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by John Jay Hilfiger
Graphing Data with R
Preface
Who Is This Book For?
Why R?
How to Use This Book
Conventions Used in This Book
Using Code Examples
Safari® Books Online
How to Contact Us
Acknowledgments
I. Getting Started with R
1. R Basics
Downloading the Software
Try Some Simple Tasks
User Interface
Installing a Package: A GUI Interface
Data Structures
Sample Datasets
The Working Directory
Putting Data into R
Typing into a Command Line
Using the Data Editor
Reading from an External File
Sourcing a Script
User-Written Functions
A Taste of Things to Come
Exercise 1-4
2. An Overview of R Graphics
Exporting a Graph
Exploratory Graphs and Presentation Graphs
Graphics Systems in R
Base Graphics and grid
lattice
ggplot2
Special Applications/Graphs Incorporated into Packages
User-Written Graphic Functions
II. Single-Variable Graphs
3. Strip Charts
A Simple Graph
Data Can Be Beautiful
Exercise 3-1
Exercise 3-2
4. Dot Charts
Basic Dot Chart
Exercise 4-1
Exercise 4-2
5. Box Plots
The Box Plot
Nimrod Again
Making the Data Beautiful
Exercise 5-1
Exercise 5-2
6. Stem-and-Leaf Plots
Basic Stem-and-Leaf Plot
Exercise 6-1
Exercise 6-2
7. Histograms
Simple Histograms
Histograms with a Second Variable
Exercise 7-1
Exercise 7-2
8. Kernel Density Plots
Density Estimation
Choosing a Bandwidth
Comparing Two or More Density Plots
A Background That Is Not White
The Cumulative Distribution Function
Exercise 8-1
Exercise 8-2
9. Bar Plots (Bar Charts)
Basic Bar Plot
Spine Plot
Bar Spacing and Orientation
Exercise 9-1
Exercise 9-2
10. Pie Charts
Ordinary Pie Chart
Fan Plot
Exercise 10-1
Exercise 10-2
11. Rug Plots
The Rug Plot
Exercise 11-1
III. Two-Variable Graphs
12. Scatter Plots and Line Charts
Basic Scatter Plots
Line Charts
Templates
Enhanced Scatter Plots
Exercise 12-1
Exercise 12-2
13. High-Density Plots
Working with Large Datasets
Sunflower Plot
Smooth Scatter Plot
Exercise 13-1
14. The Bland-Altman Plot
Assessing Measurement Reliability
Exercise 14-1
A Shorter Version of baplot()
15. QQ Plots
Comparing Sets of Numbers
Exercise 15-1
Exercise 15-2
IV. Multivariable Graphs
16. Scatter plot Matrices and Corrgrams
Scatter plot Matrix
Corrgram
Generalized Pairs Matrix with Mixed Quantitative and Categorical Variables
Exercise 16-1
17. Three-Dimensional Plots
3D Scatter plots
False Color Plots
Bubble Plots
Exercise 17-1
Exercise 17-2
18. Coplots (Conditioning Plots)
The Coplot
Exercise 18-1
19. Clustering: Dendrograms and Heat Maps
Clustering
Heat Maps
Exercise 19-1
Exercise 19-2
Exercise 19-3
20. Mosaic Plots
Graphing Categorical Data
Exercise 20-1
V. What Now?
21. Resources for Extending Your Knowledge of Things Graphical and R Fluency
R Graphics
General Principles of Graphics
Learning More About R
Statistics with R
Exercise 21-1
A. References
B. R Colors
C. The R Commander Graphical User Interface
D. Packages Used/Referenced
E. Importing Data from Outside of R
Some Useful Internet Data Repositories
Importing Data of Various Types into R
CSV
Statistical Packages (SPSS, SAS, Etc.)
ASCII
XML
netCDF
Web Scraping
F. Solutions to Chapter Exercises
Exercises 1-1 Through 1-4
Exercise 3-1
Exercise 3-2
Exercise 4-1
Exercise 4-2
Exercise 5-1
Exercise 5-2
Exercise 6-1
Exercise 6-2
Exercise 7-1
Exercise 8-1
Exercise 8-2
Exercise 9-1
Exercise 9-2
Exercise 10-1
Exercise 10-2
Exercise 11-1
Exercise 12-1
Exercise 12-2
Exercise 13-1
Exercise 14-1
Exercise 15-1
Exercise 15-2
Exercise 16-1
Exercise 17-1
Exercise 17-2
Exercise 18-1
Exercise 19-1
Exercise 19-2
Exercise 19-3
Exercise 20-1
Exercise 21-1
G. Troubleshooting: Why Doesn’t My Code Work?
Misspelling
Confusing Uppercase/Lowercase
Too Few (or Too Many) Parenthesis Signs
Forgetting to Load a Package
Forgetting to Install a Package
A Dataset in a Loaded Package Is Not Found
Leaving Out a Comma
Copy-and-Paste Error
Directory Problems—Cannot Load a Saved File
Missing File Extension
Do Not Assume That All Packages Use the Same Argument Abbreviations
Outdated Packages/Package Incompatibility
H. R Functions Introduced in This Book
Data Input/Output
Datasets
Graphical Functions 1—Creates Graph
Graphical Functions 2—Adds Features to Existing Graph
Miscellaneous
Packages
Statistics
User-Defined Functions and Scripts
Workspace and Directories
Index
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