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by Mark Gardener
Beginning R: The Statistical Programming Language
Cover
Contents
Chapter 1: Introducing R: What It Is and How to Get It
Getting the Hang of R
The R Website
Downloading and Installing R from CRAN
Running the R Program
Finding Your Way with R
Getting Help via the CRAN Website and the Internet
The Help Command in R
Anatomy of a Help Item in R
Command Packages
Standard Command Packages
What Extra Packages Can Do for You
How to Get Extra Packages of R Commands
Running and Manipulating Packages
Summary
Chapter 2: Starting Out: Becoming Familiar with R
Some Simple Math
Use R Like a Calculator
Storing the Results of Calculations
Reading and Getting Data into R
Using the combine Command for Making Data
Using the scan Command for Making Data
Reading Bigger Data Files
Viewing Named Objects
Viewing Previously Loaded Named-Objects
Removing Objects from R
Types of Data Items
Number Data
Text Items
Converting Between Number and Text Data
The Structure of Data Items
Vector Items
Data Frames
Matrix Objects
List Objects
Examining Data Structure
Working with History Commands
Using History Files
Editing History Files
Saving Your Work in R
Saving the Workspace on Exit
Saving Data Files to Disk
Reading Data Files from Disk
Saving Data to Disk as Text Files
Summary
Chapter 3: Starting Out: Working With Objects
Manipulating Objects
Manipulating Vectors
Manipulating Matrix and Data Frames
Manipulating Lists
Viewing Objects within Objects
Looking Inside Complicated Data Objects
Opening Complicated Data Objects
Quick Looks at Complicated Data Objects
Viewing and Setting Names
Rotating Data Tables
Constructing Data Objects
Making Lists
Making Data Frames
Making Matrix Objects
Re-ordering Data Frames and Matrix Objects
Forms of Data Objects: Testing and Converting
Testing to See What Type of Object You Have
Converting from One Object Form to Another
Summary
Chapter 4: Data: Descriptive Statistics and Tabulation
Summary Commands
Summarizing Samples
Summary Statistics for Vectors
Cumulative Statistics
Summary Statistics for Data Frames
Summary Statistics for Matrix Objects
Summary Statistics for Lists
Summary Tables
Making Contingency Tables
Selecting Parts of a Table Object
Converting an Object into a Table
Testing for Table Objects
Complex (Flat) Tables
Testing “Flat” Table Objects
Summary Commands for Tables
Cross Tabulation
Summary
Chapter 5: Data: Distribution
Looking at the Distribution of Data
Stem and Leaf Plot
Histograms
Density Function
Types of Data Distribution
The Shapiro-Wilk Test for Normality
The Kolmogorov-Smirnov Test
Quantile-Quantile Plots
Summary
Chapter 6: Simple Hypothesis Testing
Using the Student’s t-test
Two-Sample t-Test with Unequal Variance
Two-Sample t-Test with Equal Variance
One-Sample t-Testing
Using Directional Hypotheses
Formula Syntax and Subsetting Samples in the t-Test
The Wilcoxon U-Test (Mann-Whitney)
Two-Sample U-Test
One-Sample U-Test
Using Directional Hypotheses
Formula Syntax and Subsetting Samples in the U-test
Paired t- and U-Tests
Correlation and Covariance
Simple Correlation
Covariance
Significance Testing in Correlation Tests
Formula Syntax
Tests for Association
Multiple Categories: Chi-Squared Tests
Single Category: Goodness of Fit Tests
Summary
Chapter 7: Introduction to Graphical Analysis
Box-whisker Plots
Basic Boxplots
Customizing Boxplots
Horizontal Boxplots
Scatter Plots
Basic Scatter Plots
Adding Axis Labels
Plotting Symbols
Setting Axis Limits
Using Formula Syntax
Adding Lines of Best-Fit to Scatter Plots
Pairs Plots (Multiple Correlation Plots)
Line Charts
Line Charts Using Numeric Data
Line Charts Using Categorical Data
Pie Charts
Cleveland Dot Charts
Bar Charts
Single-Category Bar Charts
Multiple Category Bar Charts
Horizontal Bars
Bar Charts from Summary Data
Copy Graphics to Other Applications
Use Copy/Paste to Copy Graphs
Save a Graphic to Disk
Summary
Chapter 8: Formula Notation and Complex Statistics
Examples of Using Formula Syntax for Basic Tests
Formula Notation in Graphics
Analysis of Variance (ANOVA)
One-Way ANOVA
Simple Post-hoc Testing
Extracting Means from aov() Models
Two-Way ANOVA
Extracting Means and Summary Statistics
Interaction Plots
More Complex ANOVA Models
Other Options for aov()
Summary
Chapter 9: Manipulating Data and Extracting Components
Creating Data for Complex Analysis
Data Frames
Matrix Objects
Creating and Setting Factor Data
Making Replicate Treatment Factors
Adding Rows or Columns
Summarizing Data
Simple Column and Row Summaries
Complex Summary Functions
Summary
Chapter 10: Regression (Linear Modeling)
Simple Linear Regression
Linear Model Results Objects
Similarity between lm() and aov()
Multiple Regression
Formulae and Linear Models
Model Building
Curvilinear Regression
Logarithmic Regression
Polynomial Regression
Plotting Linear Models and Curve Fitting
Best-Fit Lines
Confidence Intervals on Fitted Lines
Summarizing Regression Models
Diagnostic Plots
Summary of Fit
Summary
Chapter 11: More About Graphs
Adding Elements to Existing Plots
Error Bars
Adding Legends to Graphs
Adding Text to Graphs
Adding Points to an Existing Graph
Adding Various Sorts of Lines to Graphs
Matrix Plots (Multiple Series on One Graph)
Multiple Plots in One Window
Splitting the Plot Window into Equal Sections
Splitting the Plot Window into Unequal Sections
Exporting Graphs
Using Copy and Paste to Move a Graph
Saving a Graph to a File
Using the Device Driver to Save a Graph to Disk
Summary
Chapter 12: Writing Your Own Scripts: Beginning to Program
Copy and Paste Scripts
Make Your Own Help File as Plain Text
Using Annotations with the # Character
Creating Simple Functions
One-Line Functions
Using Default Values in Functions
Simple Customized Functions with Multiple Lines
Storing Customized Functions
Making Source Code
Displaying the Results of Customized Functions and Scripts
Displaying Messages as Part of Script Output
Summary
Appendix: Answers to Exercises
Chapter 1
Exercise 1 Solution
Exercise 2 Solution
Exercise 3 Solution
Exercise 4 Solution
Exercise 5 Solution
Chapter 2
Exercise 1 Solution
Exercise 2 Solution
Chapter 3
Exercise 1 Solution
Exercise 2 Solution
Exercise 3 Solution
Exercise 4 Solution
Chapter 4
Exercise 1 Solution
Exercise 2 Solution
Exercise 3 Solution
Chapter 5
Exercise 1 Solution
Exercise 2 Solution
Chapter 6
Exercise 1 Solution
Exercise 2 Solution
Exercise 3 Solution
Exercise 4 Solution
Exercise 5 Solution
Chapter 7
Exercise 1 Solution
Exercise 2 Solution
Exercise 3 Solution
Exercise 4 Solution
Exercise 5 Solution
Chapter 8
Exercise 1 Solution
Exercise 2 Solution
Exercise 3 Solution
Exercise 4 Solution
Exercise 5 Solution
Chapter 9
Exercise 1 Solution
Exercise 2 Solution
Exercise 3 Solution
Exercise 4 Solution
Exercise 5 Solution
Chapter 10
Exercise 1 Solution
Exercise 2 Solution
Exercise 3 Solution
Exercise 4 Solution
Exercise 5 Solution
Chapter 11
Exercise 1 Solution
Exercise 2 Solution
Exercise 3 Solution
Exercise 4 Solution
Chapter 12
Exercise 1 Solution
Exercise 2 Solution
Exercise 3 Solution
Exercise 4 Solution
Exercise 5 Solution
Introduction
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