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Preface; The Recipes; A Note on Terminology; Software and Platform Notes; Other Resources; Conventions Used in This Book; Using Code Examples; Safari® Books Online; How to Contact Us; Acknowledgments;
Chapter 1: Getting Started and Getting Help;
1.1 Introduction;
1.2 Downloading and Installing R;
1.3 Starting R;
1.4 Entering Commands;
1.5 Exiting from R;
1.6 Interrupting R;
1.7 Viewing the Supplied Documentation;
1.8 Getting Help on a Function;
1.9 Searching the Supplied Documentation;
1.10 Getting Help on a Package;
1.11 Searching the Web for Help;
1.12 Finding Relevant Functions and Packages;
1.13 Searching the Mailing Lists;
1.14 Submitting Questions to the Mailing Lists;
Chapter 2: Some Basics;
2.1 Introduction;
2.2 Printing Something;
2.3 Setting Variables;
2.4 Listing Variables;
2.5 Deleting Variables;
2.6 Creating a Vector;
2.7 Computing Basic Statistics;
2.8 Creating Sequences;
2.9 Comparing Vectors;
2.10 Selecting Vector Elements;
2.11 Performing Vector Arithmetic;
2.12 Getting Operator Precedence Right;
2.13 Defining a Function;
2.14 Typing Less and Accomplishing More;
2.15 Avoiding Some Common Mistakes;
Chapter 3: Navigating the Software;
3.1 Introduction;
3.2 Getting and Setting the Working Directory;
3.3 Saving Your Workspace;
3.4 Viewing Your Command History;
3.5 Saving the Result of the Previous Command;
3.6 Displaying the Search Path;
3.7 Accessing the Functions in a Package;
3.8 Accessing Built-in Datasets;
3.9 Viewing the List of Installed Packages;
3.10 Installing Packages from CRAN;
3.11 Setting a Default CRAN Mirror;
3.12 Suppressing the Startup Message;
3.13 Running a Script;
3.14 Running a Batch Script;
3.15 Getting and Setting Environment Variables;
3.16 Locating the R Home Directory;
3.17 Customizing R;
Chapter 4: Input and Output;
4.1 Introduction;
4.2 Entering Data from the Keyboard;
4.3 Printing Fewer Digits (or More Digits);
4.4 Redirecting Output to a File;
4.5 Listing Files;
4.6 Dealing with "Cannot Open File" in Windows;
4.7 Reading Fixed-Width Records;
4.8 Reading Tabular Data Files;
4.9 Reading from CSV Files;
4.10 Writing to CSV Files;
4.11 Reading Tabular or CSV Data from the Web;
4.12 Reading Data from HTML Tables;
4.13 Reading Files with a Complex Structure;
4.14 Reading from MySQL Databases;
4.15 Saving and Transporting Objects;
Chapter 5: Data Structures;
5.1 Introduction;
5.2 Appending Data to a Vector;
5.3 Inserting Data into a Vector;
5.4 Understanding the Recycling Rule;
5.5 Creating a Factor (Categorical Variable);
5.6 Combining Multiple Vectors into One Vector and a Factor;
5.7 Creating a List;
5.8 Selecting List Elements by Position;
5.9 Selecting List Elements by Name;
5.10 Building a Name/Value Association List;
5.11 Removing an Element from a List;
5.12 Flatten a List into a Vector;
5.13 Removing NULL Elements from a List;
5.14 Removing List Elements Using a Condition;
5.15 Initializing a Matrix;
5.16 Performing Matrix Operations;
5.17 Giving Descriptive Names to the Rows and Columns of a Matrix;
5.18 Selecting One Row or Column from a Matrix;
5.19 Initializing a Data Frame from Column Data;
5.20 Initializing a Data Frame from Row Data;
5.21 Appending Rows to a Data Frame;
5.22 Preallocating a Data Frame;
5.23 Selecting Data Frame Columns by Position;
5.24 Selecting Data Frame Columns by Name;
5.25 Selecting Rows and Columns More Easily;
5.26 Changing the Names of Data Frame Columns;
5.27 Editing a Data Frame;
5.28 Removing NAs from a Data Frame;
5.29 Excluding Columns by Name;
5.30 Combining Two Data Frames;
5.31 Merging Data Frames by Common Column;
5.32 Accessing Data Frame Contents More Easily;
5.33 Converting One Atomic Value into Another;
5.34 Converting One Structured Data Type into Another;
Chapter 6: Data Transformations;
6.1 Introduction;
6.2 Splitting a Vector into Groups;
6.3 Applying a Function to Each List Element;
6.4 Applying a Function to Every Row;
6.5 Applying a Function to Every Column;
6.6 Applying a Function to Groups of Data;
6.7 Applying a Function to Groups of Rows;
6.8 Applying a Function to Parallel Vectors or Lists;
Chapter 7: Strings and Dates;
7.1 Introduction;
7.2 Getting the Length of a String;
7.3 Concatenating Strings;
7.4 Extracting Substrings;
7.5 Splitting a String According to a Delimiter;
7.6 Replacing Substrings;
7.7 Seeing the Special Characters in a String;
7.8 Generating All Pairwise Combinations of Strings;
7.9 Getting the Current Date;
7.10 Converting a String into a Date;
7.11 Converting a Date into a String;
7.12 Converting Year, Month, and Day into a Date;
7.13 Getting the Julian Date;
7.14 Extracting the Parts of a Date;
7.15 Creating a Sequence of Dates;
Chapter 8: Probability;
8.1 Introduction;
8.2 Counting the Number of Combinations;
8.3 Generating Combinations;
8.4 Generating Random Numbers;
8.5 Generating Reproducible Random Numbers;
8.6 Generating a Random Sample;
8.7 Generating Random Sequences;
8.8 Randomly Permuting a Vector;
8.9 Calculating Probabilities for Discrete Distributions;
8.10 Calculating Probabilities for Continuous Distributions;
8.11 Converting Probabilities to Quantiles;
8.12 Plotting a Density Function;
Chapter 9: General Statistics;
9.1 Introduction;
9.2 Summarizing Your Data;
9.3 Calculating Relative Frequencies;
9.4 Tabulating Factors and Creating Contingency Tables;
9.5 Testing Categorical Variables for Independence;
9.6 Calculating Quantiles (and Quartiles) of a Dataset;
9.7 Inverting a Quantile;
9.8 Converting Data to Z-Scores;
9.9 Testing the Mean of a Sample (t Test);
9.10 Forming a Confidence Interval for a Mean;
9.11 Forming a Confidence Interval for a Median;
9.12 Testing a Sample Proportion;
9.13 Forming a Confidence Interval for a Proportion;
9.14 Testing for Normality;
9.15 Testing for Runs;
9.16 Comparing the Means of Two Samples;
9.17 Comparing the Locations of Two Samples Nonparametrically;
9.18 Testing a Correlation for Significance;
9.19 Testing Groups for Equal Proportions;
9.20 Performing Pairwise Comparisons Between Group Means;
9.21 Testing Two Samples for the Same Distribution;
Chapter 10: Graphics;
10.1 Introduction;
10.2 Creating a Scatter Plot;
10.3 Adding a Title and Labels;
10.4 Adding a Grid;
10.5 Creating a Scatter Plot of Multiple Groups;
10.6 Adding a Legend;
10.7 Plotting the Regression Line of a Scatter Plot;
10.8 Plotting All Variables Against All Other Variables;
10.9 Creating One Scatter Plot for Each Factor Level;
10.10 Creating a Bar Chart;
10.11 Adding Confidence Intervals to a Bar Chart;
10.12 Coloring a Bar Chart;
10.13 Plotting a Line from x and y Points;
10.14 Changing the Type, Width, or Color of a Line;
10.15 Plotting Multiple Datasets;
10.16 Adding Vertical or Horizontal Lines;
10.17 Creating a Box Plot;
10.18 Creating One Box Plot for Each Factor Level;
10.19 Creating a Histogram;
10.20 Adding a Density Estimate to a Histogram;
10.21 Creating a Discrete Histogram;
10.22 Creating a Normal Quantile-Quantile (Q-Q) Plot;
10.23 Creating Other Quantile-Quantile Plots;
10.24 Plotting a Variable in Multiple Colors;
10.25 Graphing a Function;
10.26 Pausing Between Plots;
10.27 Displaying Several Figures on One Page;
10.28 Opening Additional Graphics Windows;
10.29 Writing Your Plot to a File;
10.30 Changing Graphical Parameters;
Chapter 11: Linear Regression and ANOVA;
11.1 Introduction;
11.2 Performing Simple Linear Regression;
11.3 Performing Multiple Linear Regression;
11.4 Getting Regression Statistics;
11.5 Understanding the Regression Summary;
11.6 Performing Linear Regression Without an Intercept;
11.7 Performing Linear Regression with Interaction Terms;
11.8 Selecting the Best Regression Variables;
11.9 Regressing on a Subset of Your Data;
11.10 Using an Expression Inside a Regression Formula;
11.11 Regressing on a Polynomial;
11.12 Regressing on Transformed Data;
11.13 Finding the Best Power Transformation (Box-Cox Procedure);
11.14 Forming Confidence Intervals for Regression Coefficients;
11.15 Plotting Regression Residuals;
11.16 Diagnosing a Linear Regression;
11.17 Identifying Influential Observations;
11.18 Testing Residuals for Autocorrelation (Durbin-Watson Test);
11.19 Predicting New Values;
11.20 Forming Prediction Intervals;
11.21 Performing One-Way ANOVA;
11.22 Creating an Interaction Plot;
11.23 Finding Differences Between Means of Groups;
11.24 Performing Robust ANOVA (Kruskal-Wallis Test);
11.25 Comparing Models by Using ANOVA;
Chapter 12: Useful Tricks;
12.1 Introduction;
12.2 Peeking at Your Data;
12.3 Widen Your Output;
12.4 Printing the Result of an Assignment;
12.5 Summing Rows and Columns;
12.6 Printing Data in Columns;
12.7 Binning Your Data;
12.8 Finding the Position of a Particular Value;
12.9 Selecting Every nth Element of a Vector;
12.10 Finding Pairwise Minimums or Maximums;
12.11 Generating All Combinations of Several Factors;
12.12 Flatten a Data Frame;
12.13 Sorting a Data Frame;
12.14 Sorting by Two Columns;
12.15 Stripping Attributes from a Variable;
12.16 Revealing the Structure of an Object;
12.17 Timing Your Code;
12.18 Suppressing Warnings and Error Messages;
12.19 Taking Function Arguments from a List;
12.20 Defining Your Own Binary Operators;
Chapter 13: Beyond Basic Numerics and Statistics;
13.1 Introduction;
13.2 Minimizing or Maximizing a Single-Parameter Function;
13.3 Minimizing or Maximizing a Multiparameter Function;
13.4 Calculating Eigenvalues and Eigenvectors;
13.5 Performing Principal Component Analysis;
13.6 Performing Simple Orthogonal Regression;
13.7 Finding Clusters in Your Data;
13.8 Predicting a Binary-Valued Variable (Logistic Regression);
13.9 Bootstrapping a Statistic;
13.10 Factor Analysis;
Chapter 14: Time Series Analysis;
14.1 Introduction;
14.2 Representing Time Series Data;
14.3 Plotting Time Series Data;
14.4 Extracting the Oldest or Newest Observations;
14.5 Subsetting a Time Series;
14.6 Merging Several Time Series;
14.7 Filling or Padding a Time Series;
14.8 Lagging a Time Series;
14.9 Computing Successive Differences;
14.10 Performing Calculations on Time Series;
14.11 Computing a Movi