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Part Ⅰ．The R Language 3

1．Introduction 3

Chapter Goals 3

What Is R? 3

Installing R 4

Choosing an IDE 5

Emacs+ESS 5

Eclipse/Architect 6

RStudio 6

Revolution-R 7

Live-R 7

Other IDEs and Editors 7

Your First Program 8

How to Get Help in R 8

Installing Extra Related Software 11

Summary 11

Test Your Knowledge:Quiz 12

Test Your Knowledge:Exercises 12

2．A Scientific Calculator 13

Chapter Goals 13

Mathematical Operations and Vectors 13

Assigning Variables 17

Special Numbers 19

Logical Vectors 20

Summary 22

Test Your Knowledge:Quiz 22

Test Your Knowledge:Exercises 23

3．Inspecting Variables and Your Workspace 25

Chapter Goals 25

Classes 25

Different Types of Numbers 26

Other Common Classes 27

Checking and Changing Classes 30

Examining Variables 33

The Work space 36

Summary 37

Test Your Knowledge:Quiz 37

Test Your Knowledge:Exercises 37

4．Vectors,Matrices,and Arrays 39

Chapter Goals 39

Vectors 39

Sequences 41

Lengths 42

Names 42

Indexing Vectors 43

Vector Recycling and Repetition 45

Matrices and Arrays 46

Creating Arrays and Matrices 46

Rows,Columns,and Dimensions 48

Row,Column,and Dimension Names 50

Indexing Arrays 51

Combining Matrices 51

Array Arithmetic 52

Summary 54

Test Your Knowledge:Quiz 55

Test Your Knowledge:Exercises 55

5．Lists and Data Frames 57

Chapter Goals 57

Lists 57

Creating Lists 57

Atomic and Recursive Variables 60

List Dimensions and Arithmetic 60

Indexing Lists 61

Converting Between Vectors and Lists 64

Combining Lists 65

NULL 66

Pairlists 70

Data Frames 70

Creating Data Frames 71

Indexing Data Frames 74

Basic Data Frame Manipulation 75

Summary 77

Test Your Knowledge:Quiz 77

Test Your Knowledge:Exercises 78

6．Environments and Functions 79

Chapter Goals 79

Environments 79

Functions 82

Creating and Calling Functions 82

Passing Functions to and from Other Functions 86

Variable Scope 89

Summary 91

Test Your Knowledge:Quiz 91

Test Your Knowledge:Exercises 91

7．Strings and Factors 93

Chapter Goals 93

Strings 93

Constructing and Printing Strings 94

Formatting Numbers 95

Special Characters 97

Changing Case 98

Extracting Substrings 98

Splitting Strings 99

File Paths 100

Factors 101

Creating Factors 101

Changing Factor Levels 103

Dropping Factor Levels 103

Ordered Factors 104

Converting Continuous Variables to Categorical 105

Converting Categorical Variables to Continuous 106

Generating Factor Levels 107

Combining Factors 107

Summary 108

Test Your Knowledge:Quiz 108

Test Your Knowledge:Exercises 108

8．Flow Control and Loops 111

Chapter Goals 111

Flow Control 111

if and else 112

Vectorized if 114

Multiple Selection 115

Loops 116

repeat Loops 116

while Loops 118

for Loops 120

Summary 122

Test Your Knowledge:Quiz 122

Test Your Knowledge:Exercises 122

9．Advanced Looping 125

Chapter Goals 125

Replication 125

Looping Over Lists 127

Looping Over Arrays 132

Multiple-Input Apply 135

Instant Vectorization 136

Split-Apply-Combine 136

The plyr Package 138

Summary 141

Test Your Knowledge:Quiz 141

Test Your Knowledge:Exercises 141

10．Packages 143

Chapter Goals 143

Loading Packages 144

The Search Path 146

Libraries and InstaLled Packages 146

Installing Packages 148

Maintaining Packages 150

Summary 150

Test Your Knowledge:Quiz 151

Test Your Knowledge:Exercises 151

11．Dates and Times 153

Chapter Goals 153

Date and Time Classes 154

POSIX Dates and Times 154

The Date Class 155

Other Date Classes 156

Conversion to and from Strings 156

Parsing Dates 156

Formatting Dates 157

Time Zones 158

Arithmetic with Dates and Times 160

Lubridate 161

Summary 165

Test Your Knowledge:Quiz 165

Test Your Knowledge:Exercises 166

Part Ⅱ．The Data Analysis Workflow 169

12．Getting Data 169

Chapter Goals 169

Built-in Datasets 169

Reading Text Files 170

CSV and Tab-Delimited Files 170

Unstructured Text Files 175

XML and HTML Files 175

JSON and YAML Files 176

Reading Binary Files 179

Reading Excel Files 179

Reading SAS,Stata,SPSS,and MATLAB Files 181

Reading Other File Types 181

Web Data 182

Sites with an API 182

Scraping Web Pages 184

Accessing Databases 185

Summary 188

Test Your Knowledge:Quiz 189

Test Your Knowledge:Exercises 189

13．Cleaning and Transforming 191

Chapter Goals 191

Cleaning Strings 191

Manipulating Data Frames 196

Adding and Replacing Columns 196

Dealing with Missing Values 197

Converting Between Wide and Long Form 198

Using SQL 200

Sorting 201

Functional Programming 202

Summary 204

Test Your Knowledge:Quiz 205

Test Your Knowledge:Exercises 205

14．Exploring and Visualizing&v 207

Chapter Goals 207

Summary Statistics 207

The Three Plotting Systems 211

Scatterplots 212

Take 1:base Graphics 213

Take 2:lattice Graphics 218

Take 3:ggplot2 Graphics 224

Line Plots 230

Histograms 238

Box Plots 249

Bar Charts 253

Other Plotting Packages and Systems 260

Summary 261

Test Your Knowledge:Quiz 261

Test Your Knowledge:Exercises 262

15．Distributions and Modeling 263

Chapter Goals 263

Random Numbers 264

The sample Function 264

Sampling from Distributions 265

Distributions 266

Formulae 267

A First Model:Linear Regressions 268

Comparing and Updating Models 271

Plotting and Inspecting Models 276

Other Model Types 280

Summary 282

Test Your Knowledge:Quiz 282

Test Your Knowledge:Exercises 282

16．Programming 285

Chapter Goals 285

Messages,Warnings,and Errors 286

Error Handling 289

Debugging 292

Testing 294

RUnit 295

testthat 298

Magic 299

Turning Strings into Code 299

Turning Code into Strings 301

Object-Oriented Programming 302

S3 Classes 303

Reference Classes 305

Summary 310

Test Your Knowledge:Quiz 310

Test Your Knowledge:Exercises 311

17．Making Packages 313

Chapter Goals 313

Why Create Packages? 313

Prerequisites 313

The Package Directory Structure 314

Your First Package 315

Documenting Packages 317

Checking and Building Packages 320

Maintaining Packages 321

Summary 323

Test Your Knowledge:Quiz 323

Test Your Knowledge:Exercises 324

Part Ⅲ．Appendixes 327

A．Properties of Variables 327

B．Other Things to Do in R 331

C．Answers to Quizzes 333

D．Solutions to Exercises 341

Bibliography 365

Index 367