An Introduction to R Draft 2 The Berkeley R Project Department of Statistics, UC Berkeley VIGRE John Jimenez Devon Shurick The Berkeley R Project The Berkeley R Project [email protected] [email protected] December 27, 2008 1 CONTENTS CONTENTS Contents 1 Introduction 2 1.1 What is R? . 2 1.2 What can I do with R? . 2 1.3 How Can I Get a Copy? . 4 1.4 The Focus of this Tutorial, and other References . 4 2 Objects 6 2.1 Introduction . 6 2.2 Numbers . 7 2.3 Vectors . 8 2.3.1 Creating Vectors . 8 2.3.2 Logical and Comparison Operators . 9 2.3.3 Indexing Vectors . 10 2.3.4 Vector Arithmetic . 11 2.4 Matrices . 11 2.5 More on indexing . 12 2.5.1 Random Sampling, with sample and more on Matrices . 13 2.5.2 Introduction to apply ............................... 16 2.6 Strings . 16 2.6.1 Manipulating Strings . 17 2.7 Factors . 18 2.8 List . 19 2.9 Data Frames . 21 2.9.1 attach and detach ................................ 23 2.10 Tables . 23 2.11 Operators . 24 2.12 Other Things You Must Know About R . 24 2.13 Functions . 26 2.13.1 Examples . 26 3 Plotting 32 3.1 Histograms . 32 3.1.1 colors . 34 3.2 Box-Plots : . 34 3.3 Scatter-Plots : . 35 3.4 Putting Multiple Graphs in One Figure . 38 3.4.1 par . 38 3.4.2 split.screen . 39 3.4.3 Replacing a Screen . 39 3.4.4 Split Screens within Split Screens . 41 3.5 abline . 42 3.6 lines . 43 3.7 Putting it all together . 44 3.8 QQ-Plots : . 45 3.8.1 qqnorm : . 45 3.8.2 qqmath (requires installation of lattice package) : . 46 3.8.3 qqplot : . 47 3.8.4 Adjusting the qqline . 47 3.9 Linear Regression . 47 2 CONTENTS CONTENTS 3.9.1 Additional Information . 52 3.10 Saving Plots . 52 3.11 Adding Text : . 52 3.11.1 text ........................................ 52 3.12 Fine Tuning Plots . 55 3.12.1 mtext ........................................ 55 3.12.2 par revisited . 56 4 Packages 57 4.1 Introduction . 57 4.2 Listing Loaded and Installed Packages . 57 4.2.1 .packages ..................................... 58 4.2.2 library ....................................... 59 4.3 Listing all R packages . 59 4.4 Installing Packages . 60 4.4.1 From the Command Line : 60 4.4.2 Using a Graphical User Interface (GUI) 60 4.5 Removing Packages . 60 5 Setting up your working environment and profile 61 6 Help R help you 61 6.1 help.start . 61 6.2 help . 62 6.2.1 Graphical User Interface (GUI) Specific Tip . 63 6.2.2 Mac OS X . 63 6.2.3 Windows OS . 63 6.3 apropos and find . 63 6.3.1 searching for functions and their packages . 63 6.3.2 searching for lost objects : 64 6.4 help.search . 64 6.5 RSiteSearch . 66 6.6 Summary . 66 7 Reading Data Into R 66 7.1 read.table . 66 7.1.1 setwd . 69 7.1.2 An Example of Cleaning Data . 69 7.2 The Rest of the read Family: . 71 7.3 scan . 72 7.4 Missing Values . 72 8 Probability 72 8.1 Binomial . 73 8.2 Normal Distribution . 74 3 LIST OF FIGURES LIST OF FIGURES 9 Scripting 78 9.0.1 From the Command Line . 78 9.0.2 Mac : From the GUI . 80 9.0.3 Windows : From the GUI . 80 9.0.4 source . 80 10 Functions 80 10.1 Introduction . 80 10.2 Functional Form . 81 10.3 Naming Functions . 81 10.4 Functions and Loops . 82 10.4.1 for loops . 82 10.4.2 On the Myth of loops being bad form in R ................... 84 10.4.3 repeat loops . 84 10.4.4 replicate . 85 10.5 Examples of Homemade Functions : . 86 10.5.1 Uploading a set of Packages . 86 10.5.2 Adjusting the QQ-line for Comparisons with Theoretical Distributions . 86 10.5.3 adjusting qqline for two sample comparison . 87 10.5.4 A More Adjustable QQ-line : . ..