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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 ï¿½Flatï¿½ Contingency Tables | |

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Making Selective ï¿½Flatï¿½ Contingency Tables | |

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Testing ï¿½Flatï¿½ 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 | |