Software for data analysis: programming with R

1. Introduction: Principles and Concepts

1.1. Exploration: The Mission

1.2. Trustworthy Software: The Prime Directive

1.3. Concepts for Programming with R

1.4. The R System and the S Language

2. Using R

2.1. Starting R

2.2. An Interactive Session

2.3. The Language

2.4. Objects and Names

2.5. Functions and Packages

2.6. Getting R

2.7. Online Information About R

2.8. What's Hard About Using R?

3. Programming with R: The Basics

3.1. From Commands to Functions

3.2. Functions and Functional Programming

3.3. Function Objects and Function Calls

3.4. The Language

3.5. Debugging

3.6. Interactive Tracing and Editing

3.7. Conditions: Errors and Warnings

3.8. Testing R Software

4. R Packages

4.1. Introduction: Why Write a Package?

4.2. The Package Concept and Tools

4.3. Creating a Package

4.4. Documentation for Packages

4.5. Testing Packages

4.6. Package Namespaces

4.7. Including C Software in Packages

4.8. Interfaces to Other Software

5. Objects

5.1. Objects, Names, and References

5.2. Replacement Expressions

5.3. Environments

5.4. Non-local Assignments; Closures

5.5. Connections

5.6. Reading and Writing Objects and Data

6. Basic Data and Computations

6.1. The Evolution of Data in the S Language

6.2. Object Types

6.3. Vectors and Vector Structures

6.4. Vectorizing Computations

6.5. Statistical Data: Data Frames

6.6. Operators: Arithmetic, Comparison, Logic

6.7. Computations on Numeric Data

6.8. Matrices and Matrix Computations

6.9. Fitting Statistical models

6.10. Programming Random Simulations

7. Data Visualization and Graphics

7.1. Using Graphics in R

7.2. The x-y Plot

7.3. The Common Graphics Model

7.4. The graphics Package

7.5. The grid Package

7.6. Trellis Graphics and the lattice Package

8. Computing with Text

8.1. Text Computations for Data Analysis

8.2. Importing Text Data

8.3. Regular Expressions

8.4. Text Computations in R

8.5. Using and Writing Perl

8.6. Examples of Text Computations

9. New Classes

9.1. Introduction: Why Classes?

9.2. Programming with New Classes

9.3. Inheritance and Inter-class Relations

9.4. Virtual Classes

9.5. Creating and Validating Objects

9.6. Programming with S3 Classes

9.7. Example: Binary Trees

9.8. Example: Data Frames

10. Methods and Generic Functions

10.1. Introduction: Why Methods?

10.2. Method Definitions

10.3. New Methods for Old Functions

10.4. Programming Techniques for Methods

10.5. Generic Functions

10.6. How Method Selection Works

11. Interfaces I: C and Fortran

11.1. Interfaces to C and Fortran

11.2. Calling R-Independent Subroutines

11.3. Calling R-Dependent Subroutines

11.4. Computations in C++

11.5. Loading and Registering Compiled Routines

12. Interfaces II: Other Systems

12.1. Choosing an Interface

12.2. Text- and File-Based Interfaces

12.3. Functional Interfaces

12.4. Object-Based Interfaces

12.5. Interfaces to OOP Languages

12.6. Interfaces to C++

12.7. Interfaces to Databases and Spreadsheets

12.8. Interfaces without R

13. How R Works

13.1. The R Program

13.2. The R Evaluator

13.3. Calls to R Functions

13.4. Calls to Primitive Functions

13.5. Assignments and Replacements

13.6. The Language

13.7. Memory Management for R Objects

A. Some Notes on the History of S

Bibliography

Index

Index of R Functions and Documentation

Index of R Classes and Types