=FALSE, auto.key=list(columns=4)) plot(graph1, position=c(0, .3, 1, 1)) plot(graph2, position=c(0, 0, 1, .3), newpage=FALSE) Here, position=c(xmin, ymin, xmax, ymax), where the x-y coordinate system for the page is a rectangle with dimensions ranging from 0 to 1 on both the x and y axes, and the origin (0,0) at the bottom left. (Again, the resulting graph is omitted to save space.) You can also change the order of the panels in a lattice graph. The index.cond= option in a high-level lattice graph function specifies the order of the conditioning variable levels. For the voice.part factor, the levels are > levels(singer$voice.part) [1] "Bass 2" "Bass 1" "Tenor 2" "Tenor 1" "Alto 2" "Alto 1" [7] "Soprano 2" "Soprano 1" Adding index.cond=list(c(2, 4, 6, 8, 1, 3, 5, 7)) would place the "1" voice parts together, followed by "2" voice parts. When there are two conditioning variables, include two vectors in the list. In listing 16.5, adding index.cond=list(c(1, 2), c(2, 1)) would reverse the order of treatments in figure 16.7. To learn more about lattice graphs, take a look the excellent text by Sarkar (2008) and its supporting website at http://lmdvr.r-forge.r-project.org. The Trellis Graphics User’s Manual (http://cm.bell-labs.com/cm/ms/departments/sia/doc/trellis.user. pdf) is also an excellent source of information. In the next section, we’ll explore a second comprehensive alternative to R’s native graphic system. This one is based on the ggplot2 package. Download from Wow! eBook 390 CHAPTER 16 Advanced graphics 16.3 The ggplot2 package The ggplot2 package implements a system for creating graphics in R based on a com- prehensive and coherent grammar. This provides a consistency to graph creation often lacking in R, and allows the user to create graph types that are innovative and novel. The simplest approach for creating graphs in ggplot2 is through the qplot() or quick plot function. The format is qplot(x, y, data=, color=, shape=, size=, alpha=, geom=, method=, formula=, facets=, xlim=, ylim=, xlab=, ylab=, main=, sub=) where the parameters/options are defined in table 16.4. Table 16.4 qplot options Option Description alpha Alpha transparency for overlapping elements expressed as a fraction between 0 (complete transparency) and 1 (complete opacity). color , shape , size , fill Associates the levels of variable with symbol color, shape, or size. For line plots, color associates levels of a variable with line color. For density and box plots, fill associates fill colors with a variable. Legends are drawn automatically. data Specifies a data frame. facets Creates a trellis graph by specifying conditioning variables. Its value is expressed as rowvar ~ colvar (see the example in figure 16.10). To create trellis graphs based on a single conditioning variable, use rowvar~. or .~colvar. geom Specifies the geometric objects that define the graph type. The geom option is expressed as a character vector with one or more entries. geom values include "point", "smooth", "boxplot", "line", "histogram", "density", "bar", and "jitter". main , sub Character vectors specifying the title and subtitle. method , formula If geom="smooth", a loess fit line and confidence limits are added by default. When the number of observations is greater than 1,000, a more efficient smoothing algorithm is employed. Methods include "lm" for regression, "gam" for generalized additive models, and "rlm" for robust regression. The formula parameter gives the form of the fit. For example, to add simple linear regression lines, you’d specify geom="smooth", method="lm", formula=y~x. Changing the formula to y~poly(x,2) would produce a quadratic fit. Note that the formula uses the letters x and y, not the names of the variables. For method="gam", be sure to load the mgcv package. For method="rml", load the MASS package. x , y Specifies the variables placed on the horizontal and vertical axis. For univariate plots (for example, histograms), omit y. xlab, ylab Character vectors specifying horizontal and vertical axis labels. xlim , ylim Two-element numeric vectors giving the minimum and maximum values for the horizontal and vertical axes, respectively. Download from Wow! eBook The ggplot2 package 391 To see how qplot() works, let’s review some examples. The following code creates box plots of gas mileage by number of cylinders. The actual data points are superimposed (and jittered to reduce overlap). Box plot colors vary by number of cylinders. library(ggplot2) mtcars$cylinder <- as.factor(mtcars$cyl) qplot(cylinder, mpg, data=mtcars, geom=c("boxplot", "jitter"), fill=cylinder, main="Box plots with superimposed data points", xlab= "Number of Cylinders", ylab="Miles per Gallon") The graph is displayed in figure 16.8. As a second example, let’s create a scatter plot matrix of gas mileage by car weight and use color and symbol shape to differentiate cars with automatic transmissions from those with manual transmissions. Additionally, we’ll add separate regression lines and confidence bands for each transmission type. library(ggplot2) transmission <- factor(mtcars$am, levels=c(0, 1), labels=c("Automatic", "Manual")) qplot(wt,mpg, data=mtcars, color=transmission, shape=transmission, geom=c("point", "smooth"), method="lm", formula=y~x, xlab="Weight", ylab="Miles Per Gallon", main="Regression Example") Box plots with superimposed data points Number of Cylinders M i l e s p e r G a l l o n 15 20 25 30 Figure 16.8 Box plots of auto mileage by number of cylinders. Data points are superimposed and jittered. Download from Wow! eBook 392 CHAPTER 16 Advanced graphics Figure 16.9 Scatter plot between auto mileage and car weight, with separate regression lines and confidence bands by engine transmission type (manual, automatic) The resulting graph is provided in figure 16.9. This is a useful type of graph, not easily created using other packages. As a third example, we’ll create a faceted (trellis) graph. Each facet (panel) displays the scatter plot between gas mileage and car weight. Row facets are defined by the transmission type, whereas column facets are defined by the number of cylinders present. The size of each data point represents the car’s horsepower rating. library(ggplot2) mtcars$cyl <- factor(mtcars$cyl, levels=c(4, 6, 8), labels=c("4 cylinders", "6 cylinders", "8 cylinders")) mtcars$am <- factor(mtcars$am, levels=c(0, 1), labels=c("Automatic", "Manual")) qplot(wt,mpg, data=mtcars, facets=am~cyl, size=hp) The graph is displayed in figure 16.10. Note how simple it is to create a complex graph (actually a bubble chart). You may want to try adding shape and color options to the function call and see how the resulting graph is affected. We’ll end this section by revisiting the singer data with which we began the chapter. This code produces the graph in figure 16.11: library(ggplot2) data(singer, package="lattice") qplot(height, data=singer, geom=c("density"), facets=voice.part~., fill=voice.part) Download from Wow! eBook The ggplot2 package 393 wt m p g 15 20 25 30 15 20 25 30 4 cylinders 2 3 4 5 6 cylinders 2 3 4 5 8 cylinders 2 3 4 5 A u t o m a t i c M a n u a l hp 100 150 200 250 300 Figure 16.10 Scatter plot between auto mileage and car weight, faceted by transmission type (manual, automatic) and number of cylinders (4, 6, or 8). Symbol size represents horsepower. height d e n s i t y 0.00 0.05 0.10 0.15 0.20 0.25 0.00 0.05 0.10 0.15 0.20 0.25 0.00 0.05 0.10 0.15 0.20 0.25 0.00 0.05 0.10 0.15 0.20 0.25 0.00 0.05 0.10 0.15 0.20 0.25 0.00 0.05 0.10 0.15 0.20 0.25 0.00 0.05 0.10 0.15 0.20 0.25 0.00 0.05 0.10 0.15 0.20 0.25 60 65 70 75 B a s s 2 B a s s 1 T e n o r 2 T e n o r 1 A l t o 2 A l t o 1 S o p r a n o 2 S o p r a n o 1 voice.part Bass 2 Bass 1 Tenor 2 Tenor 1 Alto 2 Alto 1 Soprano 2 Soprano 1 Figure 16.11 Faceted density plots for singer heights by voice part Download from Wow! eBook 394 CHAPTER 16 Advanced graphics Comparing the distribution of heights is easier in this format than in the format pre- sented in figure 16.1. (Once again, this looks better when displayed in color.) We’ve only scratched the surface of this powerful graphical system. Interested readers are referred to Wickham (2009), and the ggplot2 website (http://had.co.nz/ ggplot2/) for more information. We’ll end this chapter with a review of interactive graphics and R functions that support them. 16.4 Interactive graphs The base installation of R provides limited interactivity with graphs. You can modify graphs by issuing additional program statements, but there’s little that you can do to modify them or gather new information from them using the mouse. However, there are contributed packages that greatly enhance your ability to interact with the graphs you create. In this section, we’ll focus on functions provided by the playwith , latti- cist, iplots , and rggobi packages . Be sure to install them before first use. 16.4.1 Interacting with graphs: identifying points Before getting to the specialize packages, let’s review a function in the base R installa- tion that allows you to identify and label points in scatter plots. Using the identify() function , you can label selected points in a scatter plot with their row number or row name using your mouse. Identification continues until you select Stop or right-click on the graph. For example, after issuing the following statements plot(mtcars$wt, mtcars$mpg) identify(mtcars$wt, mtcars$mpg, labels=row.names(mtcars)) the cursor will change from a pointer to a crosshair. Clicking on scatter plot points will label them until you select Stop from the Graphics Device menu or right-click on the graph and select Stop from the context menu. Many graphic functions in contributed packages (including functions from the car package discussed in chapter 8) employ this method for labeling points. Unfortunately, the identify() function doesn’t work with lattice or ggplot2 graphs . 16.4.2 playwith The playwith package provides a GTK+ graphical user interface that allows users to edit and interact with R plots. You can install the playwith package on any platform using install.packages("playwith", depend=TRUE). On platforms running Mac OS X and Linux, it’s best to also install the JGR graphic user interface (see appendix A), and run playwith from within this GUI. The playwith()function allows users to identify and label points, view all variable values for an observation, zoom and pan, add annotations (text, arrows, lines, rectangles, titles, labels), change visual elements (colors, text sizes, and so on), apply previously saved styles, and output the resulting graph in a variety of formats. This is easily demonstrated with an example. After running the following code Download from Wow! eBook Interactive graphs 395 library(playwith) library(lattice) playwith( xyplot(mpg~wt|factor(cyl)*factor(am), data=mtcars, subscripts=TRUE, type=c("r", "p")) ) the window in figure 16.12 will appear on the screen. Try out the buttons on the left, as well as the menu items. The GUI is fairly self-explanatory. Unlike the identify() func- tion, playwith() works with lattice and ggplot2 graphs as well as base R graphs. Some options in the Theme menu only work properly with base graphics. Additionally, some features work with ggplot2 graphs (such as annotating) and some don’t (such as identifying points). To learn more about the playwith package, visit the project website at http://code. google.com/p/playwith/. Figure 16.12 The playwith window. The user can edit the graph using the mouse with this GTK+ GUI. Download from Wow! eBook 396 CHAPTER 16 Advanced graphics 16.4.3 latticist The latticist package lets you explore a data set using lattice displays. It provides a graphic user interface to the graphs described in section 16.2, but it can also be used to create displays from the vcd package (see chapter 11, section 11.4). If desired, latticist and can also be integrated with playwith. For example, executing the following code library(latticist) mtcars$cyl <- factor(mtcars$cyl) mtcars$gear <- factor(mtcars$gear) latticist(mtcars, use.playwith=TRUE) will bring up the interface in figure 16.13. In addition to having the playwith functionality (point identification, annotation, zooming, panning, styles), the user can now create lattice graphs by selecting from drop-down menus and buttons. To learn more about the latticist package, see http://code.google.com/p/latticist/. Figure 16.13 playwith window with latticist functionality. The user can create lattice and vcd graphs interactively. Download from Wow! eBook Interactive graphs 397 A similar interface is available for ggplot2 graphs , through Plot Builder, a plug-in for Deducer, a popular GUI for R (see appendix A). Because it can’t be run from the R console, we won’t discuss it here. If you’re interested, visit the Deducer website at www. deducer.org. 16.4.4 Interactive graphics with the iplots package Whereas playwith and latticist allow you to interact with a single graph, the iplots package takes interaction in a different direction. This package provides inter- active mosaic plots, bar plots, box plots, par- allel plots, scatter plots, and histograms that can be linked together and color brushed. This means that you can select and identify observations using the mouse, and highlight- ing observations in one graph will automati- cally highlight the same observations in all other open graphs. You can also use the mouse to obtain information about graphic objects such as points, bars, lines, and box plots. The iplots package is implemented through Java and the primary functions are listed in table 16.5. To understand how iplots works, execute the code provided in listing 16.6. Listing 16.6 iplots demonstration library(iplots) attach(mtcars) cylinders <- factor(cyl) gears <- factor(gear) transmission <- factor(am) ihist(mpg) ibar(gears) iplot(mpg, wt) ibox(mtcars[c("mpg", "wt", "qsec", "disp", "hp")]) ipcp(mtcars[c("mpg", "wt", "qsec", "disp", "hp")]) imosaic(transmission, cylinders) detach(mtcars) Six windows containing graphs will open. Rearrange them on the desktop so that each is visible (each can be resized if necessary). A portion of the display is provided in figure 16.14. Now try the following: ■ Click on the three-gear bar in the Barchart (gears) window. The bar will turn red. In addition, all cars with three-gear engines will be highlighted in the other graphic windows. Table 16.5 iplot functions Function Description ibar() Interactive bar chart ibox() Interactive box plot ihist() Interactive histogram imap() Interactive map imosaic() Interactive mosaic plot ipcp() Interactive parallel coordinates plot iplot() Interactive scatter plot Download from Wow! eBook 398 CHAPTER 16 Advanced graphics ■ Mouse down and drag to select a rectangular region of points in the Scatter plot (wt vs mpg) window. These points will be highlighted and the corresponding observations in every other graphics window will also turn red. ■ Hold down the Ctrl key and move the mouse pointer over a point, bar, box plot, or line in one of the graphs. Details about that object will appear in a pop-up window. ■ Right-click on any object and note the options that are offered in the context menu. For example, you can right-click on the Boxplot (mpg) window and change the graph to a parallel coordinates plot (PCP). ■ You can drag to select more than one object (point, bar, and so on) or use Shift- click to select noncontiguous objects. Try selecting both the three- and five-gear bars in the Barchart (gears) window. The functions in the iplots package allow you to explore the variable distributions and relationships among variables in subgroups of observations that you select interac- tively. This can provide insights that would be difficult and time-consuming to obtain in other ways. For more information on the iplots package, visit the project website at http://rosuda.org/iplots/. Figure 16.14 An iplots demonstration created by listing 16.6. Only four of the six windows are displayed to save room. In these graphs, the user has clicked on the three-gear bar in the bar chart window. Download from Wow! eBook Summary 399 16.4.5 rggobi For our final example of interactivity, we’ll actually look beyond the R platform to the open source GGobi application (www.ggobi.org). GGobi is a comprehensive program for the visual and dynamic exploration of high-dimensional data and is freely available for Windows, Mac OS X, and Linux platforms. It offers a number of attractive features, including linked interactive scatter plots, bar charts, parallel coordinate plots, time series plots, scatter plot matrices, and 3D rotation; brushing and identification; mul- tivariate transformation methods; and sophisticated exploratory support, including guided and manual 1D and 2D tours. Happily, the rggobi package provides a seamless interface between GGobi and R. The first step in using GGobi is to download and install the appropriate software for your platform (www.ggobi.org/downloads/). Then install the rggobi package within R using install.packages("rggobi", depend=TRUE). Once you’ve installed both, you can use the ggobi() function to run GGobi from within R. This gives you sophisticated interactive graphics access to all of your R data. To see this in action, execute the following code: library(rggobi) g <- ggobi(mtcars) The GGobi interface will open and allow you to explore the mtcars dataset in a highly interactive fashion. To learn more, review the introduction, tutorial, manual, and vid- eo guides available on the GGobi website. A comprehensive overview is also provided in Cook and Swayne (2008). 16.5 Summary In this chapter, we reviewed several packages that provide access to advanced graphi- cal methods. We started with the lattice package, designed to provide a system for creating trellis graphs, followed by the ggplot2 package, based on a comprehensive grammar of graphics. Both packages are designed to provide you with a complete and comprehensive alternative to the native graphics provided with R. Each offers methods of creating attractive and meaningful visualizations of data that are difficult to gener- ate in other ways. We then explored several packages for dynamically interacting with graphs, including playwith, latticist, iplots, and rggobi. These packages allow you to interact directly with data in graphs, leading to a greater intimacy with your data and expanded opportunities for developing insights. You should now have a firm grasp of the many ways that R allows you to create visual representations of data. If a picture is worth a thousand words, and R provides a thousand ways to create a picture, then R must be worth a million words (or something to that effect). These resources are a testament to the hard and selfless work of the initial R development team and the thousands of hours of work contributed by package authors. Download from Wow! eBook 400 afterword: Into the rabbit hole We’ve covered a broad range of topics in the book, including major ones like the R development environment, data management, traditional statistical models, and statistical graphics. We’ve also covered hidden gems like resampling statistics, miss- ing values imputation, and interactive graphics. The great (or perhaps infuriating) thing about R is that there’s always more to learn. R is a large, robust, and evolving statistical platform and programming language. With so many new packages, frequent updates, and new directions, how can a user stay current? Happily, many websites support this active community and provide coverage of platform and package changes, new methodologies, and a wealth of tutorials. I’ve listed some of my favorite sites below. The R Project (http://www.r-project.org/) The official R website and your first stop for all things R. The site includes extensive documentation, including An Introduction to R, The R Language Definition, Writing R Extensions, R Data Import/Export, R Installation and Administration, and The R FAQ. The R Journal (http://journal.r-project.org/) A freely accessible refereed journal containing articles on the R project and contrib- uted packages. R Bloggers (http://www.r-bloggers.com/) A central hub (blog aggregator) collecting content from bloggers writing about R. Contains new articles daily. I’m addicted to it. Planet R (http://planetr.stderr.org) Another good site-aggregator, including information from a wide range of sources. Updated daily. Download from Wow! eBook AFTERWORD Into the rabbit hole 401 CRANberries (http://dirk.eddelbuettel.com/cranberries/) A site that aggregates information about new and updated packages, and contains links to CRAN for each. R Graph Gallery (http://addictedtor.free.fr/graphiques/) A collection of innovative graphs, along with their source code. R Graphics Manual (http://bm2.genes.nig.ac.jp/) A collection of R graphics from all R packages, arranged by topic, package, and func- tion. At last count, there were 35,000+ images! Journal of Statistical Software (http://www.jstatsoft.org/) A freely accessible refereed journal containing articles, book reviews, and code snip- pets on statistical computing. Contains frequent articles about R. Revolutions (http://blog.revolution-computing.com/) A popular, well-organized blog, dedicated to news and information about R. CRAN Task Views (http://cran.r-project.org/web/views/) Task views are guides to the use of R in different academic and research fields. They include a description of the packages and methods available for a given area. Currently there are 28 task views available (see table below). CRAN Task Views Bayesian Inference Machine Learning & Statistical Learning Chemometrics and Computational Physics Medical Image Analysis Design, Monitoring, and Analysis of Clinical Trials Multivariate Statistics Clinical Trial Design, Monitoring, and Analysis Natural Language Processing Cluster Analysis & Finite Mixture Models Official Statistics & Survey Methodology Probability Distributions Optimization and Mathematical Programming Computational Econometrics Analysis of Pharmacokinetic Data Analysis of Ecological and Environmental Data Phylogenetics, Especially Comparative Methods Design of Experiments (DoE) Psychometric Models and Methods Empirical Finance Robust Statistical Methods Statistical Genetics Statistics for the Social Sciences Graphic Displays & Dynamic Graphics Analysis of Spatial Data gRaphical Models in RSurvival Analysis High-Performance and Parallel Computing with RTime Series Analysis Download from Wow! eBook 402 AFTERWORD Into the rabbit hole R-Help Main R Mailing List (https://stat.ethz.ch/mailman/listinfo/r-help) This electronic mailing list is the best place to ask questions about R. The archives are also searchable. Be sure to read the FAQ before posting questions. Quick-R (http://www.statmethods.net) This is my R website. It’s stocked with more than 80 brief tutorials on R topics. False modesty forbids me from saying more. The R community is a helpful, vibrant, and exciting lot. Welcome to Wonderland. Download from Wow! eBook 403 appendix A Graphic user interfaces You turned here first, didn’t you? By default, R provides a simple command-line in- terface (CLI). The user enters statements at a command-line prompt (> by default) and each command is executed one at a time. For many data analysts, the CLI is one of R’s most significant limitations. There have been a number of attempts to create more graphical interfaces, ranging from code editors that interact with R (such as RStudio), to GUIs for specific functions or packages (such as BiplotGUI), to full-blown GUIs that allow the user to construct analyses through interactions with menus and dialog boxes (such as R Commander). Several of the more useful code editors are listed in table A.1. Table A.1 Integrated development environments and syntax editors Name URL Eclipse with StatET plug-in http://www.eclipse.org and http://www.walware.de/goto/statet ESS (Emacs Speaks Statistics) http://ess.r-project.org/ Komodo Edit with SciViews-K plug-in http://www.activestate.com/komodo_edit/ http://www. sciviews.org/SciViews-K/ JGR http://www.rforge.net/JGR/ Download from Wow! eBook 404 APPENDIX A Graphic user interfaces Table A.1 Integrated development environments and syntax editors (continued ) Name URL RStudio http://www.rstudio.org Tinn-R (Windows only) http://www.sciviews.org/Tinn-R/ Notepad++ with NppToR (windows only) http://notepad-plus-plus.org/ http://sourceforge.net/projects/npptor/ The code editors in table A.1 allow the user to edit and execute R code and include syntax highlighting, statement completion, object exploration, project organization, and online help. A screenshot of RStudio is provided in figure A.1. Several promising full-blown GUIs for R are listed in table A.2. The GUIs available for R are less comprehensive and mature than those offered by SAS or IBM SPSS, but they’re developing rapidly. Figure A.1 RStudio IDE Download from Wow! eBook APPENDIX A Graphic user interfaces 405 Table A.2 Comprehensive GUIs for R Name URL JGR/ Deducer http://ifellows.ucsd.edu/pmwiki/pmwiki.php?n=Main.DeducerManual R AnalyticFlow http://www.ef-prime.com/products/ranalyticflow_en/ Rattle (for data mining) http://rattle.togaware.com/ R Commander http://socserv.mcmaster.ca/jfox/Misc/Rcmdr/ Red R http://www.red-r.org/ Rkward http://rkward.sourceforge.net/ My favorite GUI for introductory statistics courses is R Commander (shown in figure A.2). Finally, there are a number of applications that allow the user to create a GUI wrapper for any given R function (including user-written functions). These include the R GUI Generator (RGG) (http://rgg.r-forge.r-project.org/), and the fgui and twiddler packages available from CRAN. GUI projects in R are undergoing rapid change and expansion. For more information, visit the R GUI Projects page at http://www.sciviews.org/_rgui/. Figure A.2 R Commander GUI Download from Wow! eBook 406 appendix B Customizing the startup environment One of the first things that programmers like to do is customize their startup envi- ronment to conform to their preferred way of working. Customizing the startup en- vironment allows you to set R options, specify a working directory, load commonly used packages, load user-written functions, set a default CRAN download site , and perform any number of housekeeping tasks. You can customize the R environment through either a site initialization file (Rprofile.site ) or a directory initialization file (.Rprofile ). These are text files containing R code to be executed at startup. At startup, R will source the file Rprofile.site from the R_HOME/etc directory , where R_HOME is an environment value. It will then look for an .Rprofile file to source in the current working directory. If R doesn’t find this file, it will look for it in the user’s home directory. You can use Sys.getenv("R_HOME") , Sys. getenv("HOME") , and getwd() to identify the location of the R_HOME, HOME, and current working directory, respectively. You can place two special functions in these files. The .First() function is executed at the start of each R session, and the .Last() function is executed at the end of each session. An example of an Rprofile.site file is shown in listing B.1. Download from Wow! eBook APPENDIX B Customizing the startup environment 407 Listing B.1 Sample Rprofile.site file options( papersize="a4") options(editor="notepad") options(pager="internal") options(tab.width = 2) options(width = 130) options(graphics.record=TRUE) options(show.signif.stars=FALSE) options(prompt="> ") options(continue="+ ") .libPaths("C:/my_R_library") local({r <- getOption("repos") r["CRAN"] <- "http://cran.case.edu/" options(repos=r)}) .First <- function(){ library(lattice) library(Hmisc) source("C:/mydir/myfunctions.R") cat("\nWelcome at", date(), "\n") } .Last <- function(){ cat("\nGoodbye at ", date(), "\n") } There are several things you should note about this file: ■ Setting a .libPaths value allows you to create a local library for packages out- side of the R directory tree. This can be useful for retaining packages during an upgrade. ■ Setting a default CRAN mirror site frees you from having to choose one each time you issue an install.packages() command . ■ The .First() function is an excellent place to load libraries that you use often, as well as source text files containing user-written functions that you apply fre- quently. ■ The .Last() function is an excellent place for any cleanup activities, including archiving command histories, program output, and data files. There are other ways to customize the startup environment, including the use of com- mand-line options and environment variables . See help(Startup) and appendix B in the Introduction to R manual (http://cran.r-project.org/doc/manuals/R-intro.pdf) for more details. Set common options Set R interactive prompt Set path for local library Set CRAN mirror default Startup function Session end function Download from Wow! eBook 408 appendix C Exporting data from R In chapter 2, we reviewed a wide range of methods for importing data into R. But there are times that you’ll want to go the other way—exporting data from R—so that data can be archived or imported into external applications. In this appendix, you’ll learn how to output an R object to a delimited text file, an Excel spreadsheet, or a statistical application (such as SPSS, SAS, or Stata). C.1 Delimited text file You can use the write.table() function to output an R object to a delimited text file. The format is write.table(x, outfile, sep=delimiter, quote=TRUE, na="NA") where x is the object and outfile is the target file. For example, the statement write.table(mydata, "mydata.txt", sep=",") would save the dataset mydata to a comma-delimited file named mydata.txt in the current working directory. Include a path (for example, “c:/myprojects/mydata. txt”) to save the output file elsewhere. Replacing sep="," with sep="\t" would save the data in a tab-delimited file. By default, strings are enclosed in quotes ("") and missing values are written as NA. Download from Wow! eBook Statistical applications 409 C.2 Excel spreadsheet The write.xlsx() function in the xlsx package can be used to save an R data frame to an Excel 2007 workbook. The format is library(xlsx) write.xlsx(x, outfile, col.Names=TRUE, row.names=TRUE, sheetName="Sheet 1", append=FALSE) For example, the statements library(xlsx) write.xlsx(mydata, "mydata.xlsx") export the data frame mydata to a worksheet (Sheet 1 by default) in an Excel work- book named mydata.xlsx in the current working directory. By default, the variable names in the dataset are used to create column headings in the spreadsheet and row names are placed in the first column of the spreadsheet. If mydata.xlsx already exists, it is overwritten. The xlsx package is a powerful tool for manipulating Excel 2007 workbooks. See the package documentation for more details. C.3 Statistical applications The write.foreign() function in the foreign package can be used to export a data frame to an external statistical application. Two files are created—a free- format text file containing the data, and a code file containing instructions for reading the data into the external statistical application. The format is write.foreign(dataframe, datafile, codefile, package=package) For example, the code library(foreign) write.foreign(mydata, "mydata.txt", "mycode.sps", package="SPSS") would export the dataframe mydata into a free-format text file named mydata.txt in the current working directory and an SPSS program named mycode.sps that can be used to read the text file. Other values of package include "SAS " and "Stata ". To learn more about exporting data from R, see the R Data Import/Export documentation, available from http://cran.r-project.org/doc/manuals/R-data.pdf. Download from Wow! eBook 410 appendix D Creating publication-quality output Research doesn’t end when the last statistical analysis or graph is completed. We need to include the results in a report that effectively communicates these findings to a teacher, supervisor, client, government agency, or journal editor. Although R creates state-of-the-art graphics, its text output is woefully retro—tables of mono- spaced text with columns lined up using spaces. There are two common approaches to creating publication quality reports in R: Sweave and odfWeave. The Sweave package allows you to embed R code and output in LaTeX documents, in order to produce high-end typeset reports in PDF, PostScript, and DVI formats. Sweave is an elegant, precise, and highly flexible system, but it requires the author to be conversant with LaTeX coding . In a similar fashion, the odfWeave package provides a mechanism for embedding R code and output in documents that follow the Open Documents Format (ODF). These reports can be further edited via an ODF word processor, such as OpenOffice Writer, and saved in either ODF or Microsoft Word format. The process is not as flexible as the Sweave approach, but it eliminates the need to learn LaTeX. We’ll look at each approach in turn. D.1 High-quality typesetting with Sweave (R + LaTeX) LaTeX is a document preparation system for high-quality typesetting (http://www. latex-project.org) that’s freely available for Windows, Mac, and Linux platforms. An author creates a text document that includes markup code for formatting the Download from Wow! eBook High-quality typesetting with Sweave (R + LaTeX) 411 content. The document is then processed through a LaTeX compiler , producing a finished document in PDF, PostScript, or DVI format. The Sweave package allows you to embed R code and output (including graphs) within the LaTeX document. This is a multistep process: 1 A special document called a noweb file (typically with the extension .Rnw) is created using any text editor. The file contains the written content, LaTeX markup code , and R code chunks. Each R code chunk starts with the delimiter <<>>= and ends with the delimiter @. 2 The Sweave() function processes the noweb file and generates a LaTeX file. During this step, the R code chunks are processed, and depending on options, replaced with LaTeX-formatted R code and output. This step can be accomplished from within R or from the command line. Within R, the format is Sweave("infile.Rnw") By default, Sweave("example.Rnw") would input the file example.Rnw from the current working directory and output the file example.tex to the same directory. Alternatively, use can use Sweave("infile.Rnw", syntax="SweaveSyntaxNoweb") Specifying this syntax option can help avoid some common parsing errors, as well as conflicts with the R2HTML package . Execution from the command line will depend on the operating system. For example, on a Linux system, this might look like$ R CMD Sweave infile.Rnw 3 The LaTeX file is then run through a LaTeX compiler, creating a PDF, PostScript, or DVI file. Popular LaTeX compilers include TeX Live for Linux, MacTeX for Mac, and proTeXt for Windows. The complete process is outlined in figure D.1. example.rnw example.rnw example.pdf PDF file Run through LaTeX compiler example.ps Postscript file example.dvi DVI file LaTex (TeX) file Text file with LaTex markup and Rcode Chunks Run through Sweave() function in R Figure D.1 Process for generating a publication-quality report using Sweave Download from Wow! eBook 412 APPENDIX D Creating publication-quality output As indicated earlier, each chunk of R code is surrounded by <<>>= and @. You can add options to each <<>>= delimiter in order to control the processing of the correspond- ing R code chunk. For example <>= summary(lm(Y~X, data=mydata)) @ would output the code, but not the results, whereas <>= plot(A) @ wouldn’t print the code but would include the graph in the output. Common delim- iter options are described in table D.1. Table D.1 Common options for R code chunks Option Description echo Include the code in the output (echo=TRUE) or not (echo=FALSE). The default is TRUE. eval Use eval=FALSE to keep the code from being evaluated/executed. The default is TRUE. fig Use fig=TRUE when the output is a graph. The default is FALSE. results Include R code output (results=verbatim), suppress the output (results=hide), or include the output and assume that it contains LaTeX markup (results=tex). The default is verbatim. Use results=tex when the output is generated by the xtable() function in the xtable package or the latex() function in the Hmisc package. By default, Sweave will add LaTeX markup code to attractively format data frames, ma- trices, and vectors. Additionally, R objects can be embedded inline using a \Sexpr{} statement . Note that lattice graphs must be embedded in a print() statement to be processed properly. The xtable() function in the xtable package can be used to format data frames and matrices more precisely. In addition, it can be used to format other R objects, including those produced by lm(), glm(), aov(), table(), ts(), and coxph(). Use method(xtable) to view a comprehensive list. When formatting R output using xtable() , be sure to include the results=tex option in the code chunk delimiter. It’s easier to see how this all works with an example. Consider the noweb file in listing D.1. This is a reworking of the one-way ANOVA example in section 8.3. LaTeX markup code begins with a backslash (\). The exception is \Sexpr{}, which is a Sweave addition. R related code is presented in bold italics. Listing D.1 A sample noweb file (example.nrw) \documentclass[12pt]{article} \title{Sample Report} Download from Wow! eBook High-quality typesetting with Sweave (R + LaTeX) 413 \author{Robert I. Kabacoff, Ph.D.} \date{} \begin{document} \maketitle <>= library(multcomp) library(xtable) attach(cholesterol) @ \section{Results} Cholesterol reduction was assessed in a study that randomized \Sexpr{nrow(cholesterol)} patients to one of \Sexpr{length(unique(trt))} treatments. Summary statistics are provided in Table \ref{table:descriptives}. <>= descTable <- data.frame("Treatment" = sort(unique(trt)), "N" = as.vector(table(trt)), "Mean" = tapply(response, list(trt), mean, na.rm=TRUE), "SD" = tapply(response, list(trt), sd, na.rm=TRUE) ) print(xtable(descTable, caption = "Descriptive statistics for each treatment group", label = "table:descriptives"), caption.placement = "top", include.rownames = FALSE) @ The analysis of variance is provided in Table \ref{table:anova}. <>= fit <- aov(response ~ trt) print(xtable(fit, caption = "Analysis of variance", label = "table:anova"), caption.placement = "top") @ \noindent and group differences are plotted in Figure \ref{figure:tukey}. \begin{figure}\label{figure:tukey} \begin{center} <>= par(mar=c(5,4,6,2)) tuk <- glht(fit, linfct=mcp(trt="Tukey")) plot(cld(tuk, level=.05),col="lightgrey",xlab="Treatment", ylab="Response") box("figure") @ \caption{Distribution of response times and pairwise comparisons.} \end{center} \end{figure} \end{document} Download from Wow! eBook 414 APPENDIX D Creating publication-quality output Sample Report Robert I.Kabacoﬀ,Ph.D. 1 Results Cholesterol reduction was assessed in a study that randomized 50 patients to one of 5 treatments.Summary statistics are provided in Table 1. Table 1:Descriptive statistics for each treatment group Treatment NMean SD 1time 10 5.78 2.88 2times 10 9.22 3.48 4times 10 12.37 2.92 drugD 10 15.36 3.45 drugE 10 20.95 3.35 The analysis of variance is provided in Table 2. Table 2:Analysis of variance Df Sum Sq Mean Sq F value Pr(>F) trt 4 1351.37 337.84 32.43 0.0000 Residuals 45 468.75 10.42 and group diﬀerences are plotted in Figure 1. Figure D.2 Page 1 of the report created from the sample noweb file in listing D.1. The noweb file was processed through the Sweave() function in R and the resulting TeX file was processed through a LaTeX compiler to produce a PDF document. After processing the noweb file through the Sweave() function in R and processing the resulting TeX file through a LaTeX compiler, the PDF document in figures D.2 and D.3 is generated. ● ● 1time 2times 4times drugD drugE 510 1 5 2 0 2 5 Treatment R e s p o n s e a a b b c c d Figure 1:Distribution of response times and pairwise comparisons. Figure D.3 Page 2 of the report created from the sample noweb file in listing D.1. Download from Wow! eBook Joining forces with OpenOffice using odfWeave 415 To learn more about Sweave, visit the Sweave home page (www.stat.uni-muenchen. de/~leisch/Sweave/). An excellent presentation is also provided by Theresa Scott (http://biostat.mc.vanderbilt.edu/TheresaScott). To learn more about LaTeX, check out the article "The Not So Short Introduction to LaTeX 2e,” available on the LaTeX home page (www.latex-project.org). D.2 Joining forces with OpenOffice using odfWeave Sweave provides a means of embedding R code and output in a LaTeX document that’s compiled into a PDF, PostScript, or DVI file. Although beautiful, the final document isn’t editable. Additionally, many recipients require reports in a format such as Word. odfWeave provides a mechanism for embedding R code and output in OpenOffice documents. Instead of placing R code chunks in a LaTeX document, the user places R code chunks in an OpenOffice ODT file (see figure D.3.). An advantage is that the ODT file can be created with a WYSIWYG editor such as OpenOffice Writer (www. OpenOffice.org); there’s no need to learn a markup language. Once the noweb document is created as an ODT file, you process it through the odfWeave() function in the odfWeave package . Unlike Sweave, odfWeave has to be downloaded, installed before first use (install.packages("odfWeave")), and loaded in each session in which it will be used. For example, library(odfWeave) infile <- "example.odt" outfile <- "example-out.odt" odfWeave(infile, outfile) will take the example.odt file displayed in figure D.4 and produce the example-out. odt file displayed in figure D.5. Adding options(SweaveSyntax="SweaveSyntaxNo web") before the odfWeave() statement may help reduce parsing errors on some platforms. There are several differences between Sweave and odfWeave: ■ The xtable() function doesn’t work with odfWeave. By default, odfWeave will render data frames, matrices, and vectors in an attractive format. Optionally, the odfTable() function can be used to format these objects with a high degree of control. ■ ODF documents use XML markup rather than LaTeX. Therefore, the code chunk option result=tex should never be used. Use result=xml for code chunks that use odfTable(). ■ The infile and outfile names should be different. Unlike Sweave, odfWeave("example.odt") would overwrite the noweb document with the fi- nal report. Download from Wow! eBook 416 APPENDIX D Creating publication-quality output If you look at Figure D.4, you’ll note that the ANOVA table isn’t attractively formatted (as it was in Sweave). Rather, the table is in the standard monospaced font produced by R. This is because odfWeave doesn’t have a formatting function for the objects My Sample Report Robert I. Kabacoff, Ph.D. <>= library(multcomp) library(xtable) attach(cholesterol) @ 1 Results Cholesterol reduction was assessed in a study that randomized \Sexpr{nrow(cholesterol)} patients to one of \Sexpr{length(unique(trt))} treatments. Summary statistics are provided in Table 1. Table 1. Descriptive Statistics for each treatment group <>= descTable <- data.frame("Treatment" = sort(unique(trt)), "N" = as.vector(table(trt)), "Mean" = tapply(response, list(trt), mean, na.rm=TRUE), "SD" = tapply(response, list(trt), sd, na.rm=TRUE) ) odfTable(descTable) @ The analysis of variance is provided Table 2. Table 2. Analysis of Variance <>= fit <- aov(response ~ trt) summary(fit) @ and group differences are plotted in Figure 1. <>= par(mar=c(5,4,6,2)) tuk <- glht(fit, linfct=mcp(trt="Tukey")) plot(cld(tuk, level=.05),col="lightgrey",xlab="Treatment", ylab="Response") box("figure") @ Figure1. Distribution of response times and pair-wise comparisons. Figure D.4 Initial noweb file (example.odt) to be processed through odfWeave Download from Wow! eBook Joining forces with OpenOffice using odfWeave 417 My Sample Report Robert I. Kabacoff, Ph.D. 1 Results Cholesterol reduction was assessed in a study that randomized 50 patients to one of 5 treatments. Summary statistics are provided in Table 1. Table 1. Descriptive Statistics for each treatment group Treatment N Mean SD 1time 1time 10 5.782 2.878 2times 2times 10 9.225 3.483 4times 4times 10 12.375 2.923 drugD drugD 10 15.361 3.455 drugE drugE 10 20.948 3.345 The analysis of variance is provided Table 2. Table 2. Analysis of Variance Df Sum Sq Mean Sq F value Pr(>F) trt 4 1351.37 337.84 32.433 9.819e-13 *** Residuals 45 468.75 10.42 --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 and group differences are plotted in Figure 1. Figure D.5 Final report in ODF format (example-out.odt). Page 2 is similar to the second page of the Sweave output in figure D.2 and is omitted to save space returned by lm(), glm(), and so forth. To properly format these results, we’d have to pull the components out of the object in question (fit in this case), and arrange them in a matrix or data frame. Once you have your report in ODF format, you can continue to edit it, tighten up the formatting, and save the results to an ODT, HTML, DOC, or DOCX file format. To learn more, read the odfWeave manual and vignette. Download from Wow! eBook 418 APPENDIX D Creating publication-quality output D.3 Comments There are several advantages to the Sweave and odfWeave approaches described here. By embedding the code needed to perform the statistical analyses directly into the final report, you document exactly how the results were calculated. Six months from now, you can easily see what was done. You can also modify the statistical analyses or add new data and immediately regenerate the report with minimum effort. Additionally, you avoid the need to cut and paste and reformat the results. Unfortunately, you gain these advantages by putting in significantly more work at the front-end. There are other disadvantages as well. In the case of LaTeX, you need to learn a typesetting language. In the case of ODF, you need to use a program like OpenOffice that may not be standard in your work environment. For good or ill, Microsoft Word and PowerPoint are the current report and presentation standards in the business world. The packages R2wd and R2PPT can be used to dynamically create Word and PowerPoint documents with inserted R output, but they are in their formative stages of development. I’m looking forward to seeing fully developed implementations. Download from Wow! eBook 419 appendix E Matrix Algebra in R Many of the functions described in this book operate on matrices. The manipula- tion of matrices is built deeply into the R language. Table E.1 describes operators and functions that are particularly important for solving linear algebra problems. In the following table, A and B are matrices, x and b are vectors, and k is a scalar. Table E.1 R functions and operators for matrix algebra Operator or Function Description + - * / ^ Element-wise addition, subtraction, multiplication, division, and exponentiation, respectively. A %*% BMatrix multiplication. A %o% BOuter product. AB'. cbind(A, B, …)Combine matrices or vectors horizontally. chol(A)Choleski factorization of A. If R <- chol(A), then chol(A) contains the upper triangular factor, such that R’R = A. colMeans(A)Returns a vector containing the column means of A. crossprod(A)A’A. crossprod(A,B)A’B. Download from Wow! eBook 420 APPENDIX E Matrix Algebra in R Table E.1 R functions and operators for matrix algebra (continued ) Operator or Function Description colSums(A)Returns a vector containing the column sums of A. diag(A)Returns a vector containing the elements of the principal diagonal. diag(x)Creates a diagonal matrix with the elements of x in the principal diagonal. diag(k)If k is a scalar, this creates a k x k identity matrix. eigen(A)Eigenvalues and eigenvectors of A. If y <- eigen(A), then y$val are the eigenvalues of A and y$vec are the eigenvectors of A. ginv(A)Moore-Penrose Generalized Inverse of A. (Requires the MASS package). qr(A)QR decomposition of A. If y <- qr(A), then y$qr has an upper triangle containing the decomposition and a lower triangle that contains information on the decomposition, y$rank is the rank of A, y$qraux is a vector containing additional information on Q, and y$pivot contains information on the pivoting strategy used. rbind(A, B, …)Combines matrices or vectors vertically. rowMeans(A)Returns a vector containing the row means of A. rowSums(A)Returns a vector containing the row sums of A. solve(A)Inverse of A where A is a square matrix. solve(A, b)Solves for vector x in the equation b = Ax. svd(A)Single value decomposition of A. If y <- svd(A), then y$d is a vector containing the singular values of A, y$u is a matrix with columns containing the left singular vectors of A, and y$v is a matrix with columns containing the right singular vectors of A. t(A)Transpose of A. There are several user-contributed packages that are particularly useful for matrix al- gebra. The matlab package contains wrapper functions and variables used to replicate MATLAB function calls as closely as possible. These functions can help port MATLAB applications and code to R. There’s also a useful cheat sheet for converting MATLAB statements to R statements at http://mathesaurus.sourceforge.net/octave-r.html. The Matrix package contains functions that extend R in order to support highly dense or sparse matrices. It provides efficient access to BLAS (Basic Linear Algebra Subroutines), Lapack (dense matrix), TAUCS (sparse matrix), and UMFPACK (sparse matrix) routines. Finally, the matrixStats package provides methods for operating on the rows and columns of matrices, including functions that calculate counts, sums, products, central tendency, dispersion, and more. Each is optimized for speed and efficient memory use. Download from Wow! eBook 421 appendix F Packages used in this book R derives much of its breadth and power from the contributions of selfless authors. Table F.1 lists the user-contributed packages described in this book, along with the chapter(s) in which they appear. Table F.1 Contributed packages used in this book Package Authors Description Chapters AER Christian Kleiber and Achim Zeileis Functions, data sets, examples, demos, and vignettes from the book Applied Econometrics with R by Christian Kleiber and Achim Zeileis 13 Amelia James Honaker, Gary King, and Matthew Blackwell Amelia II: A program for missing data via multiple imputation 15 arrayImpute Eun-kyung Lee, Dankyu Yoon, and Taesung Park Missing imputation for microarray data 15 arrayMissPattern Eun-kyung Lee and Taesung Park Exploratory analysis of missing patterns for microarray data 15 Download from Wow! eBook 422 APPENDIX F Packages used in this book Table F.1 Contributed packages used in this book (continued ) Package Authors Description Chapters boot S original by Angelo Canty. R port by Brian Ripley. Bootstrap functions 12 ca Michael Greenacre and Oleg Nenadic Simple, multiple and joint correspondence analysis 7 car John Fox and Sanford Weisberg Companion to Applied Regression 1, 8, 9, 10, 11 cat Ported to R by Ted Harding and Fernando Tusell. Original by Joseph L. Schafer. Analysis of categorical- variable datasets with missing values 15 coin Torsten Hothorn, Kurt Hornik, Mark A. van de Wiel, and Achim Zeileis Conditional inference procedures in a permutation test framework 12 corrgram Kevin Wright Plot a correlogram 11 corrperm Douglas M. Potter Permutation tests of correlation with repeated measurements 12 doBy Søren Højsgaard with contributions from Kevin Wright and Alessandro A. Leidi. Group-wise computations of summary statistics, general linear contrasts and other utilities 7 effects John Fox and Jangman Hong Effect displays for linear, generalized linear, multinomial-logit, and proportional-odds logit models 8, 9 FactoMineR Francois Husson, Julie Josse, Sebastien Le, and Jeremy Mazet Multivariate exploratory data analysis and data mining with R 14 FAiR Ben Goodrich Factor analysis using a genetic algorithm 14 fCalendar Diethelm Wuertz and Yohan Chalabi Functions for chronological and calendarical objects 4 foreign R-core members, Saikat DebRoy, Roger Bivand, and others Read data stored by Minitab, S, SAS, SPSS, Stata, Systat, dBase, and others 2 gclus Catherine Hurley Clustering graphics 1, 11 Download from Wow! eBook APPENDIX F Packages used in this book 423 Table F.1 Contributed packages used in this book (continued ) Package Authors Description Chapters glmPerm Wiebke Werft and Douglas M. Potter Permutation test for inference in generalized linear models 12 gmodels Gregory R. Warnes. Includes R source code and/or documentation contributed by Ben Bolker, Thomas Lumley, and Randall C Johnson. Contributions from Randall C. Johnson are Copyright (2005) SAIC-Frederick, Inc. Various R programming tools for model fitting 7 gplots Gregory R. Warnes. Includes R source code and/or documentation contributed by Ben Bolker, Lodewijk Bonebakker, Robert Gentleman, Wolfgang Huber Andy Liaw, Thomas Lumley, Martin Maechler, Arni Magnusson, Steffen Moeller, Marc Schwartz, and Bill Venables Various R programming tools for plotting data 6, 9 grid Paul Murrell A rewrite of the graphics layout capabilities, plus some support for interaction 16 gvlma Edsel A. Pena and Elizabeth H. Slate Global validation of linear models assumptions 8 hdf5 Marcus G. Daniels Interface to the NCSA HDF5 library 2 hexbin Dan Carr, ported by Nicholas Lewin-Koh and Martin Maechler Hexagonal binning routines 11 HH Richard M. Heiberger Support software for Statistical Analysis and Data Display by Heiberger and Holland 9 Hmisc Frank E Harrell Jr, with contributions from many other users Harrell miscellaneous functions for data analysis, high-level graphics, utility operations, and more 2, 3, 7 Download from Wow! eBook 424 APPENDIX F Packages used in this book Table F.1 Contributed packages used in this book (continued ) Package Authors Description Chapters kmi Arthur Allignol Kaplan-Meier multiple imputation for the analysis of cumulative incidence functions in the competing risks setting 15 lattice Deepayan Sarkar Lattice graphics 16 latticist Felix Andrews GUI for exploratory visualization 16 lavaan Yves Rosseel Functions for latent variable models, including confirmatory factor analysis, structural equation modeling, and latent growth curve models 14 lcda Michael Buecker Latent class discriminant analysis 14 leaps Thomas Lumley using Fortran code by Alan Miller Regression subset selection including exhaustive search 8 lmPerm Bob Wheeler Permutation tests for linear models 12 logregperm Douglas M. Potter Permutation test for inference in logistic regression 12 longitudinalData Christophe Genolini Tools for longitudinal data 15 lsa Fridolin Wild Latent semantic analysis 14 ltm Dimitris Rizopoulos Latent trait models under item response theory 14 lubridate Garrett Grolemund and Hadley Wickham Functions to identify and parse date-time data, extract and modify components of a date-time, perform accurate math on date-times, and handle time zones and Daylight Savings Time 4 MASS S original by Venables and Ripley. R port by Brian Ripley, following earlier work by Kurt Hornik and Albrecht Gebhardt. Functions and datasets to support Venables and Ripley’s Modern Applied Statistics with S (4th edition) 4, 5, 7, 8, 9, 12 Download from Wow! eBook APPENDIX F Packages used in this book 425 Table F.1 Contributed packages used in this book (continued ) Package Authors Description Chapters mlogit Yves Croissant Estimation of the multinomial logit model 13 multcomp Torsten Hothorn, Frank Bretz Peter Westfall, Richard M. Heiberger, and Andre Schuetzenmeister Simultaneous tests and confidence intervals for general linear hypotheses in parametric models, including linear, generalized linear, linear mixed effects, and survival models 9, 12 mvnmle Kevin Gross, with help from Douglas Bates ML estimation for multivariate normal data with missing values 15 mvoutlier Moritz Gschwandtner and Peter Filzmoser Multivariate outlier detection based on robust methods 9 ncdf , ncdf4 David Pierce Interface to Unidata netCDF data files 2 nFactors Gilles Raiche Parallel analysis and non graphical solutions to the Cattell scree test 14 npmc Joerg Helms and Ullrich Munzel Nonparametric multiple comparisons 7 OpenMx Steven Boker, Michael Neale, Hermine Maes, Michael Wilde, Michael Spiegel, Timothy R. Brick, Jeffrey Spies, Ryne Estabrook, Sarah Kenny, Timothy Bates, Paras Mehta, and John Fox Advanced structural equation modeling. 14 pastecs Frederic Ibanez, Philippe Grosjean, and Michele Etienne Package for the analysis of space-time ecological series 7 piface Russell Lenth, R package interface by Tobias Verbeke Java applets for power and sample size assessment 10 playwith Felix Andrews A GTK+ graphical user interface for editing and interacting with R plots 16 poLCA Drew Linzer and Jeffrey Lewis Polytomous variable latent class analysis 14 Download from Wow! eBook 426 APPENDIX F Packages used in this book Table F.1 Contributed packages used in this book (continued ) Package Authors Description Chapters psych William Revelle Procedures for psychological, psychometric, and personality research 7, 14 pwr Stephane Champely Basic functions for power analysis 10 qcc Luca Scrucca Quality control charts 13 randomLCA Ken Beath Random effects latent class analysis 14 Rcmdr John Fox, with contributions from Liviu Andronic, Michael Ash, Theophilius Boye, Stefano Calza, Andy Chang, Philippe Grosjean, Richard Heiberger, G. Jay Kerns, Renaud Lancelot, Matthieu Lesnoff, Uwe Ligges, Samir Messad, Martin Maechler, Robert Muenchen, Duncan Murdoch, Erich Neuwirth, Dan Putler, Brian Ripley, Miroslav Ristic, and Peter Wolf. R Commander, a platform- independent basic-statistics graphical user interface for R, based on the tcltk package 11 reshape Hadley Wickham Flexibly reshape data 4, 5, 7 rggobi Duncan Temple Lang, Debby Swayne, Hadley Wickham, and Michael Lawrence An interface between R and GGobi 16 rgl Daniel Adler and Duncan Murdoch 3D visualization device system (OpenGL) 11 RJDBC Simon Urbanek Provides access to databases through the JDBC interface 2 rms Frank E. Harrell, Jr.Regression modeling strategies - about 225 function that assist with and streamline regression modeling, testing, estimations, validation, graphics, prediction, and typesetting 13 Download from Wow! eBook APPENDIX F Packages used in this book 427 Table F.1 Contributed packages used in this book (continued ) Package Authors Description Chapters robust Jiahui Wang, Ruben Zamar, Alfio Marazzi, Victor Yohai, Matias Salibian-Barrera, Ricardo Maronna, Eric Zivot, David Rocke, Doug Martin, Martin Maechler, and Kjell Konis A package of robust methods 13 RODBC Brian Ripley and Michael Lapsley ODBC database access 2 ROracle David A. James and Jake Luciani Oracle database interface for R 2 rrcov Valentin Todorov Robust location and scatter estimation and robust multivariate analysis with high breakdown point 9 sampling Yves Tillé and Alina Matei Functions for drawing and calibrating samples 4 scatterplot3d Uwe Ligges Plots a three dimensional (3D) point cloud 11 sem John Fox with contributions from Adam Kramer and Michael Friendly Structural equation models 14 SeqKnn Ki-Yeol Kim and Gwan-Su Yi, CSBio lab., Information and Communications University Sequential KNN imputation method 15 sm Adrian Bowman and Adelchi Azzalini. Ported to R by B. D. Ripley up to version 2.0, version 2.1 by Adrian Bowman and Adelchi Azzalini, version 2.2 by Adrian Bowman. Smoothing methods for nonparametric regression and density estimation 6, 9 vcd David Meyer, Achim Zeileis, and Kurt Hornik Functions for visualizing categorical data 1, 6, 7, 11, 12 vegan Jari Oksanen, F. Guillaume Blanchet, Roeland Kindt, Pierre Legendre, R. B. O’Hara, Gavin L. Simpson, Peter Solymos, M. Henry H. Stevens, and Helene Wagner Ordination methods, diversity analysis, and other functions for community and vegetation ecologists 9 Download from Wow! eBook 428 APPENDIX F Packages used in this book Table F.1 Contributed packages used in this book (continued ) Package Authors Description Chapters VIM Matthias Templ, Andreas Alfons, and Alexander Kowarik Visualization and imputation of missing values 15 xlsx Adrian A. Dragulescu Read, write, and format Excel 2007 (xlsx) files 2 XML Duncan Temple Lang Tools for parsing and generating XML within R and S-Plus 2 Download from Wow! eBook 429 appendix G Working with large datasets R holds all of its objects in virtual memory. For most of us, this design decision has led to a zippy interactive experience, but for analysts working with large datasets, it can lead to slow program execution and memory-related errors. Memory limits will depend primarily on the R build (32 versus 64-bit) and for 32-bit Windows, on the OS version involved. Error messages starting with cannot allocate vector of size typically indicate a failure to obtain sufficient contiguous memory, while error messages starting with cannot allocate vector of length indicate that an address limit has been exceeded. When working with large datasets, try to use a 64-bit build if at all possible. For all builds, the number of elements in a vector is limited to 2,147,483,647 (see ?Memory for more information). There are three issues to consider when working with large datasets: (a) efficient programming to speed execution, (b) storing data externally to limit memory issues, and (c) using specialized statistical routines designed to efficiently analyze massive amounts of data. We will briefly consider each. G.1 Efficient programming There are a number of programming tips that improve performance when working with large datasets. ■ Vectorize calculations when possible. Use R’s built-in functions for manipulat- ing vectors, matrices, and lists (for example, sapply, lappy, and mapply) and avoid loops (for and while) when feasible. Download from Wow! eBook 430 APPENDIX G Working with large datasets ■ Use matrices rather than data frames (they have less overhead). ■ When using the read.table() family of functions to input external data into data frames, specify the colClasses and nrows options explicitly, set comment. char = "", and specify "NULL" for columns that aren’t needed. This will decrease memory usage and speed up processing considerably. When reading external data into a matrix, use the scan() function instead. ■ Test programs on subsets of the data, in order to optimize code and remove bugs, before attempting a run on the full dataset. ■ Delete temporary objects and objects that are no longer needed. The call rm(list=ls()) will remove all objects from memory, providing a clean slate. Specific objects can be removed with rm(object) . ■ Use the function .ls.objects() described in Jeromy Anglim’s blog entry “Memory Management in R: A Few Tips and Tricks” (jeromyanglim.blogspot. com), to list all workspace objects sorted by size (MB). This function will help you find and deal with memory hogs. ■ Profile your programs to see how much time is being spent in each function. You can accomplish this with the Rprof() and summaryRprof() functions. The system.time() function can also help. The profr and prooftools packages provide functions that can help in analyzing profiling output. ■ The Rcpp package can be used to transfer R objects to C++ functions and back when more optimized subroutines are needed. With large datasets, increasing code efficiency will only get you so far. When bumping up against memory limits, you can also store our data externally and use specialized analysis routines. G.2 Storing data outside of RAM There are several packages available for storing data outside of R’s main memory. The strategy involves storing data in external databases or in binary flat files on disk, and then accessing portions as they are needed. Several useful packages are described in table G.1. Table G.1 R packages for accessing large datasets Package Description ff Provides data structures that are stored on disk but behave as if they were in RAM. bigmemory Supports the creation, storage, access, and manipulation of massive matrices. Matrices are allocated to shared memory and memory- mapped files. filehash Implements a simple key-value database where character string keys are associated with data values stored on disk. Download from Wow! eBook Analytic packages for large datasets 431 Table G.1 R packages for accessing large datasets (continued ) Package Description ncdf , ncdf4 Provides an interface to Unidata netCDF data files. RODBC , RMySQL , ROracle , RPostgreSQL , RSQLite Each provides access to external relational database management systems. The packages above help overcome R’s memory limits on data storage. However, spe- cialized methods are also needed when attempting to analyze large datasets in a rea- sonable length of time. Some of the most useful are described below. G.3 Analytic packages for large datasets R provides several packages for the analysis of large datasets: ■ The biglm and speedglm packages fit linear and generalized linear models to large datasets in a memory efficient manner. This offers lm() and glm() type functionality when dealing with massive datasets. ■ Several packages offer analytic functions for working with the massive matri- ces produced by the bigmemory package . The biganalytics package offers k-means clustering, column statistics, and a wrapper to biglm. The bigtabu- late package provides table() , split() , and tapply() functionality and the bigalgebra package provides advanced linear algebra functions. ■ The biglars package offers least-angle regression, lasso, and stepwise regres- sion for datasets that are too large to be held in memory, when used in conjunc- tion with the ff package . ■ The Brobdingnag package can be used to manipulate large numbers (numbers larger than 2^1024). Working with datasets in the gigabyte to terabyte range can be challenging in any lan- guage. For more information on the methods available within R, see the CRAN Task View: High-Performance and Parallel Computing with R (cran.r-project.org/web/views/). Download from Wow! eBook 432 appendix H Updating an R installation As consumers, we take for granted that we can update a piece of software via a “Check for updates…” option. In chapter 1, I noted that the update.packages() function can be used to download and install the most recent version of a contrib- uted package. Unfortunately, there’s no corresponding function for updating the R installation itself. If you want to update an R installation from version 4.1.0 to 5.1.1, you must get creative. (As I write this, the current version is actually 2.13.0, but I want this book to appear hip and current for years to come). Downloading and installing the latest version of R from CRAN (http://cran.r- project.org/bin/) is relatively straightforward. The complicating factor is that customizations (including previously installed contributed packages) will not be included in the new installation. In my current set-up, I have 248 contributed packages installed. I really don’t want to have to write their names down and reinstall them by hand the next time I upgrade my R installation. There has been much discussion on the web concerning the most elegant and efficient way to update an R installation. The method described below is neither elegant nor efficient, but I find that it works well on a variety of platforms (Windows, Mac, and Linux). In this approach, the installed.packages() function is used to save a list of packages to a location outside of the R directory tree, and then the list is used with the install.packages() function to download and install the latest contributed packages into the new R installation. Here are the steps: Download from Wow! eBook APPENDIX H Updating an R installation 433 1 If you have a customized Rprofile.site file (see appendix B), save a copy outside of R. 2 Launch your current version of R and issue the following statements oldip <- installed.packages()[,1] save(oldip, file="path/installedPackages.Rdata") where path is a directory outside of R. 3 Download and install the newer version of R. 4 If you saved a customized version of the Rprofile.site file in step 1, copy it into the new installation. 5 Launch the new version of R, and issue the following statements load("path/installedPackages.Rdata") newip <- installed.packages()[,1] for(i in setdiff(oldip, newip)) install.packages(i) where path is the location specified in step 2. 6 Delete the old installation (optional). This approach will install only packages that are available from the CRAN. It won’t find packages obtained from other locations. You’ll have to find and download these separately. Luckily, the process will display a list of packages that can’t be installed. Dur- ing my last installation, globaltest and Biobase couldn’t be found. Since I got them from the Bioconductor site, I was able to install them via the code source(http://bioconductor.org/biocLite.R) biocLite("globaltest") biocLite("Biobase") Step 6 involves the optional deletion of the old installation. On a Windows machine, more than one version of R can be installed at a time. If desired, uninstall the older version via Start > Control Panel > Uninstall a Program. On Mac and Linux platforms, the new version of R will overwrite the older version. To delete any rem- nants on a Mac, use the Finder to go to the /Library/Frameworks/R.frameworks/ versions/ directory and delete the folder representing the older version. On a Linux platform, it’s probably best to leave well enough alone. Clearly, updating an existing version of R is more involved than is desirable for such a sophisticated piece of software. I’m hopeful that someday this appendix will simply say “Select the Check for Updates… option” to update an R installation. Download from Wow! eBook Download from Wow! eBook 435 index Symbol ! operator 77 != operator 77 # symbol 8 %a symbol 81 %A symbol 81 %B symbol 82 %b symbol 82 %d symbol 81 %m symbol 81 %Y symbol 82 %y symbol 82 * operator 75, 178 ** operator 75 ... option 58, 61 . symbol 178 / operator 75 : symbol 178 ? function 11 ?? function 11 ^ operator 75, 178, 181 ~ symbol 178 + operator 75, 178 < operator 77 <<- operator 29 <= operator 77 == operator 77 > operator 77 >= operator 77 -1 symbol 178 brackets 29 3D pie charts 127 3D scatter plots 274–278 A abline( ) function 60, 265 abs( ) function 93 absolute widths 67 acos( ) function 93 acosh( ) function 93 AER package 421 aggr( ) function, VIM package 357 aggregate( ) function 113, 240 aggregating data 112–113 AIC( ) function 179, 208 all subsets regression 210, 213 alpha option 390 alternative= option 255 Amelia package 365, 369, 421 analyses, excluding missing values from 80–81 analysis of covariance (ANCOVA) one-way 230–233 assessing test assumptions 232 visualizing results 232–233 overview 222 analysis of variance (ANOVA) 219–245, 252–253 fitting models 222–225 aov( ) function 222–223 order of formula terms 223–225 MANOVA 239–243 assessing test assumptions 241–242 robust 242–243 one-way 225–230 assessing test assumptions 229–230 multiple comparisons 227–229 one-way ANCOVA 230–233 assessing test assumptions 232 visualizing results 232–233 as regression 243–245 repeated measures 237–239 terminology of 220–222 two-way factorial 234–236 analytic packages, for large datasets 431 ANCOVA. See analysis of covariance ancova( ) function, HH package 232 AND operator 77 annotating datasets 42 annotations 62–64 ANOVA. See analysis of variance anova( ) function 179, 208 Anova( ) function, car package 225, 239 aov( ) function 222–223 append option 13 apply( ) function 102–103 apropos( ) function 11 aq.plot( ) function, mvoutlier package 242 arithmetic operators 75 arrayImpute package 370 421 arrayMissPattern package 370, 421 arrays 26–27 Arthritis dataset 19 as.character( ) function 83 ASCII file 35 as.datatype( )function 84 as.Date( ) function 81, 88 asin( ) function 93 asinh( ) function 93 aspect option 378 assumptions linear model, global validation of 199 of MANOVA tests, assessing 241–242 of OLS regression, assessing 188–199 of one-way ANCOVA tests, assessing 232 of one-way ANOVA tests, assessing 229–230 asypow package 261 Download from Wow! eBook 436 INDEX at option 58 atan( ) function 93 atanh( ) function 93 attach( ) function 28, 30, 88 auto.key option 384 avPlots( ) function 193, 203 axes 57, 60 axes option 57 axis( ) function 57 B background color (bg) option 61 backslash character 13, 102 bar plots 120–125 fitting labels in 124 for mean values 122–123 simple 120–121 spinograms 124–125 stacked and grouped 121–122 tweaking 123–124 barplot( ) function 120, 122–123 base package 274 batch processing 17 Beta distribution 97 bg option. See background color option bg parameter 52 biganalytics package 431 biglars package 431 bigmemory package 430–431 bigtabulate package 431 Binomial distribution 97 bitro.diameter variable 339 bivariate relationships 184 block comments 33 bmp( ) function 47 boot package 422 bootstrap package 214 bootstrapping 89, 303–309 box plots 133–138 parallel, comparing groups with 134–137 violin variation of 137–138 box type (bty) option 61 boxplot( ) function 47, 238 boxplots option 267 boxplot.stats( ) function 133 boxTidwell( ) function 206 Box-Tidwell transformations 206 breaks option 128 Brobdingnag package 431 bty option. See box type option bubble plots 278–279 by function 146 by option 113 byrow option 25 bzfile( ) function 36 C c( ) function 9, 24, 43 ca package 422 car package 225, 230, 239, 266, 268 case identifiers 23, 30 case-wise deletion 364–365 cast( ) function 114–115 casting 114, 116 cat( ) function 101, 111 cat package 370, 422 categorical variables 23 Cauchy distribution 97 cbind( ) function 43, 85, 105–106, 240 ceiling( ) function 93 cex ( ) option 61 cex parameter 51, 53 cex.axis parameter 53 cex.lab parameter 53 cex.main parameter 53 cex.names option 123 cex.sub parameter 53 CFA. See confirmatory factor analysis character functions 99–101 character variables, converting date values to 83 Chi-square tests 255–256 Chi-squared (noncentral) distribution 97 class( ) function 43 cld( ) function 228 CLI. See command-line interface close( ) function 40 cm.colors( ) function 53 cmdscale( ) function 350 code editors, list of 403–404 coefficients( ) function 179 coin package 422 col option 52, 58, 122, 134, 136, 359, 378 col.axis parameter 52 colClasses option 36, 430 col.corrgram( ) function 287 colfill vector 132 col.lab parameter 52 col.main parameter 52 color option 139, 390 colorRampPalett( ) function 287 colors, graphical parameters 52–53 colors( ) function 53 col.sub parameter 52 columns adding 85 data frames 27 combine objects. See c( ) function combining graphs. See page arrangement of graphs command prompt 7 command-line interface (CLI) 403 command-line options 407 command-line prompt 403 comments, # symbol 8, 33 common factors 342 comparisons, multiple 227–229 complete( ) function 369 complete-case analysis 364–365 complete.cases( ) function 356–357, 364 components, principal extracting 339 rotating 339–341 scores 341–342 selecting number to extract 335 comprehensive GUIs, for R 405 Comprehensive R Archive Network (CRAN) 7, 406 conditional execution 107–109 if-else construct 108–109 ifelse construct 109 repetition and looping 107–108 switch construct 109 conditioning variables 376, 379–380 confint( ) function 179, 188 confirmatory factor analysis (CFA) 349 constant residual variance 191 contrasts( ) function 244 contr.helmert function 244 control flow 107–109 Download from Wow! eBook INDEX 437 contr.poly function 244 contr.SAS function 244 contr.sum function 244 contr.treatment function 244 conversions, type 83–84 Cook’s distance 18, 189–191, 202–204, 317 cooks.distance( ) function 18 cor( ) function 184 corrective measures 205–207 deleting observations 205 variables adding or deleting 207 transforming 205–207 correlations tests of significance 162–164, 253 types 159–162 using to assess missing data patterns 360–361 correlograms 283, 287 corrgram( ) function, corrgram package 284 corrgram package 284, 422 corrperm package 422 cos( ) function 93 cosh( ) function 93 cov( ) function 240 cov2cor( ) function 343 Cox proportional hazards regression 175 cpairs( ) function 269–270 CRAN. See Comprehensive R Archive Network crimedat dataframe 40 cross-tabulations 151–155 crossval( ) function 214 cross-validation 213, 215 crPlots( ) function 193, 196 curly braces 107 cut( ) function 78, 101, 379 D D plots, Cook. See Cook’s distance D values, Cook. See Cook’s distance data exporting of 408–409 delimited text ﬁle 408 Excel spreadsheet 409 missing. See missing data for statistical applications 409 long format 114 time-stamping 82 data( ) function 11 data frames 22–23, 27–30 applying functions to 102–103 attach( ), detach( ), and with( ) functions 28–30 case identifiers 30 using SQL statements to manipulate 89–90 data management aggregating 112–113 control flow 107–109 conditional execution 108–109 repetition and looping 107–108 datasets merging 85–86 subsetting 86–89 date values 81–83 example 73–75 functions 93–103 applying to matrices and data frames 102–103 character 99–101 mathematical 93–94 probability 96–99 statistical 94–96 missing values 79–81 excluding from analyses 80–81 recoding values to missing 80 restructuring reshape package 113–116 transpose 112 sorting 84–85 type conversions 83–84 user-written functions 109–111 using SQL statements to manipulate data frames 89–90 variables creating new 75–76 recoding 76–78 renaming 78–79 data objects applying functions to 102 functions for working with 42–44 data option 299, 300, 306, 308, 319, 323, 325, 328, 365, 368, 375 data storage, outside of RAM 430–431 data structures 23–33 arrays 26–27 data frames 27–30 attach( ), detach( ), and with( ) functions 28–30 case identiﬁers 30 factors 30-31 lists 32–33 matrices 24–26 vectors 24 data type, converting from one to another 84 database interface (DBI) related packages 41 database management systems (DBMSs), accessing 39–41 DBI-related packages 41 ODBC interface 39–40 data.frame( ) function 27 datasets annotating 42 data structures 23–33 arrays 26–27 factors 30–31 frames 27–30 lists 32–33 matrices 24–26 vectors 24 description of 22–23 functions for working with data objects 42–44 input 33–42 accessing DBMSs 39–41 entering data from keyboard 34–35 importing data 35–39, 41–42 webscraping 37 large 18, 429–431 analytic packages for 431 efﬁcient programming 429–430 storing data outside of RAM 430–431 merging 85–86 adding columns 85 adding rows 86 subsetting 86–89 excluding variables 86–87 random samples 89 selecting observations 87–88 Download from Wow! eBook 438 INDEX selecting variables 86 subset( ) function 88–89 transposing 112 date( )function 82 date values 81–83 DBI related packages. See database interface related packages DBMSs, accessing. See database management systems, accessing deleting old versions of R 433 deletion, pairwise 370–371 delimited text files exporting data to 408 importing data from 35–36 demo( ) function 9–10 density( ) function 130 densityplot( ) function 386 dependent variable 220 detach( ) function 28, 30 dev.new( ) function 47 dev.next( ) function 47 dev.off( ) function 13, 47 dev.prev( ) function 47 dev.set( ) function 47 diagnostics, regression 188–200 enhanced approach 192–198 global validation of linear model assumption 199 multicollinearity 199–200 typical approach 189–192 diag.panel option 285 diff( ) function 95 difftime( )function 83 dim( ) function 43 dimensions of an array 26 of graphs and margins 54–56 dimnames 26 dir.create( ) function 13 directory initialization file 406 distribution functions, normal 97–98 dmat.color( ) function, gclus package 270 doBy package 422 dollar sign character 33 dot plots 138, 140 dotchart( ) function 138 Durbin-Watson test 196 durbinWatsonTest( ) function 193, 196 E echo option 412 edit( ) function 34–35 EFA. See exploratory factor analysis effect( ) function 187, 231 defined for ANOVA 252 defined for chi-square tests 255 defined for correlation 253 defined for linear models 253, 254 defined for test of proportions 254 defined for t-test 250 effect size 248–260 effect size benchmarks 257–258 effects library 231 effects package 187, 231, 422 environment, customizing startup 406–407 environment variables 407 errors, independence of 196 escape character 13, 102 ES.w2( ) function 255 eval option 412 example( ) function 11 example.Rnw file 411 Excel, Microsoft accessing files with RODBC 36 exporting data to spreadsheet 409 importing data from 36–37 excluding missing values from analyses 80–81 observations 87–89 variables 86–87 exp( ) function 94 exploratory factor analysis (EFA) 331–334, 342–349 deciding number of common factors to extract 343–344 FactoMineR package 349 factors extracting common 344–345 rotating 345–348 scores 349 FAiR package 349 GPArotation package 349 nFactors package 349 other latent variable models 349–351 exponential distribution 97, 315 exponentiation operator 75 exporting data 408–409 delimited text file 408 Excel spreadsheet 409 for statistical applications 409 expression( ) function 386 expression statement 107 extracting common factors 344–345 principal components 339 F F distribution 97 fa( ) function 333, 344, 349 facets, ggplot2 package 390–394 facets option 390 factanal( ) function 333 FactoMineR package 349, 422 factor( ) function 30, 42 factor intercorrelation matrix 346 factor pattern matrix 346 factor structure matrix 346 factorial ANOVA design 221 factor.plot( ) function 333, 347 factors as dimensions in principal components or factor analysis deciding number of common to extract 343–344 extracting common 344–345 rotating 345–348 scores 349 as R data structures 23–24, 30–31 fa.diagram( ) function 333, 347 FAiR package 349, 422 family parameter 54 fan plots 127–128 fan.plot( ) function 127 fa.parallel( ) function 333, 335, 343 fCalendar package 83, 422 ff package 430–431 fg parameter 52 Download from Wow! eBook INDEX 439 fgui package 405 fig graphical parameter 69–71 fig option, in Sweave 412 figures, creating with fine control 69–72 file( ) function 36 filehash package 430 fill option 390 fine control, creating figure arrangements with 69–72 First( ) function 406–407 fit lines 5 fitted( ) function 179 fitting ANOVA models 222–225 aov( ) function 222–223 order of formula terms 223–225 fitting regression models, with lm( ) function 178–179 fix( ) function 35, 43, 78 FlexMix package 350 floor( ) function 93 fmi, fraction of missing information 367–368 font families changing 54 examples on Windows platform 64 font parameter 54 font.axis parameter 54 font.lab parameter 54 font.main parameter 54 font.sub parameter 54 for loop 108 foreign package 38, 409, 422 format( ) function 82 formulas, in R 178, 223–225 frame.plot option 57 freq option 128 frequency tables 149–155 Friedman test 168 functions applying to data objects 102 character 99–101 date 81–83 for debugging 111 mathematical 93–94 numeric 93–99 other useful 101 probability 96–99 for saving graphic output 14 statistical 94–96 type conversion 84 user-written 109–111 G Gamma distribution 97 gap package 261 gclus package 16, 269–270, 422 gcolor option 138 generalizability 174 genome-wide association studies (GWAS) 261 geom option 390 geometric distribution 97 geostatistical data 14 getwd( ) function 12, 406 GGobi program 399 ggplot2 package 374–375, 390–394 Gibbs sampling 366 glht( ) function, multcomp package 227 glm( ) function 431 glmPerm package 423 global validation, of linear model assumption 199 gls( ) function, nlme package 239 gmodels package 423 GPArotation package 349 gplots package 123, 226, 235, 423 graph dimensions 54, 56 graphic output 13–14 graphic user interfaces (GUIs) 5, 403–405 IDEs for 403–404 for R 405 graphical parameters 49–56 colors 52–53 graph and margin dimensions 54–56 reference lines 60 symbols and lines 50–51 text characteristics 53–54 graphics 373–399 four systems of 374–375 ggplot2 package 390–394 interactive graphs 394–399 identifying points 394 iplots package 397–398 latticist package 396–397 playwith package 394–395 rggobi package 399 lattice package 375–389 graphic parameters 387–388 page arrangement 388–389 panel functions 381–383 variables 379–380, 383–387 parameters 387–388 graphs axis and text options 56–64 annotations 62–64 axes 57–60 legend 60–62 reference lines 60 titles 57 bar plots 120–125 for mean values 122–123 simple 120–121 spinograms 124–125 stacked and grouped 121–122 tweaking 123–124 box plots 133–138 parallel 134–137 violin variation of 137–138 combining 65–72 creating 46 dot plots 138–140 example 48 graphical parameters 49–56 colors 52–53 graph and margin dimensions 54–56 symbols and lines 50–51 text characteristics 53–54 histograms 128–130 interactive 394–399. See also intermediate graphs identifying points 394 iplots package 397–398 latticist package 396–397 playwith package 394–395 rggobi package 399 kernel density plots 130–132 pie charts 125–128 single enhanced 69 gray( ) function 53 grep( ) function 37, 100 grid function 374 grid package 374, 423 grouped bar plots 121–122 grouping variables 383–387 groups option dot plots 138 lattice package 378, 384 gsub( ) function 37 GUIs. See graphic user interfaces gvlma( ) function 199 gvlma package 193, 199, 423 GWAS. See genome-wide association studies gzfile( ) function 36 Download from Wow! eBook 440 INDEX H hat statistic 201 HDF5 files. See Hierarchical Data Format files hdf5 package 39, 423 head( ) function 43 header value 35 heat.colors( )function 53 height variable 339 height vector 120 heights option 67 help ( ) or ? function 11 help facilities 11, 16 help.search( ) or ?? function 11 help.start( ) function 11 hexbin( ) function 272 hexbin package 272, 423 HH package 232, 235–236, 423 Hierarchical Data Format (HDF5) files 39 high-density scatter plots 271–274 high-leverage observations 201–202 hist( ) command 47 hist( ) function 66 histograms 128–130 of bootstrapped statistics 306–308 in ggplot2 plots 390 in iplots 397 in lattice plots 375, 377 in scatterplot matrices 269 of studentized residuals 195 history( ) function 12 Hmisc package 38, 59, 370, 423 homoscedasticity 191, 197–198 regression 190 statistical assumption 177 horiz option 120 hsv( ) function 53 hypergeometric distribution 97 hypothesis testing 247–249 I I( ) operator 178, 181 ibar( ) function 397 ibox( ) function 397 identify( ) function 394–395 IDEs. See integrated development environments id.method option 193, 266 IDPmisc package 273–274 if-else construct 108–109 ifelse construct 109 if-else control structure 108 ihist( ) function 397 imap( ) function 397 imosaic( ) function 397 importing data from database management systems 39–41 from delimited text file 35–36 from HDF5 files 39 from the keyboard 34–35 from Microsoft Excel 36–37 from netCDF files 39 from SAS datasets 38 from SPSS datasets 38 from Stata datasets 38–39 via Stat/Transfer application 41–42 from web pages 39 from XML files 37 imputation multiple 365–369 simple 371–372 incomplete data. See missing data independence, of errors 177, 190, 196 index.cond option 378 indices in R, 33 infile 17 influencePlot( ) function 193, 204 influential observations 190, 202, 204 input 13–14, 18 installations, updating 432–433 installed.packages( ) function 16, 432, 433 installing packages 116 R application 7 setting default CRAN site 407 install.packages( ) function 16, 407, 432 integrated development environments (IDEs) 403–404 interaction2wt( ) function, HH package 235–236 interaction.plot( ) function 235, 238 interactions, multiple linear regression with 186–188 interactive graphs 394–399 identifying points 394 iplots package 397–398 latticist package 396–397 playwith package 394–395 rggobi package 399 intermediate graphs 263 bubble plots 278–279 correlograms 283–287 line charts 280–283 mosaic plots 288 scatter plots 264–279 3D, 274–277 high-density 271–274 matrices 267–271 ipairs( ) function, IDPmisc package 274 ipcp( ) function 397 iplot( ) function 273, 397 iplots package 394, 397–398 is.datatype( ) function 84 is.infinite( ) function 355 is.na( ) function 79, 355 is.nan( ) function 355 isoMDS( ) function 350 isTRUE( ) operator 77 J JGR/Deducer GUI 405 jpeg( ) function 47 K kernel density estimation 6 kernel density plots 130, 132 key (or auto.key) option 378 keyboards, entering data from 34–35 k-fold cross-validation 214 kmi package 370, 424 Kruskal-Wallis test 168 L labels, fitting in bar plots 124 labels option 58, 193, 266 lapply( ) function 103 las option 58 Last( ) function 406–407 latent variable models 349, 351 LaTeX documents, R code + (Sweave package) 410–415 Download from Wow! eBook INDEX 441 lattice package 48, 374–375, 378–381, 424 graphic parameters 387–388 graphs types 377 page arrangement 388–389 panel functions 381–383 variables conditioning 379–380 grouping 383–387 latticist package 396–397, 424 lavaan package 350, 424 layout( ) function 65–69 layout option 378 lcda package 350, 424 lcm( ) function 67 lcmm package 350 leadership data frame 86 leaps package 211, 424 legend( ) function 60, 132 legend option 60 legend.plot option 266 legends 60–62 in bar plots 122 in kernel density plots 131–132 in lattice plots 384–386 in line plots 282–283 in mosaic plots 289 in scatter plots 264, 273 legend.text parameter 122 length( ) function 43, 101, 143, 148 level option, cld( ) function 228 leverage value, of observations 190 .libPaths( ) function 15, 407 library( ) function 15–16 line( ) function 59 line charts 280–283 linear models 253–254, 257 assumption, global validation of 199 versus nonlinear model 183 linear regression multiple 184–186 simple 179–181 linearity 196–197 regression 190 statistical assumption 177 lines graphical parameters 50–51 reference 60 lines( ) function 123, 129–130, 282 link function 315 list( ) function 32 lists 32–33 list-wise deletion 81 listwise deletion 364–365 lm( ) function 178–179, 184–188 lme4 package 239 lmer( ) function, lme4 package 239 lmfit list object 18 lmPerm package 424 load( ) function 12, 13 loadhistory( ) function 12 location option 60, 62 locator() function 132 loess( ) function 266 log( ) function 93 log10( ) function 93 logical operators 76 logistic regression 175, 314, 315, 317–323 extensions 323 fitting 317–320 interpreting parameters 320–322 overdispersion 322–323 lognormal distribution 97 logregperm package 424 long data format 116 longitudinalData package 370, 424 looping, repetition and 107–108 lower.panel option 285 lowess( ) function 265–266 ls( ) function 12, 43 lsa package 350, 424 .ls.objects( ) function 430 ltm package 424 lty option 58, 378 lty parameter 51 lty.smooth option 183–184, 268–269 lubridate package 83, 424 lwd option 378 lwd parameter 51 M mad( ) function 94 mai parameter 55 main option 378, 390 Mallows Cp statistic 211 MANCOVA. See multivariate analysis of covariance Mann-Whitney U test 166–167 MANOVA. See multivariate analysis of variance manova( ) function 241 MAR. See missing at random mar parameter 55 margin dimensions 54–56 marginplot( ) function, VIM package 359 MASS package 98, 209, 350, 424 math annotations 64 mathematical functions 93–94 matrices 24–26 applying functions to 102–103 matrix algebra with R 419–420 of scatter plots 267–271 matrix function 24–25 matrixplot( ) function, VIM package 358 max( ) function 95 MCAR. See missing completely at random md.pattern( ) function, mice package 357 MDS. See multidimensional scaling mean( ) function 94, 102, 105, 356 mean substitution 371 mean values, bar plots for 122–123 median( ) function 94 melt( ) function 114–115 melting 114 merging datasets 85–86 adding columns 85 adding rows 86 metafile format, Windows 47 method option 390 mfrow parameter 65 MI. See multiple imputation mi package 365, 369 mice( ) function 366 mice package 353, 357, 365, 369 Microsoft Excel, importing data from 36–37 min( ) function 95 minor.tick( ) function 59 minus sign 87 missing at random (MAR) 354 missing completely at random Download from Wow! eBook 442 INDEX (MCAR) 354 missing data 352–372 approaches for dealing with incomplete data 363–364 complete-case analysis 364–365 exploring patterns 356–361 exploring missing data visually 357–359 missing values 357, 360–361 identifying 355–356 multiple imputation 365–369 pairwise deletion 370–371 rational approaches for correcting 363–364 simple imputation 371 steps in dealing with 353–355 understanding sources and impact of 362–363 missing values 79–81 excluding from analyses 80–81 recoding values to missing 80 mix package 370 mixed-model ANOVA design 221 mlogit package 425 mode( ) function 43 MODULUS operator 75 mosaic( ) function, vcd library 288 mosaic plots 288 mosaicplot( ) function 288 mtcars data frame 29, 46, 377 mtext( ) function 59, 62 multcomp package 227, 231, 425 multicollinearity 199–200 multidimensional scaling (MDS) 350 multiline comments 33 multiple comparisons nonparametric 169 parametric one-way ANCOVA 231 one-way ANOVA 227–229 multiple graphs per page. See page arrangement of graphs multiple imputation (MI) 365, 369 multiple linear regression 175, 179, 184–188 multiple regression 184 multivariate analysis of covariance (MANCOVA) 222 multivariate analysis of variance (MANOVA) 222, 239–243 assessing test assumptions 241–242 robust 242–243 multivariate normal data, generating 98–99 multivariate regression 175 mvnmle package 370, 425 mvoutlier package 242, 425 mvrnorm( ) function 98 N NA. See not available names( ) function 43, 79 names.arg argument 123 NaN. See not a number na.omit( ) function 81, 364 na.rm option 80 ncdf package 39, 425, 431 ncdf4 package 39, 425, 431 nchar( ) function 100 ncvTest( ) function 193, 197 netCDF files. See network Common Data Form files netCDF library, Unidata 39 network Common Data Form (netCDF) files 39 new option 70 nFactors package 349, 425 NHST. See null hypothesis significance testing nlme package 239 NMAR. See not missing at random nonlinear model, versus linear model 183 nonlinear regression 175 nonparametric regression 175 nonparametric tests 166–170 nonstochastic imputation 371–372 no.readonly option 49 normal data, generating multivariate 98–99 normal distribution functions 97–98 normal Q-Q plot 190 normality 193, 196 regression 190 statistical assumption 177 not a number (NaN) 79, 355 not available (NA) 79, 355 not missing at random (NMAR) 355 notched box plots 134–135 noweb file 411, 414 npmc package 425 nrows option 430 null hypothesis significance testing (NHST) 246 O obcConnectExcel( ) function 37 objects 23 oblique rotation 340, 345 observations deleting 205 deleting with na.omit( ) function 81 selecting 87–88 unusual 200–204 high leverage 201–202 inﬂuential 202–204 outliers 200–201 ODBC interface. See Open Database Connectivity interface odbcConnect( ) function 40 ODF. See Open Documents Format odfTable( ) function 415 odfWeave package 410–415 OLS regression. See ordinary least squares regression one-way analysis of covariance (ANCOVA) 230–233 assessing test assumptions 232 visualizing results 232–233 one-way analysis of variance (ANOVA) 225–230 assessing test assumptions 229–230 multiple comparisons 227–229 power and effect size 252, 257 terminology 220–221 one-way between-groups Download from Wow! eBook INDEX 443 ANOVA design 220 one-way within-groups ANOVA design 220–221 Open Database Connectivity (ODBC) interface 39–40 Open Documents Format (ODF) 410 openMx package 350, 425 OpenOffice documents, creating reports with odfWeave package 415–417 OpenOffice ODT file 415 options( ) function 12, 245 OR operator 77 order( ) function 84, 107 order of formula terms 223, 225 order.clusters( ) function 17 ordered factor 31 order.single( ) function, gclus package 270 ordinary least squares (OLS) regression 175–218 cross-validation 213–215 fitting regression models with lm( ) function 178–179 multiple linear regression 184–186 multiple linear regression with interactions 186–188 polynomial regression 181–184 regression diagnostics 188–207 simple linear regression 179–181 variable (model) selection 207–213 variable importance 215–217 orthogonal rotation 340, 345 outlier observation 190 outliers 200–201 outlierTest( ) function 193, 200, 230 output graphic 13–14 text 13 using as input 18 P packages 14–17 analytic, for large datasets 431 description of 15–16 function of 16–17 installing 16 list of 421–428 loading 16 updating 432 page arrangement of graphs with base graphics 65–71 with lattice graphs 388–389 pairs( ) function 267 pairwise deletion 370–371 pamm package 261 pan package 370 panel functions 381, 383 panel option 285, 378 panel.abline( ) function 383 panel.ellipse option 285 panel.grid( ) function 381 panel.lmline( ) function 381 panel.loess( ) function 383 panel.minmax option 285 panel.pie option 285 panel.pts option 285 panel.rug( ) function 381 panel.shade option 285 panel.txt option 285 panel.xyplot( ) function 381, 383 par( ) function 49–50, 53–56, 59–61, 64–67, 69–70, 124 parallel analysis approach 335 parallel box plots, comparing groups with 134–137 parameters, graphic 387–388 paste( ) function 86, 100 pastecs package 425 PCA. See principal components analysis pch parameter 49–51 pdf( ) function 47 pedantics package 261 period character 33 PHYS variable 334 pie charts 125–128 pie3D( ) function 127 piface package 260, 425 pin parameter 55 playwith package 394–396, 425 plot( ) function 47–48, 59, 282, 388–389 plot3d( ) function, rgl package 277 plotmath( ) function 64 plotmeans( ) function, gplots package 226, 235 plot.new( ) function 71 plotrix package 127 plots, power analysis 258–259 plotting symbols, with pch parameter 51 pmm. See predictive mean matching png( ) function 47 points, identifying 394 poisson regression 175, 324–330 fitting 325 interpreting parameters 326 overdispersion 327 robust 330 with varying time periods 329 zero-inflated 329 poLC package 350 poLCA package 425 polygon( ) function 130 polynomial regression 175, 179, 181, 184 pool( ) function 366 pos option 58, 62 position option 379 postscript( ) function 47 power analysis 246–262, 313 hypothesis testing 247–249 implementing with pwr package 249–258 ANOVA 252–253 Chi-square tests 255–256 correlations 253 effect size benchmarks 257–258 linear models 253–254 tests of proportions 254–255 t-tests 250–252 plots 258–259 specialized packages 260–262 powerGWASinteraction package 261 powerpkg package 261 powerSurvEpi package 261 predict( ) function 179 predictive mean matching (pmm) 368 pretty() function 101 primary variables, in lattice functions 376 principal( ) function 333, 336, 341 Download from Wow! eBook 444 INDEX principal components analysis (PCA) 331–351 other latent variable models 349–351 principal components extracting 339 obtaining scores 341–342 rotating 339–341 selecting number of components to extract 335 princomp( ) function 333 print( ) statement 412 probability functions 96–99 generating multivariate normal data 98–99 setting seed for random number generation 98 profr package 430 prooftools package 430 proportions, tests of 254–255 ps parameter 54 pseudo-random numbers 96–99 multivariate normal 98–99 probability distributions 96–97 setting the seed 98 psych package 333, 426 publication-quality reports OpenOffice documents with odfWeave package 415–417 typesetting with Sweave package (R code + LaTeX documents) 410–415 pundat dataframe 40 pwr package, implementing power analysis with 249–258 ANOVA 252–253 Chi-square tests 255–256 correlations 253 effect size benchmarks 257–258 linear models 253–254 tests of proportions 254–255 t-tests 250–252 pwr.2p2n.test function 250 pwr.2p.test( ) function 250, 254 pwr.anova.test( ) function 250, 252, 257 pwr.chisq.test( ) function 250, 255 pwr.f2.test( ) function 250, 253 PwrGSD package 261 pwr.p.test function 250 pwr.r.test( ) function 250, 253, 258 pwr.t2n.test function 250, 252 pwr.t.test( ) function 250 Q q( ) function 9, 12 qcc package 426 qplot( ) function 390–393 qqPlot( ) function 193 quadratic regression 184 quantile( ) function 95, 105 quartzFonts( )function 54 R R AnalyticFlow GUI 405 R CMD BATCH statement 17 R code + LaTeX documents (Sweave package), typesetting with 410–415 R Commander GUI 405 R Data Import/Export manual 34 .R extension 17 R GUI Generator (RGG) 405 R GUI Projects page 405 R icon 8 R language batch processing 17 example 18 getting help 11 getting started 8–10 input 13 large datasets and 18 obtaining and installing 7 output graphic 13–14 text 13 using as input 18 packages 14–17 description of 15–16 function of 16–17 installing 16 loading 16 reasons to use 5–7 workspace 11–13 R programming, common mistakes in 17 R statements 107 R_HOME value 406 R_HOME/etc directory 406 R2HTML package 411 rainbow( ) function 53, 127 Random Access Memory (RAM), storing data outside of 430–431 random number generation, setting seed for 98 random samples 89 randomized block design 223 randomLCA package 350, 426 range( ) function 95 Rattle (for data mining) GUI 405 rbind( ) function 43, 86, 232 Rcmdr package 277, 426 Rcpp package 430 RCurl package 37 .RData file 13 readLines( ) function 37 read.spss( ) function 38 read.ssd( ) function 38 read.table( ) function 35–36, 430 read.xlsx( ) function 37 recode( ) function 78 recodevar( ) function 78 recoding, values to missing 80 Red R GUI 405 reference lines 60 regression 173–218 ANOVA as 243–245 corrective measures 205–207 deleting observations 205 variables 205–207 diagnostics 188–200 enhanced approach 192–198 global validation of linear model assumption 199 multicollinearity 199–200 typical approach 189–192 measuring performance 213–218 cross-validation 213–215 relative importance 215–218 OLS 177–188 ﬁtting regression models with lm( ) function 178–179 multiple linear regression 184–186 polynomial regression 181–184 Download from Wow! eBook INDEX 445 simple linear regression 179–181 selecting model 207–213 comparing models 208–209 variable selection 209–213 unusual observations 200–204 high leverage 201–202 inﬂuential 202–204 outliers 200–201 varieties of 174–177 regression diagnostics 188–207 regsubsets( ) function 210 relaimpo package 215 relative importance, of variables 215–218 relative weights 216 relative widths 67 relweights( ) function 216 rename( ) function 78 rep( ) function 101 repeated measures, ANOVA 221, 237–239 repetition, and looping 107–108 reports, publication-quality OpenOfice documents with odfWeave package 415–417 typesetting with Sweave package (R code + LaTeX documents) 410–415 resampling statistics 89, 291–303 reshape package 78–79, 113–116, 426 casting 114–116 melting 114 residplot( ) function 195 residual versus leverage plot 190 residuals( ) function 179 restructuring data reshape package 113–116 casting 114–116 melting 114 transpose 112 results option, Sweave 412 RGG. See R GUI Generator rggobi package 394, 399, 426 rgl package 277, 426 .Rhistory file 13 RJDBC package 426 Rkward GUI 405 rm( ) function 12, 43, 430 rms package 426 RMySQL package 41, 431 robust MANOVA 242–243 robust package 427 Robust regression 175 RODBC package 36–40, 427–431 ROracle package 41, 427–431 rotating 3D scatter plots 277 factors 345–348 principal components 339–341 round( ) function 93 .Rout extension 17 rownames 23 row.names option 30, 36 rows, adding 86 RPostgreSQL package 41, 431 Rprof( ) function 430 .Rprofile file 406 Rprofile.site file 406–407, 433 rrcov package 242, 427 RSiteSearch( ) function 11 RSQLite package 41, 431 R-square statistic 214 rug plots 6, 129 runif( ) function 98 S sample( ) function 89 sample size quantity 248 samples, random 89 sampling package 427 sapply( ) function 103, 106 sas.get( ) function 38 save( ) function 12 savehistory( ) function 12 save.image( ) function 12 scalar values 33 scale( ) function 96, 104, 215 scales option 379 scan( ) function 430 scatter plots 264–279 3D 274–277 high-density 271–274 matrices 267–271 scatter3d( ) function, Rcmdr package 277 scatterplot( ) function 183, 193, 266 scatterplot3d( ) function, scatterplot3d package 274 scatterplot3d package 274, 427 scatterplotMatrix( ) function 6, 184, 193, 268 scores factors 349 principal components 342 scores option 341 scree( ) function 333 sd( ) function 94 search( ) command 16 seed, setting for random number generation 98 SELECT statements 40, 89 selecting observations 87–88 variables 86 SEM. See structural equation modeling sem package 350, 427 seq( ) function 101 SeqKnn package 370, 427 sequence, in for statements 107–108 set.seed( ) function 98 setwd( ) function 12–13 Sexpr statement 412 shadow matrix 360 shape option 390 show.settings( ) function 387 shrinkage( ) function 214 side option 58, 62 signif( ) function 93 significance levels 248 simple imputation 371–372 simple linear regression 175, 179, 181 simulate option 196 sin( ) function 93 singer dataset 392 sinh( ) function 93 sink( ) function 13, 15 site initialization file 406 size option, in ggplot2 390 sm packages 130–131, 427 sm.density.compare( ) function 130, 132 smoothScatter( ) function, base package 272, 274 software, updating 432–433 sorting, data management 84–85 Download from Wow! eBook 446 INDEX source( ) function 13–15 speedglm package 431 sphericity 239 spine( ) function 124 spinning 3D scatter plots 277 spinograms 124–125 split( ) function, in bigtabulate package 431 split option, in lattice plots 379, 388 splitting output 13 spread option 183, 269 spreadLevelPlot( ) function 193, 197, 206 SPSS datasets. See Statistical Package for the Social Sciences datasets, importing data from spss. get( ) function 38 SQL. See Structured Query Language sqldf( ) function 89 sqldf package 90 sqlDrop( ) function 40 sqlFetch( ) function 40 sqlQuery( ) function 40 sqlSave( ) function 40 sqrt( ) function 93 ssize.fdr package 261 stacked bar plots 121–122 standardizing data 96 startup environment customizing 406–407 Stata datasets exporting data to 409 importing data from 38–39 statements, in R 107 state.x77 dataset 184 Statistical Analysis System (SAS) datasets, importing data from 38 statistical applications, exporting data for 409 statistical functions 94–96 Statistical Package for the Social Sciences (SPSS) datasets, importing data from 38 Stat/Transfer application, importing data via 41–42 stepAIC( ) function 209 stepwise regression 209–210 stop( ) function 111 storage, outside of RAM 430–431 str( ) function 31, 43 stringsAsFactors option 36 strip option 379 strsplit( ) function 100, 106 structural equation modeling (SEM) 349 Structured Query Language (SQL) 89–90 sub( ) function 100 sub option 390 subset( ) function 88–89 subsets( ) function 211 subsetting datasets 86–89 selecting observations 87–88 selecting variables 86 subset( ) function 88–89 substr( ) function 100 sum( ) function 81, 95, 356 sum of squares Type I (sequential) 224 Type II (hierarchical) 224 Type III (marginal) 224 summary( ) function 31, 179, 188 summary.aov( ) function 241 summaryRprof( ) function 430 Sweave( ) function 411, 414 Sweave package (R code + LaTeX documents), typesetting with 410–415 switch construct 109–110 symbols graphical parameters 50–51 plotting with pch parameter 51 in R formulas 178 symbols( ) function 278 Sys.Date( ) function 82 Sys.getenv( ) function 406 system.time( ) function 430 T t( ) function 112 tab-delimited files 36 table( ) function 120–121, 431 tabulating missing values 357 tail( ) function 43 tan( ) function 93 tanh( ) function 93 tapply( ) function 431 tck option 58 terrain.colors( )function 53 Test of proportions 257 TeX file 414 text( ) function 62–64 text characteristics, graphical parameters 53–54 text files, delimited exporting data to 408 importing data from 35–36 text options annotations 62–64 legend 60–62 titles 57 text output 13 text.col ( ) option 61 text.panel option 285 tick marks 59–60 tick.ratio 59 tiff( ) function 47 time-series regression 175 time-stamping data 82 title( ) function 57, 123, 132 title option 60 titles 57 tolower( ) function 100 topo.colors( )function 53 toupper( ) function 100 transform( ) function 76 transformations, of variables 205–207 transmission disequilibrium test (TDT) 261 transpose 112 trellis.par.get( ) function 387 trellis.par.set( ) function 387 trt2times variable 245 trunc( ) function 93 t-tests dependent groups 165–166 independent groups 164–165 power 250–252, 257 twiddler package 405 two-way ANOVA design 221 two-way factorial ANOVA 223, 234–236 type conversions 83–84 Type I (sequential) approach 224 Type II (hierarchical) approach 224 Type III (marginal) approach 224 type option 379 U unbalanced design 220 Unidata netCDF library 39 Download from Wow! eBook INDEX 447 uniquenesses 337 unz( ) function 36 update( ) function 379 update.packages( ) function 16, 432 updating installations 432–433 upper.panel option 285 url( ) function 36 user-written functions 109, 111 V validation, of linear model assumption 199 value labels 42 var( ) function 94 variable <- expression statement 75 variable labels 42 variable[condition] <- expression statement 77 variables adding or deleting 207 conditioning 379–380 creating new 75–76 data frames 27 excluding 86–87 grouping 383–387 recoding 76–78 renaming 78–79 selecting 86, 209–213 in stepwise regression 209–210 in subsets regression 210–213 transforming 205–207 variance inflation factor (VIF) 200 varimax rotation 340 varwidth option 134 vcd package 18–19, 120, 124, 288, 427 vcov( ) function 179 vectors 24 vegan package 427 VIF. See variance inflation factor vif( ) function 193, 200 vignette( ) function 11 VIM package 353, 359, 428 violin plots 137–138 vioplot( ) function 137 vioplot package 137 W warning( ) function 111 webscraping 37 which( )function 88 while loop 108 widths option 67 Wilcoxon rank sum test 166–167 Wilks.test( ) function, rrcov package 242 Windows metafile format 47 windowsFont( ) function 54 win.metafile( ) function 47 with( ) function 28, 30, 77, 366 within( ) function 77 workspace 11, 13 write.foreign( ) function 409 write.table( ) function 408 write.xlsx( ) function 409 X xaxt option 57 xfig( ) function 47 xlab option 120, 379, 390 xlim option 379, 390 xlsx package 37, 409, 428 XML files, importing data from 37 XML package 37, 428 xtable( ) function 412, 415 xtable package 412 xyplot( ) function 381 xzfile( ) function 36 Y yaxt option 57 ylab option 120, 379, 390 ylim option 379, 390 Download from Wow! eBook Download from Wow! eBook Robert I. Kabacoff Ris a powerful language for statistical computing and graph- ics that can handle virtually any data-crunching task. It runs on all important platforms and provides thousands of useful specialized modules and utilities. Th is makes R a great way to get meaningful information from mountains of raw data. R in Action is a language tutorial focused on practical problems. It presents useful statistics examples and includes elegant meth- ods for handling messy, incomplete, and nonnormal data that are diffi cult to analyze using traditional methods. And statistical analysis is only part of the story. You’ll also master R’s extensive graphical capabilities for exploring and presenting data visually. What’s Inside Practical data analysis, step by step Interfacing R with other soft ware Using R to visualize data Over 130 graphs Eight reference appendixes Dr. Rob Kabacoff is a seasoned researcher who specializes in data analysis. He has taught graduate courses in statistical program- ming and manages the Quick-R website at statmethods.net. For access to the book’s forum and a free ebook for owners of this book, go to manning.com/RinAction$59.99 / Can \$68.99 [INCLUDING eBOOK] R IN ACTION DATA/STATISTICS/PROGRAMMING MANNING SEE INSERT “Lucid and engaging ... a fun way to learn R!” —Amos A. Folarin University College London “Finally, a book that brings R to the real world.” —Charles Malpas University of Melbourne “R from a programmer’s point of view.” —Philipp K. Janert Principal Value, LLC “A great balance of targeted tutorials and in-depth examples.” —Landon Cox, 360VL, Inc. “An excellent introduction and reference from the author of the best R website.” —Christopher Williams University of Idaho

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