IN ACTION Data analysis and graphics with R Robert I Kabacoff MANNING 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 20 Baldwin Road PO Box 261 Shelter Island, NY 11964 Development editor: Sebastian Stirling Copyeditor: Liz Welch Typesetter: Composure Graphics Cover designer: Marija Tudor ISBN: 9781935182399 Printed in the United States of America 10 MAL 16 15 14 13 12 11 Download from Wow! eBook brief contents Part I Getting started 1 Part II ■ ■ ■ ■ ■ Introduction to R Creating a dataset 21 Getting started with graphs 45 Basic data management 73 Advanced data management 91 Basic methods 117 ■ ■ Basic graphs 119 Basic statistics 141 Part III Intermediate methods 171 10 11 12 ■ ■ ■ ■ ■ Regression 173 Analysis of variance 219 Power analysis 246 Intermediate graphs 263 Resampling statistics and bootstrapping 291 v Download from Wow! eBook vi BRIEF CONTENTS Part IV Advanced methods 311 13 14 15 16 ■ ■ ■ ■ Generalized linear models 313 Principal components and factor analysis 331 Advanced methods for missing data 352 Advanced graphics 373 Download from Wow! eBook contents preface xv acknowledgments xvii about this book xix about the cover illustration xxiv Part I Getting started .1 Introduction to R 1.1 1.2 1.3 Why use R? Obtaining and installing R Working with R 7 Getting started Getting help 11 Input and output 13 ■ 1.4 Packages The workspace 11 14 What are packages? 15 Loading a package 16 1.5 1.6 1.7 ■ ■ ■ Installing a package 16 Learning about a package 16 Batch processing 17 Using output as input—reusing results Working with large datasets 18 18 vii Download from Wow! eBook viii CONTENTS 1.8 1.9 Working through an example Summary 20 Creating a dataset 2.1 2.2 2.3 21 Understanding datasets Data structures 23 Vectors 24 Factors 30 18 ■ ■ 22 Matrices 24 Lists 32 ■ Arrays 26 ■ Data frames 27 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 Variable labels 42 2.5 2.6 ■ 42 Value labels 42 Useful functions for working with data objects Summary 43 Getting started with graphs 3.1 3.2 3.3 45 Working with graphs 46 A simple example 48 Graphical parameters 49 Symbols and lines 50 Colors 52 Graph and margin dimensions 54 ■ 3.4 ■ Text characteristics 53 Adding text, customized axes, and legends Titles 57 Axes 57 Text annotations 62 ■ 3.5 42 ■ Reference lines 60 ■ 56 Legend 60 Combining graphs 65 Creating a figure arrangement with fine control 69 3.6 Summary 71 Basic data management 73 4.1 4.2 4.3 A working example 73 Creating new variables 75 Recoding variables 76 Download from Wow! eBook ix CONTENTS 4.4 4.5 Renaming variables Missing values 79 78 Recoding values to missing 80 4.6 Date values Excluding missing values from analyses 80 ■ 81 Converting dates to character variables 83 4.7 4.8 4.9 Going further 83 Type conversions 83 Sorting data 84 Merging datasets 85 Adding columns 85 4.10 ■ ■ Adding rows 85 Subsetting datasets 86 Selecting (keeping) variables 86 Excluding (dropping) variables 86 Selecting observations 87 The subset() function 88 Random samples 89 ■ ■ 4.11 4.12 Using SQL statements to manipulate data frames Summary 90 Advanced data management 5.1 5.2 ■ 91 A data management challenge 92 Numerical and character functions 93 Mathematical functions 93 Statistical functions 94 Character functions 99 Other useful functions 101 matrices and data frames 102 ■ ■ 5.3 5.4 Part II ■ Probability functions 96 Applying functions to 103 Conditional execution 108 112 Aggregating data 112 ■ The reshape package 113 Summary 116 Basic methods 117 Basic graphs 6.1 ■ User-written functions 109 Aggregation and restructuring Transpose 112 5.7 ■ ■ A solution for our data management challenge Control flow 107 Repetition and looping 107 5.5 5.6 119 Bar plots 120 Simple bar plots 120 Stacked and grouped bar plots 121 Tweaking bar plots 123 Spinograms 124 ■ ■ 6.2 6.3 89 Pie charts 125 Histograms 128 Download from Wow! eBook ■ Mean bar plots 122 index Symbol ! operator 77 != operator 77 # symbol %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