R-For Data Analysis Training Course

Getting the Hang of R

• The R Website
• Downloading and Installing R from CRAN
• Installing R on Your Windows Computer
• Installing R on Your Macintosh Computer
• Installing R on Your Linux Computer

Running the R program

Finding Your Way with R

• Getting Help via the CRAN Website and the Internet
• The Help Command in R
• Help for Windows Users
• Help for Macintosh Users
• Help for Linux Users
• Help For All Users
• 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
• How to Install Extra Packages for Windows Users
• How to Install Extra Packages for Macintosh Users
• How to Install Extra Packages for Linux Users
• Running and Manipulating Packages
• Loading Packages
• Windows-Specific Package Commands
• Macintosh-Specific Package Commands
• Removing or Unloading Packages

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
• Entering Numerical Items as Data
• Entering Text Items as Data
• Using the scan Command for Making Data
• Entering Text as Data
• Using the Clipboard to Make Data
• Reading a File of Data from a Disk
• Reading Bigger Data Files
• The read.csv() Command
• Alternative Commands for Reading Data in R
• Missing Values in Data Files

Viewing Named Objects

• Viewing Previously Loaded Named-Objects
• Viewing All Objects
• Viewing Only Matching Names
• 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
• Viewing the Previous Command History
• Saving and Recalling Lists of Commands
• Alternative History Commands in Macintosh OS
• Editing History Files

Saving Your Work in R

• Saving the Workspace on Exit
• Saving Data Files to Disk
• Save Named Objects
• Save Everything
• Reading Data Files from Disk
• Saving Data to Disk as Text Files
• Writing Vector Objects to Disk
• Writing Matrix and Data Frame Objects to Disk
• CONTENTS Writing List Objects to Disk
• Converting List Objects to Data Frames

Manipulating Objects

• Manipulating Vectors
• Selecting and Displaying Parts of a Vector
• Sorting and Rearranging a Vector
• Returning Logical Values from a Vector
• Manipulating Matrix and Data Frames
• Selecting and Displaying Parts of a Matrix or Data Frame
• Sorting and Rearranging a Matrix or Data Frame
• 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
• Convert a Matrix to a Data Frame
• Convert a Data Frame into a Matrix
• Convert a Data Frame into a List
• Convert a Matrix into a List
• Convert a List to Something Else

Summary Commands

Summarizing Samples

• Summary Statistics for Vectors
• Summary Commands With Single Value Results
• Summary Commands With Multiple Results
• Cumulative Statistics
• Simple Cumulative Commands
• Complex Cumulative Commands
• Summary Statistics for Data Frames
• Generic Summary Commands for Data Frames
• Special Row and Column Summary Commands
• The apply() Command for Summaries on Rows or Columns
• Summary Statistics for Matrix Objects
• Summary Statistics for Lists

Summary Tables

• Making Contingency Tables
• Creating Contingency Tables from Vectors
• Creating Contingency Tables from Complicated Data
• Creating Custom Contingency Tables
• Creating Contingency Tables from Matrix Objects
• Selecting Parts of a Table Object
• Converting an Object into a Table
• Testing for Table Objects
• Complex (Flat) Tables
• Making “Flat” Contingency Tables
• Making Selective “Flat” Contingency Tables
• Testing “Flat” Table Objects
• Summary Commands for Tables
• Cross Tabulation
• Testing Cross-Table (xtabs) Objects
• A Better Class Test
• Recreating Original Data from a Contingency Table

Summary Tables

Looking at the Distribution of Data

• Stem and Leaf Plot
• Histograms
• Density Function
• Using the Density Function to Draw a Graph
• Adding Density Lines to Existing Graphs
• Types of Data Distribution
• The Normal Distribution
• Other Distributions
• Random Number Generation and Control
• Random Numbers and Sampling
• The Shapiro-Wilk Test for Normality
• The Kolmogorov-Smirnov Test
• Quantile-Quantile Plots
• A Basic Normal Quantile-Quantile Plot
• Adding a Straight Line to a QQ Plot
• Plotting the Distribution of One Sample Against Another

Using the Student’s t-test

• Two-Sample t-Test with Unequal Variance
• Two-Sample t-Test with Equal Variance
• One-Sample t-Testing 183 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
• Monte Carlo Simulation
• Yates’ Correction for 2 n 2 Tables
• Single Category: Goodness of Fit Tests

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
• Stacked Bar Charts
• Grouped 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
• Windows
• Macintosh
• Linux

Examples of Using Formula Syntax for Basic Tests

Formula Notation in Graphics

Analysis of Variance (ANOVA)

• One-Way ANOVA
• Stacking the Data before Running Analysis of Variance
• Running aov() Commands
• Simple Post-hoc Testing
• Extracting Means from aov() Models
• Two-Way ANOVA
• More about Post-hoc Testing
• Graphical Summary of ANOVA
• Graphical Summary of Post-hoc Testing
• Extracting Means and Summary Statistics
• Model Tables
• Table Commands
• Interaction Plots
• More Complex ANOVA Models
• Other Options for aov()
• Replications and Balance

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
• The rowsum() Command
• The apply() Command
• Using tapply() to Summarize Using a Grouping Variable
• The aggregate() Command

Simple Linear Regression

• Linear Model Results Objects
• Coefficients
• Fitted Values
• Residuals
• Formula
• Best-Fit Line
• Similarity between lm() and aov()
>

Multiple Regression

• Formulae and Linear Models
• Model Building
• Adding Terms with Forward Stepwise Regression
• Removing Terms with Backwards Deletion
• Comparing Models

Curvilinear Regression

• Logarithmic Regression
• Polynomial Regression

Plotting Linear Models and Curve Fitting

• Best-Fit Lines
• Adding Line of Best-Fit with abline()
• Calculating Lines with fitted()
• Producing Smooth Curves using spline()
• Confidence Intervals on Fitted Lines

Summarizing Regression Models

• Diagnostic Plots
• Summary of Fit

Adding Elements to Existing Plots

• Linear Model Results Objects
• Error Bars 364 Using the segments() Command for Error Bars
• Using the arrows() Command to Add Error Bars
• Adding Legends to Graphs
• Color Palettes
• Placing a Legend on an Existing Plot
• Adding Text to Graphs
• Making Superscript and Subscript Axis Titles
• Orienting the Axis Labels
• Making Extra Space in the Margin for Labels
• Setting Text and Label Sizes
• Adding Text to the Plot Area
• Adding Text in the Plot Margins
• Creating Mathematical Expressions
• Adding Points to an Existing Graph
• Adding Various Sorts of Lines to Graphs
• Adding Straight Lines as Gridlines or Best-Fit Lines
• Making Curved Lines to Add to Graphs
• Plotting Mathematical Expressions
• Adding Short Segments of Lines to an Existing Plot
• Adding Arrows to an Existing Graph

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
• Windows
• Macintosh
• Linux
• Using the Device Driver to Save a Graph to Disk
• PNG Device Driver
• PDF Device Driver
• Copying a Graph from Screen to Disk File
• Making a New Graph Directly to a Disk File

Copy and Paste Scripts

• Make Your Own Help File as Plaintext
• 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
• Simple Screen Text
• Display a Message and Wait for User Intervention

Case study 1 - wildfire activity in the western united states

• Exercise 1 Have the number of wildfires increased or decreased in the past few decades?
• Exercise 2 Has the acreage burned increased over time?
• Exercise 3 is the size of individual wildfire increased over time?
• Exercise 4 has the length of the fire season increased over time?
• Exercise 5 does the average wildfire size differ by federal organization?

Case study 2- single family residential home and rental value

• Exercise 1 what is the trend for home value in the Austin metro area
• Exercise 2 what is the trend for rental rates in the Austin metro area?
• Exercise 3 determining the price-rent ratio for the Austin metropolitan area
• Exercise 4 comparing residential home values in Austin to other texas and u.s. Metropolitan areas