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Contents
Introduction .......................................................................................................................................................1
1. Starting Up .....................................................................................................................................................3
1.1 Getting started under Windows ............................................................................................................3
1.2 Using the Console (or Command Line) Window ..................................................................................5
1.3 A Short R Session.................................................................................................................................5
1.4 Further Notational Details ...................................................................................................................7
1.5 On-line Help ........................................................................................................................................7
1.6 Exercise ...............................................................................................................................................8
2. An Overview of R ..........................................................................................................................................9
2.1 The Uses of R.............................................................................................................................................9
2.2 The Look and Feel of R.............................................................................................................................11
2.3 R Objects .................................................................................................................................................12
*2.4 Looping..................................................................................................................................................12
2.5 R Functions..............................................................................................................................................13
2.6 Vectors.....................................................................................................................................................14
2.7 Data Frames............................................................................................................................................16
2.8 Common Useful Functions .......................................................................................................................18
2.9 Making Tables .........................................................................................................................................19
2.10 The R Directory Structure ......................................................................................................................19
2.11 More Detailed Information....................................................................................................................20
2.11 Exercises................................................................................................................................................20
3. Plotting .........................................................................................................................................................21
3.1 plot () and allied functions.......................................................................................................................21
3.2 Fine control – Parameter settings ............................................................................................................22
3.3 Adding points, lines and text.....................................................................................................................23
3.4 Identification and Location on the Figure Region ...................................................................................25
3.5 Plots that show the distribution of data values.........................................................................................26
3.6 Other Useful Plotting Functions...............................................................................................................29
3.7 Plotting Mathematical Symbols................................................................................................................31
3.8 Guidelines for Graphs ..............................................................................................................................31
3.9 Exercises..................................................................................................................................................32
3.10 References..............................................................................................................................................33
4. Lattice graphics, and coplot() ......................................................................................................................35
4.1 Examples that Present Panels of Scatterplots – Using xyplot().........................................................35
4.2 Using coplot() ...................................................................................................................................37
4.3 Exercises..................................................................................................................................................37
ii
5. Linear (Multiple Regression) Models and Analysis of Variance ..............................................................39
5.1 The Model Formula in Straight Line Regression .....................................................................................39
5.2 Regression Objects ..................................................................................................................................40
5.3 Model Formulae, and the X Matrix ..........................................................................................................41
5.4 Multiple Linear Regression Models..........................................................................................................43
5.5 Polynomial and Spline Regression ...........................................................................................................45
5.6 Using Factors in R Models .......................................................................................................................48
5.7 Multiple Lines – Different Regression Lines for Different Species...........................................................51
5.8 aov models (Analysis of Variance) ...........................................................................................................52
5.9 Exercises..................................................................................................................................................54
5.10 References..............................................................................................................................................55
6. Multivariate and Tree-Based Methods.......................................................................................................57
6.1 Multivariate EDA, and Principal Components Analysis ..........................................................................57
6.2 Cluster Analysis.......................................................................................................................................58
6.3 Discriminant Analysis..............................................................................................................................58
6.4 Decision Tree models (Tree-based models)..............................................................................................60
6.5 Exercises..................................................................................................................................................60
6.6 References................................................................................................................................................60
*7. R Data Structures ......................................................................................................................................63
7.1 Vectors.....................................................................................................................................................63
7.2 Missing Values.........................................................................................................................................63
7.3 Data frames .............................................................................................................................................64
7.4 Data Entry ...............................................................................................................................................65
7.5 Factors and Ordered Factors...................................................................................................................67
7.6 Ordered Factors ......................................................................................................................................68
7.7 Lists..........................................................................................................................................................68
*7.8 Matrices and Arrays ...............................................................................................................................69
7.9 Different Types of Attachments.................................................................................................................70
7.10 Exercises................................................................................................................................................70
8. Useful Functions ..........................................................................................................................................73
8.1 Confidence Intervals and Tests.................................................................................................................73
8.2 Matching and Ordering ............................................................................................................................73
8.3 String Functions ......................................................................................................................................73
8.4 Application of a Function to the Columns of an Array or Data Frame....................................................74
*8.5 tapply() ..................................................................................................................................................74
8.6 Splitting Vectors and Data Frames Down into Lists – split()...................................................................76
*8.7 Merging Data Frames ............................................................................................................................76
8.8 Dates........................................................................................................................................................76
8.9 Exercises..................................................................................................................................................77
9. Writing Functions and other Code..............................................................................................................79
9.1 Syntax and Semantics ...............................................................................................................................79
9.2 Issues for the Writing and Use of Functions.............................................................................................80
9.3 Functions as aids to Data Management ...................................................................................................81
9.4 A Simulation Example ..............................................................................................................................81
9.5 Exercises..................................................................................................................................................82
*10. GLM, and General Non-linear Models...................................................................................................85
10.1 A Taxonomy of Extensions to the Linear Model .....................................................................................85
10.2 Logistic Regression................................................................................................................................86
10.3 glm models (Generalized Linear Regression Modelling) .......................................................................90
10.4 Models that Include Smooth Spline Terms .............................................................................................90
10.5 Non-linear Models.................................................................................................................................90
10.6 Model Summaries ..................................................................................................................................90
10.7 Further Elaborations.............................................................................................................................91
10.8 Exercises................................................................................................................................................91
10.9 References..............................................................................................................................................91
*11. Multi-level Models, Time Series and Survival Analysis ........................................................................93
11.1 Multi-Level Models, Including Repeated Measures Models...................................................................93
11.2 Time Series Models................................................................................................................................97
11.3 Survival Analysis ...................................................................................................................................98
11.4 Exercises................................................................................................................................................98
11.5 References..............................................................................................................................................98
*12. Advanced Programming Topics ..............................................................................................................99
12.1. Methods ................................................................................................................................................99
12.2 Extracting Arguments to Functions ........................................................................................................99
12.3 Parsing and Evaluation of Expressions................................................................................................100
12.4 Plotting a mathematical expression......................................................................................................101
12.4 Searching R functions for a specified token..........................................................................................102
13. R Resources..............................................................................................................................................103
13.1 R Packages for Windows ......................................................................................................................103
13.2 Literature written by expert users.........................................................................................................103
13.3 The R-help electronic mail discussion list ............................................................................................104
13.4 Competing Systems – XLISP-STAT.......................................................................................................104
14. Appendix 1................................................................................................................................................105
14.1 Data Sets Referred to in these Notes ....................................................................................................105
14.2 Answers to Selected Exercises ..............................................................................................................105
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