Beginning R

Dr. Mark Gardener is an ecologist, lecturer, and writer working in the UK. He is currently self-employed and runs courses in ecology, data analysis, and R for a variety of organizations.

• Introduction xxi Chapter 1: Introducing R: What It Is and How to Get It 1Getting the Hang of R 2The R Website 3Downloading and Installing R from CRAN 3Installing R on Your Windows Computer 4Installing R on Your Macintosh Computer 7Installing R on Your Linux Computer 7Running the R Program 8Finding Your Way with R 10Getting Help via the CRAN Website and the Internet 10The Help Command in R 10Help for Windows Users 11Help for Macintosh Users 11Help for Linux Users 13Help For All Users 13Anatomy of a Help Item in R 14Command Packages 16Standard Command Packages 16What Extra Packages Can Do for You 16How to Get Extra Packages of R Commands 18How to Install Extra Packages for Windows Users 18How to Install Extra Packages for Macintosh Users 18How to Install Extra Packages for Linux Users 19Running and Manipulating Packages 20Loading Packages 21Windows-Specific Package Commands 21Macintosh-Specific Package Commands 21Removing or Unloading Packages 22Summary 22Chapter 2: Starting Out: Becoming Familiar with R 25Some Simple Math 26Use R Like a Calculator 26Storing the Results of Calculations 29Reading and Getting Data into R 30Using the combine Command for Making Data 30Entering Numerical Items as Data 30Entering Text Items as Data 31Using the scan Command for Making Data 32Entering Text as Data 33Using the Clipboard to Make Data 33Reading a File of Data from a Disk 35Reading Bigger Data Files 37The read.csv() Command 37Alternative Commands for Reading Data in R 39Missing Values in Data Files 40Viewing Named Objects 41Viewing Previously Loaded Named-Objects 42Viewing All Objects 42Viewing Only Matching Names 42Removing Objects from R 44Types of Data Items 45Number Data 45Text Items 45Converting Between Number and Text Data 46The Structure of Data Items 47Vector Items 48Data Frames 48Matrix Objects 49List Objects 49Examining Data Structure 49Working with History Commands 51Using History Files 52Viewing the Previous Command History 52Saving and Recalling Lists of Commands 52Alternative History Commands in Macintosh OS 52Editing History Files 53Saving Your Work in R 54Saving the Workspace on Exit 54Saving Data Files to Disk 54Save Named Objects 54Save Everything 55Reading Data Files from Disk 56Saving Data to Disk as Text Files 57Writing Vector Objects to Disk 58Writing Matrix and Data Frame Objects to Disk 58Writing List Objects to Disk 59Converting List Objects to Data Frames 60Summary 61Chapter 3: Starting Out: Working With Objects 65Manipulating Objects 65Manipulating Vectors 66Selecting and Displaying Parts of a Vector 66Sorting and Rearranging a Vector 68Returning Logical Values from a Vector 70Manipulating Matrix and Data Frames 70Selecting and Displaying Parts of a Matrix or Data Frame 71Sorting and Rearranging a Matrix or Data Frame 74Manipulating Lists 76Viewing Objects within Objects 77Looking Inside Complicated Data Objects 77Opening Complicated Data Objects 78Quick Looks at Complicated Data Objects 80Viewing and Setting Names 82Rotating Data Tables 86Constructing Data Objects 86Making Lists 87Making Data Frames 88Making Matrix Objects 89Re-ordering Data Frames and Matrix Objects 92Forms of Data Objects: Testing and Converting 96Testing to See What Type of Object You Have 96Converting from One Object Form to Another 97Convert a Matrix to a Data Frame 97Convert a Data Frame into a Matrix 98Convert a Data Frame into a List 99Convert a Matrix into a List 100Convert a List to Something Else 100Summary 104Chapter 4: Data: Descriptive Statistics and Tabulation 107Summary Commands 108Summarizing Samples 110Summary Statistics for Vectors 110Summary Commands With Single Value Results 110Summary Commands With Multiple Results 113Cumulative Statistics 115Simple Cumulative Commands 115Complex Cumulative Commands 117Summary Statistics for Data Frames 118Generic Summary Commands for Data Frames 119Special Row and Column Summary Commands 119The apply() Command for Summaries on Rows or Columns 120Summary Statistics for Matrix Objects 120Summary Statistics for Lists 121Summary Tables 122Making Contingency Tables 123Creating Contingency Tables from Vectors 123Creating Contingency Tables from Complicated Data 123Creating Custom Contingency Tables 126Creating Contingency Tables from Matrix Objects 128Selecting Parts of a Table Object 130Converting an Object into a Table 132Testing for Table Objects 133Complex (Flat) Tables 134Making “Flat” Contingency Tables 134Making Selective “Flat” Contingency Tables 138Testing “Flat” Table Objects 139Summary Commands for Tables 139Cross Tabulation 142Testing Cross-Table (xtabs) Objects 144A Better Class Test 144Recreating Original Data from a Contingency Table 145Switching Class 146Summary 147Chapter 5: Data: Distrib ution 151Looking at the Distribution of Data 151Stem and Leaf Plot 152Histograms 154Density Function 158Using the Density Function to Draw a Graph 159Adding Density Lines to Existing Graphs 160Types of Data Distribution 161The Normal Distribution 161Other Distributions 164Random Number Generation and Control 166Random Numbers and Sampling 168The Shapiro-Wilk Test for Normality 171The Kolmogorov-Smirnov Test 172Quantile-Quantile Plots 174A Basic Normal Quantile-Quantile Plot 174Adding a Straight Line to a QQ Plot 174Plotting the Distribution of One Sample Against Another 175Summary 177Chapter 6: Si mple Hypothesis Testing 181Using the Student’s t-test 181Two-Sample t-Test with Unequal Variance 182Two-Sample t-Test with Equal Variance 183One-Sample t-Testing 183Using Directional Hypotheses 183Formula Syntax and Subsetting Samples in the t-Test 184The Wilcoxon U-Test (Mann-Whitney) 188Two-Sample U-Test 189One-Sample U-Test 189Using Directional Hypotheses 189Formula Syntax and Subsetting Samples in the U-test 190Paired t- and U-Tests 193Correlation and Covariance 196Simple Correlation 197Covariance 199Significance Testing in Correlation Tests 199Formula Syntax 200Tests for Association 203Multiple Categories: Chi-Squared Tests 204Monte Carlo Simulation 205Yates’ Correction for 2 n 2 Tables 206Single Category: Goodness of Fit Tests 206Summary 210Chapter 7: Introduction to Graphical Analysis 215Box-whisker Plots 215Basic Boxplots 216Customizing Boxplots 217Horizontal Boxplots 218Scatter Plots 222Basic Scatter Plots 222Adding Axis Labels 223Plotting Symbols 223Setting Axis Limits 224Using Formula Syntax 225Adding Lines of Best-Fit to Scatter Plots 225Pairs Plots (Multiple Correlation Plots) 229Line Charts 232Line Charts Using Numeric Data 232Line Charts Using Categorical Data 233Pie Charts 236Cleveland Dot Charts 239Bar Charts 245Single-Category Bar Charts 245Multiple Category Bar Charts 250Stacked Bar Charts 250Grouped Bar Charts 250Horizontal Bars 253Bar Charts from Summary Data 253Copy Graphics to Other Applications 256Use Copy/Paste to Copy Graphs 257Save a Graphic to Disk 257Windows 257Macintosh 258Linux 258Summary 259Chapter 8: Formula Notation and Complex Statistic s 263Examples of Using Formula Syntax for Basic Tests 264Formula Notation in Graphics 266Analysis of Variance (ANOVA) 268One-Way ANOVA 268Stacking the Data before Running Analysis of Variance 269Running aov() Commands 270Simple Post-hoc Testing 271Extracting Means from aov() Models 271Two-Way ANOVA 273More about Post-hoc Testing 275Graphical Summary of ANOVA 277Graphical Summary of Post-hoc Testing 278Extracting Means and Summary Statistics 281Model Tables 281Table Commands 283Interaction Plots 283More Complex ANOVA Models 289Other Options for aov() 290Replications and Balance 290Summary 292Chapter 9: Manipulating Data and Extracting Components 295Creating Data for Complex Analysis 295Data Frames 296Matrix Objects 299Creating and Setting Factor Data 300Making Replicate Treatment Factors 304Adding Rows or Columns 306Summarizing Data 312Simple Column and Row Summaries 312Complex Summary Functions 313The rowsum() Command 314The apply() Command 315Using tapply() to Summarize Using a Grouping Variable 316The aggregate() Command 319Summary 323Chapter 10: Regression (Li near Modeling) 327Simple Linear Regression 328Linear Model Results Objects 329Coefficients 330Fitted Values 330Residuals 330Formula 331Best-Fit Line 331Similarity between lm() and aov() 334Multiple Regression 335Formulae and Linear Models 335Model Building 337Adding Terms with Forward Stepwise Regression 337Removing Terms with Backwards Deletion 339Comparing Models 341Curvilinear Regression 343Logarithmic Regression 344Polynomial Regression 345Plotting Linear Models and Curve Fitting 347Best-Fit Lines 348Adding Line of Best-Fit with abline() 348Calculating Lines with fitted() 348Producing Smooth Curves using spline() 350Confidence Intervals on Fitted Lines 351Summarizing Regression Models 356Diagnostic Plots 356Summary of Fit 357Summary 359Chapter 11: More About Graphs 363Adding Elements to Existing Plots 364Error Bars 364Using the segments() Command for Error Bars 364Using the arrows() Command to Add Error Bars 368Adding Legends to Graphs 368Color Palettes 370Placing a Legend on an Existing Plot 371Adding Text to Graphs 372Making Superscript and Subscript Axis Titles 373Orienting the Axis Labels 375Making Extra Space in the Margin for Labels 375Setting Text and Label Sizes 375Adding Text to the Plot Area 376Adding Text in the Plot Margins 378Creating Mathematical Expressions 379Adding Points to an Existing Graph 382Adding Various Sorts of Lines to Graphs 386Adding Straight Lines as Gridlines or Best-Fit Lines 386Making Curved Lines to Add to Graphs 388Plotting Mathematical Expressions 390Adding Short Segments of Lines to an Existing Plot 393Adding Arrows to an Existing Graph 394Matrix Plots (Multiple Series on One Graph) 396Multiple Plots in One Window 399Splitting the Plot Window into Equal Sections 399Splitting the Plot Window into Unequal Sections 402Exporting Graphs 405Using Copy and Paste to Move a Graph 406Saving a Graph to a File 406Windows 406Macintosh 406Linux 406Using the Device Driver to Save a Graph to Disk 407PNG Device Driver 407PDF Device Driver 407Copying a Graph from Screen to Disk File 408Making a New Graph Directly to a Disk File 408Summary 410Chapter 12: Writing Your Own Scripts: Beginning to Program 415Copy and Paste Scripts 416Make Your Own Help File as Plaintext 416Using Annotations with the # Character 417Creating Simple Functions 417One-Line Functions 417Using Default Values in Functions 418Simple Customized Functions with Multiple Lines 419Storing Customized Functions 420Making Source Code 421Displaying the Results of Customized Functions and Scripts 421Displaying Messages as Part of Script Output 422Simple Screen Text 422Display a Message and Wait for User Intervention 424Summary 428Appendix: Answers to Exerci ses 433Index 461