John M. Chambers

Statistics and Computing
Series Editors:
J. Chambers
D. Hand
W. Härdle

Library of Congress Control Number: 2008922937

Contents
1 Introduction: Principles and Concepts 1
1.1 Exploration: The Mission . . . . . . . . . . . . . . . . . . . . 1
1.2 Trustworthy Software: The Prime Directive . . . . . . . . . . 3
1.3 Concepts for Programming with R . . . . . . . . . . . . . . . 4
1.4 The R System and the S Language . . . . . . . . . . . . . . . 9
2 Using R 11
2.1 Starting R . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
2.2 An Interactive Session . . . . . . . . . . . . . . . . . . . . . . 13
2.3 The Language . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
2.4 Objects and Names . . . . . . . . . . . . . . . . . . . . . . . . 24
2.5 Functions and Packages . . . . . . . . . . . . . . . . . . . . . 25
2.6 Getting R . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
2.7 Online Information About R . . . . . . . . . . . . . . . . . . . 31
2.8 What’s Hard About Using R? . . . . . . . . . . . . . . . . . . 34
3 Programming with R: The Basics 37
3.1 From Commands to Functions . . . . . . . . . . . . . . . . . 37
3.2 Functions and Functional Programming . . . . . . . . . . . . 43
3.3 Function Objects and Function Calls . . . . . . . . . . . . . . 50
3.4 The Language . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
3.5 Debugging . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
3.6 Interactive Tracing and Editing . . . . . . . . . . . . . . . . . 67
3.7 Conditions: Errors and Warnings . . . . . . . . . . . . . . . . 74
3.8 Testing R Software . . . . . . . . . . . . . . . . . . . . . . . . 76
4 R Packages 79
4.1 Introduction: Why Write a Package? . . . . . . . . . . . . . . 79
4.2 The Package Concept and Tools . . . . . . . . . . . . . . . . 80
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4.3 Creating a Package . . . . . . . . . . . . . . . . . . . . . . . . 85
4.4 Documentation for Packages . . . . . . . . . . . . . . . . . . . 95
4.5 Testing Packages . . . . . . . . . . . . . . . . . . . . . . . . . 101
4.6 Package Namespaces . . . . . . . . . . . . . . . . . . . . . . . 103
4.7 Including C Software in Packages . . . . . . . . . . . . . . . . 108
4.8 Interfaces to Other Software . . . . . . . . . . . . . . . . . . . 108
5 Objects 111
5.1 Objects, Names, and References . . . . . . . . . . . . . . . . . 111
5.2 Replacement Expressions . . . . . . . . . . . . . . . . . . . . 115
5.3 Environments . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
5.4 Non-local Assignments; Closures . . . . . . . . . . . . . . . . 125
5.5 Connections . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
5.6 Reading and Writing Objects and Data . . . . . . . . . . . . 135
6 Basic Data and Computations 139
6.1 The Evolution of Data in the S Language . . . . . . . . . . . 140
6.2 Object Types . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
6.3 Vectors and Vector Structures . . . . . . . . . . . . . . . . . . 143
6.4 Vectorizing Computations . . . . . . . . . . . . . . . . . . . . 157
6.5 Statistical Data: Data Frames . . . . . . . . . . . . . . . . . . 166
6.6 Operators: Arithmetic, Comparison, Logic . . . . . . . . . . . 184
6.7 Computations on Numeric Data . . . . . . . . . . . . . . . . . 191
6.8 Matrices and Matrix Computations . . . . . . . . . . . . . . . 200
6.9 Fitting Statistical models . . . . . . . . . . . . . . . . . . . . 218
6.10 Programming Random Simulations . . . . . . . . . . . . . . . 221
7 Data Visualization and Graphics 237
7.1 Using Graphics in R . . . . . . . . . . . . . . . . . . . . . . . 238
7.2 The x-y Plot . . . . . . . . . . . . . . . . . . . . . . . . . . . 242
7.3 The Common Graphics Model . . . . . . . . . . . . . . . . . . 253
7.4 The graphics Package . . . . . . . . . . . . . . . . . . . . . . 263
7.5 The grid Package . . . . . . . . . . . . . . . . . . . . . . . . 271
7.6 Trellis Graphics and the lattice Package . . . . . . . . . . . 280
8 Computing with Text 289
8.1 Text Computations for Data Analysis . . . . . . . . . . . . . 289
8.2 Importing Text Data . . . . . . . . . . . . . . . . . . . . . . . 294
8.3 Regular Expressions . . . . . . . . . . . . . . . . . . . . . . . 298
8.4 Text Computations in R . . . . . . . . . . . . . . . . . . . . . 304
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8.5 Using and Writing Perl . . . . . . . . . . . . . . . . . . . . . . 309
8.6 Examples of Text Computations . . . . . . . . . . . . . . . . 318
9 New Classes 331
9.1 Introduction: Why Classes? . . . . . . . . . . . . . . . . . . . 331
9.2 Programming with New Classes . . . . . . . . . . . . . . . . . 334
9.3 Inheritance and Inter-class Relations . . . . . . . . . . . . . . 344
9.4 Virtual Classes . . . . . . . . . . . . . . . . . . . . . . . . . . 351
9.5 Creating and Validating Objects . . . . . . . . . . . . . . . . 359
9.6 Programming with S3 Classes . . . . . . . . . . . . . . . . . . 362
9.7 Example: Binary Trees . . . . . . . . . . . . . . . . . . . . . . 369
9.8 Example: Data Frames . . . . . . . . . . . . . . . . . . . . . . 375
10 Methods and Generic Functions 381
10.1 Introduction: Why Methods? . . . . . . . . . . . . . . . . . . 381
10.2 Method Definitions . . . . . . . . . . . . . . . . . . . . . . . . 384
10.3 New Methods for Old Functions . . . . . . . . . . . . . . . . . 387
10.4 Programming Techniques for Methods . . . . . . . . . . . . . 389
10.5 Generic Functions . . . . . . . . . . . . . . . . . . . . . . . . 396
10.6 How Method Selection Works . . . . . . . . . . . . . . . . . . 405
11 Interfaces I: C and Fortran 411
11.1 Interfaces to C and Fortran . . . . . . . . . . . . . . . . . . . . 411
11.2 Calling R-Independent Subroutines . . . . . . . . . . . . . . . 415
11.3 Calling R-Dependent Subroutines . . . . . . . . . . . . . . . . 420
11.4 Computations in C++ . . . . . . . . . . . . . . . . . . . . . . 425
11.5 Loading and Registering Compiled Routines . . . . . . . . . . 426
12 Interfaces II: Other Systems 429
12.1 Choosing an Interface . . . . . . . . . . . . . . . . . . . . . . 430
12.2 Text- and File-Based Interfaces . . . . . . . . . . . . . . . . . 432
12.3 Functional Interfaces . . . . . . . . . . . . . . . . . . . . . . . 433
12.4 Object-Based Interfaces . . . . . . . . . . . . . . . . . . . . . 435
12.5 Interfaces to OOP Languages . . . . . . . . . . . . . . . . . . 437
12.6 Interfaces to C++ . . . . . . . . . . . . . . . . . . . . . . . . . 440
12.7 Interfaces to Databases and Spreadsheets . . . . . . . . . . . 446
12.8 Interfaces without R . . . . . . . . . . . . . . . . . . . . . . . 450
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13 How R Works 453
13.1 The R Program . . . . . . . . . . . . . . . . . . . . . . . . . . 453
13.2 The R Evaluator . . . . . . . . . . . . . . . . . . . . . . . . . 454
13.3 Calls to R Functions . . . . . . . . . . . . . . . . . . . . . . . 460
13.4 Calls to Primitive Functions . . . . . . . . . . . . . . . . . . . 463
13.5 Assignments and Replacements . . . . . . . . . . . . . . . . . 465
13.6 The Language . . . . . . . . . . . . . . . . . . . . . . . . . . . 468
13.7 Memory Management for R Objects . . . . . . . . . . . . . . 471
A Some Notes on the History of S 475
Bibliography 479
Index 481
Index of R Functions and Documentation 489
Index of R Classes and Types 497