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| Introduction | |
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| Introducing R: What It Is and How to Get It | |
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| Getting the Hang of R | |
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| The R Website | |
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| Downloading and Installing R from CRAN | |
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| Installing R on Your Windows Computer | |
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| Installing R on Your Macintosh Computer | |
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| Installing R on Your Linux Computer | |
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| Running the R Program | |
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| Finding Your Way with R | |
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| Getting Help via the CRAN Website and the Internet | |
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| The Help Command in R | |
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| Help for Windows Users | |
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| Help for Macintosh Users | |
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| Help for Linux Users | |
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| Help For All Users | |
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| Anatomy of a Help Item in R | |
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| Command Packages | |
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| Standard Command Packages | |
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| What Extra Packages Can Do for You | |
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| How to Get Extra Packages of R Commands | |
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| How to Install Extra Packages for Windows Users | |
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| How to Install Extra Packages for Macintosh Users | |
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| How to Install Extra Packages for Linux Users | |
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| Running and Manipulating Packages | |
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| Loading Packages | |
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| Windows-Specific Package Commands | |
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| Macintosh-Specific Package Commands | |
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| Removing or Unloading Packages | |
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| Summary | |
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| Starting Out: Becoming Familiar with R | |
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| Some Simple Math | |
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| Use R Like a Calculator | |
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| Storing the Results of Calculations | |
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| Reading and Getting Data into R | |
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| Using the combine Command for Making Data | |
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| Entering Numerical Items as Data | |
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| Entering Text Items as Data | |
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| Using the scan Command for Making Data | |
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| Entering Text as Data | |
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| Using the Clipboard to Make Data | |
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| Reading a File of Data from a Disk | |
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| Reading Bigger Data Files | |
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| The read.csv() Command | |
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| Alternative Commands for Reading Data in R | |
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| Missing Values in Data Files | |
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| Viewing Named Objects | |
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| Viewing Previously Loaded Named-Objects | |
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| Viewing All Objects | |
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| Viewing Only Matching Names | |
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| Removing Objects from R | |
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| Types of Data Items | |
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| Number Data | |
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| Text Items | |
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| Converting Between Number and Text Data | |
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| The Structure of Data Items | |
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| Vector Items | |
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| Data Frames | |
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| Matrix Objects | |
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| List Objects | |
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| Examining Data Structure | |
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| Working with History Commands | |
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| Using History Files | |
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| Viewing the Previous Command History | |
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| Saving and Recalling Lists of Commands | |
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| Alternative History Commands in Macintosh OS | |
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| Editing History Files | |
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| Saving Your Work in R | |
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| Saving the Workspace on Exit | |
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| Saving Data Files to Disk | |
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| Save Named Objects | |
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| Save Everything | |
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| Reading Data Files from Disk | |
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| Saving Data to Disk as Text Files | |
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| Writing Vector Objects to Disk | |
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| Writing Matrix and Data Frame Objects to Disk | |
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| Writing List Objects to Disk | |
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| Converting List Objects to Data Frames | |
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| Summary | |
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| Starting Out: Working With Objects | |
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| Manipulating Objects | |
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| Manipulating Vectors | |
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| Selecting and Displaying Parts of a Vector | |
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| Sorting and Rearranging a Vector | |
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| Returning Logical Values from a Vector | |
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| Manipulating Matrix and Data Frames | |
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| Selecting and Displaying Parts of a Matrix or Data Frame | |
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| Sorting and Rearranging a Matrix or Data Frame | |
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| Manipulating Lists | |
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| Viewing Objects within Objects | |
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| Looking Inside Complicated Data Objects | |
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| Opening Complicated Data Objects | |
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| Quick Looks at Complicated Data Objects | |
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| Viewing and Setting Names | |
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| Rotating Data Tables | |
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| Constructing Data Objects | |
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| Making Lists | |
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| Making Data Frames | |
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| Making Matrix Objects | |
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| Re-ordering Data Frames and Matrix Objects | |
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| Forms of Data Objects: Testing and Converting | |
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| Testing to See What Type of Object You Have | |
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| Converting from One Object Form to Another | |
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| Convert a Matrix to a Data Frame | |
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| Convert a Data Frame into a Matrix | |
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| Convert a Data Frame into a List | |
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| Convert a Matrix into a List | |
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| Convert a List to Something Else | |
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| Summary | |
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| Data: Descriptive Statistics and Tabulation | |
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| Summary Commands | |
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| Summarizing Samples | |
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| Summary Statistics for Vectors | |
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| Summary Commands With Single Value Results | |
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| Summary Commands With Multiple Results | |
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| Cumulative Statistics | |
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| Simple Cumulative Commands | |
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| Complex Cumulative Commands | |
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| Summary Statistics for Data Frames | |
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| Generic Summary Commands for Data Frames | |
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| Special Row and Column Summary Commands | |
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| The apply() Command for Summaries on Rows or Columns | |
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| Summary Statistics for Matrix Objects | |
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| Summary Statistics for Lists | |
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| Summary Tables | |
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| Making Contingency Tables | |
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| Creating Contingency Tables from Vectors | |
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| Creating Contingency Tables from Complicated Data | |
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| Creating Custom Contingency Tables | |
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| Creating Contingency Tables from Matrix Objects | |
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| Selecting Parts of a Table Object | |
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| Converting an Object into a Table | |
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| Testing for Table Objects | |
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| Complex (Flat) Tables | |
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| Making �Flat� Contingency Tables | |
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| Making Selective �Flat� Contingency Tables | |
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| Testing �Flat� Table Objects | |
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| Summary Commands for Tables | |
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| Cross Tabulation | |
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| Testing Cross-Table (xtabs) Objects | |
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| A Better Class Test | |
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| Recreating Original Data from a Contingency Table | |
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| Switching Class | |
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| Summary | |
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| Data: Distrib ution | |
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| Looking at the Distribution of Data | |
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| Stem and Leaf Plot | |
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| Histograms | |
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| Density Function | |
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| Using the Density Function to Draw a Graph | |
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| Adding Density Lines to Existing Graphs | |
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| Types of Data Distribution | |
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| The Normal Distribution | |
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| Other Distributions | |
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| Random Number Generation and Control | |
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| Random Numbers and Sampling | |
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| The Shapiro-Wilk Test for Normality | |
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| The Kolmogorov-Smirnov Test | |
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| Quantile-Quantile Plots | |
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| A Basic Normal Quantile-Quantile Plot | |
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| Adding a Straight Line to a QQ Plot | |
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| Plotting the Distribution of One Sample Against Another | |
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| Summary | |
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| Si mple Hypothesis Testing | |
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| Using the Student’s t-test | |
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| Two-Sample t-Test with Unequal Variance | |
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| Two-Sample t-Test with Equal Variance | |
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| One-Sample t-Testing | |
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| Using Directional Hypotheses | |
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| Formula Syntax and Subsetting Samples in the t-Test | |
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| The Wilcoxon U-Test (Mann-Whitney) | |
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| Two-Sample U-Test | |
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| One-Sample U-Test | |
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| Using Directional Hypotheses | |
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| Formula Syntax and Subsetting Samples in the U-test | |
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| Paired t- and U-Tests | |
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| Correlation and Covariance | |
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| Simple Correlation | |
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| Covariance | |
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| Significance Testing in Correlation Tests | |
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| Formula Syntax | |
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| Tests for Association | |
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| Multiple Categories: Chi-Squared Tests | |
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| Monte Carlo Simulation | |
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| Yates’ Correction for 2 n 2 Tables | |
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| Single Category: Goodness of Fit Tests | |
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| Summary | |
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| Introduction to Graphical Analysis | |
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| Box-whisker Plots | |
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| Basic Boxplots | |
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| Customizing Boxplots | |
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| Horizontal Boxplots | |
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| Scatter Plots | |
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| Basic Scatter Plots | |
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| Adding Axis Labels | |
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| Plotting Symbols | |
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| Setting Axis Limits | |
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| Using Formula Syntax | |
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| Adding Lines of Best-Fit to Scatter Plots | |
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| Pairs Plots (Multiple Correlation Plots) | |
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| Line Charts | |
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| Line Charts Using Numeric Data | |
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| Line Charts Using Categorical Data | |
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| Pie Charts | |
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| Cleveland Dot Charts | |
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| Bar Charts | |
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| Single-Category Bar Charts | |
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| Multiple Category Bar Charts | |
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| Stacked Bar Charts | |
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| Grouped Bar Charts | |
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| Horizontal Bars | |
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| Bar Charts from Summary Data | |
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| Copy Graphics to Other Applications | |
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| Use Copy/Paste to Copy Graphs | |
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| Save a Graphic to Disk | |
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| Windows | |
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| Macintosh | |
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| Linux | |
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| Summary | |
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| Formula Notation and Complex Statistic s | |
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| Examples of Using Formula Syntax for Basic Tests | |
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| Formula Notation in Graphics | |
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| Analysis of Variance (ANOVA) | |
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| One-Way ANOVA | |
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| Stacking the Data before Running Analysis of Variance | |
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| Running aov() Commands | |
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| Simple Post-hoc Testing | |
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| Extracting Means from aov() Models | |
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| Two-Way ANOVA | |
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| More about Post-hoc Testing | |
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| Graphical Summary of ANOVA | |
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| Graphical Summary of Post-hoc Testing | |
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| Extracting Means and Summary Statistics | |
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| Model Tables | |
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| Table Commands | |
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| Interaction Plots | |
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| More Complex ANOVA Models | |
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| Other Options for aov() | |
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| Replications and Balance | |
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| Summary | |
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| Manipulating Data and Extracting Components | |
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| Creating Data for Complex Analysis | |
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| Data Frames | |
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| Matrix Objects | |
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| Creating and Setting Factor Data | |
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| Making Replicate Treatment Factors | |
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| Adding Rows or Columns | |
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| Summarizing Data | |
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| Simple Column and Row Summaries | |
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| Complex Summary Functions | |
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| The rowsum() Command | |
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| The apply() Command | |