An Introduction to R

Notes on R: A Programming Environment for Data Analysis and Graphics

Version 2.6.0 (2007-10-03)

W. N. Venables, D. M. Smith
and the R Development Core Team
Copyright c 1990 W. N. Venables
Copyright c 1992 W. N. Venables & D. M. Smith
Copyright c 1997 R. Gentleman & R. Ihaka
Copyright c 1997, 1998 M. Maechler
Copyright c 1999–2006 R Development Core Team

Permission is granted to make and distribute verbatim copies of this manual provided the copy-
right notice and this permission notice are preserved on all copies.
Permission is granted to copy and distribute modified versions of this manual under the condi-
tions for verbatim copying, provided that the entire resulting derived work is distributed under
the terms of a permission notice identical to this one.
Permission is granted to copy and distribute translations of this manual into another language,
under the above conditions for modified versions, except that this permission notice may be
stated in a translation approved by the R Development Core Team.
ISBN 3-900051-12-7
 i

Table of Contents

Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

1 Introduction and preliminaries . . . . . . . . . . . . . . . . . . . . . . . . . . 2

1.1 The R environment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.2 Related software and documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.3 R and statistics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.4 R and the window system . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.5 Using R interactively . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.6 An introductory session . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.7 Getting help with functions and features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.8 R commands, case sensitivity, etc. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.9 Recall and correction of previous commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
1.10 Executing commands from or diverting output to a file . . . . . . . . . . . . . . . . . . . . . . . . . . 5
1.11 Data permanency and removing objects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

2 Simple manipulations; numbers and vectors . . . . . . . . . . . . . . 7

2.1 Vectors and assignment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
2.2 Vector arithmetic . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
2.3 Generating regular sequences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
2.4 Logical vectors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
2.5 Missing values . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
2.6 Character vectors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
2.7 Index vectors; selecting and modifying subsets of a data set . . . . . . . . . . . . . . . . . . . . . . 10
2.8 Other types of objects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

3 Objects, their modes and attributes . . . . . . . . . . . . . . . . . . . . 13

3.1 Intrinsic attributes: mode and length . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
3.2 Changing the length of an object . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
3.3 Getting and setting attributes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
3.4 The class of an object . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

4 Ordered and unordered factors . . . . . . . . . . . . . . . . . . . . . . . . . 16

4.1 A specific example . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
4.2 The function tapply() and ragged arrays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
4.3 Ordered factors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

5 Arrays and matrices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

5.1 Arrays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
5.2 Array indexing. Subsections of an array . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
5.3 Index matrices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
5.4 The array() function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
5.4.1 Mixed vector and array arithmetic. The recycling rule . . . . . . . . . . . . . . . . . . . . . . 20
5.5 The outer product of two arrays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
5.6 Generalized transpose of an array . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
5.7 Matrix facilities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
5.7.1 Matrix multiplication . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
 ii

5.7.2 Linear equations and inversion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

5.7.3 Eigenvalues and eigenvectors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
5.7.4 Singular value decomposition and determinants . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
5.7.5 Least squares fitting and the QR decomposition . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
5.8 Forming partitioned matrices, cbind() and rbind() . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
5.9 The concatenation function, c(), with arrays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
5.10 Frequency tables from factors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

6 Lists and data frames. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

6.1 Lists . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
6.2 Constructing and modifying lists . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
6.2.1 Concatenating lists. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
6.3 Data frames . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
6.3.1 Making data frames . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
6.3.2 attach() and detach() . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
6.3.3 Working with data frames . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
6.3.4 Attaching arbitrary lists . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
6.3.5 Managing the search path . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29

7 Reading data from files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30

7.1 The read.table() function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
7.2 The scan() function. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
7.3 Accessing builtin datasets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
7.3.1 Loading data from other R packages. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
7.4 Editing data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32

8 Probability distributions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
8.1 R as a set of statistical tables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
8.2 Examining the distribution of a set of data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
8.3 One- and two-sample tests . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36

9 Grouping, loops and conditional execution . . . . . . . . . . . . . . 40

9.1 Grouped expressions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
9.2 Control statements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
9.2.1 Conditional execution: if statements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
9.2.2 Repetitive execution: for loops, repeat and while . . . . . . . . . . . . . . . . . . . . . . . . . 40

10 Writing your own functions . . . . . . . . . . . . . . . . . . . . . . . . . . . 42

10.1 Simple examples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
10.2 Defining new binary operators . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
10.3 Named arguments and defaults . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
10.4 The ‘...’ argument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
10.5 Assignments within functions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
10.6 More advanced examples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
10.6.1 Efficiency factors in block designs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
10.6.2 Dropping all names in a printed array . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
10.6.3 Recursive numerical integration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
10.7 Scope . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
10.8 Customizing the environment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
10.9 Classes, generic functions and object orientation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
 iii

11 Statistical models in R . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
11.1 Defining statistical models; formulae . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
11.1.1 Contrasts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
11.2 Linear models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
11.3 Generic functions for extracting model information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
11.4 Analysis of variance and model comparison . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
11.4.1 ANOVA tables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
11.5 Updating fitted models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
11.6 Generalized linear models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
11.6.1 Families . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
11.6.2 The glm() function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
11.7 Nonlinear least squares and maximum likelihood models . . . . . . . . . . . . . . . . . . . . . . . . 58
11.7.1 Least squares . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
11.7.2 Maximum likelihood . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
11.8 Some non-standard models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60

12 Graphical procedures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
12.1 High-level plotting commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
12.1.1 The plot() function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
12.1.2 Displaying multivariate data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
12.1.3 Display graphics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
12.1.4 Arguments to high-level plotting functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
12.2 Low-level plotting commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
12.2.1 Mathematical annotation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
12.2.2 Hershey vector fonts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
12.3 Interacting with graphics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
12.4 Using graphics parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
12.4.1 Permanent changes: The par() function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
12.4.2 Temporary changes: Arguments to graphics functions. . . . . . . . . . . . . . . . . . . . . . 68
12.5 Graphics parameters list . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
12.5.1 Graphical elements. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
12.5.2 Axes and tick marks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
12.5.3 Figure margins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
12.5.4 Multiple figure environment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
12.6 Device drivers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
12.6.1 PostScript diagrams for typeset documents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
12.6.2 Multiple graphics devices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
12.7 Dynamic graphics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75

13 Packages. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
13.1 Standard packages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
13.2 Contributed packages and CRAN . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
13.3 Namespaces . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76

Appendix A A sample session . . . . . . . . . . . . . . . . . . . . . . . . . . . 78

Appendix B Invoking R . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
B.1 Invoking R from the command line . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
B.2 Invoking R under Windows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
B.3 Invoking R under Mac OS X . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
B.4 Scripting with R . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
 iv

Appendix C The command-line editor . . . . . . . . . . . . . . . . . . . 87

C.1 Preliminaries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
C.2 Editing actions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
C.3 Command-line editor summary. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87

Appendix D Function and variable index . . . . . . . . . . . . . . . . . 89

Appendix E Concept index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92

Appendix F References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
Preface 1

Preface
This introduction to R is derived from an original set of notes describing the S and S-Plus
environments written by Bill Venables and David M. Smith (Insightful Corporation). We have
made a number of small changes to reflect differences between the R and S programs, and
expanded some of the material.
We would like to extend warm thanks to Bill Venables (and David Smith) for granting
permission to distribute this modified version of the notes in this way, and for being a supporter
of R from way back.
Comments and corrections are always welcome. Please address email correspondence to
[email protected].

Suggestions to the reader

Most R novices will start with the introductory session in Appendix A. This should give some
familiarity with the style of R sessions and more importantly some instant feedback on what
actually happens.
Many users will come to R mainly for its graphical facilities. In this case, Chapter 12
[Graphics], page 62 on the graphics facilities can be read at almost any time and need not wait
until all the preceding sections have been digested.
Chapter 1: Introduction and preliminaries 2

1 Introduction and preliminaries

1.1 The R environment

R is an integrated suite of software facilities for data manipulation, calculation and graphical
display. Among other things it has
• an effective data handling and storage facility,
• a suite of operators for calculations on arrays, in particular matrices,
• a large, coherent, integrated collection of intermediate tools for data analysis,
• graphical facilities for data analysis and display either directly at the computer or on hard-
copy, and
• a well developed, simple and effective programming language (called ‘S’) which includes
conditionals, loops, user defined recursive functions and input and output facilities. (Indeed
most of the system supplied functions are themselves written in the S language.)
The term “environment” is intended to characterize it as a fully planned and coherent system,
rather than an incremental accretion of very specific and inflexible tools, as is frequently the
case with other data analysis software.
R is very much a vehicle for newly developing methods of interactive data analysis. It has
developed rapidly, and has been extended by a large collection of packages. However, most
programs written in R are essentially ephemeral, written for a single piece of data analysis.

1.2 Related software and documentation

R can be regarded as an implementation of the S language which was developed at Bell Labora-
tories by Rick Becker, John Chambers and Allan Wilks, and also forms the basis of the S-Plus
systems.
The evolution of the S language is characterized by four books by John Chambers and
coauthors. For R, the basic reference is The New S Language: A Programming Environment
for Data Analysis and Graphics by Richard A. Becker, John M. Chambers and Allan R. Wilks.
The new features of the 1991 release of S are covered in Statistical Models in S edited by John
M. Chambers and Trevor J. Hastie. The formal methods and classes of the methods package are
based on those described in Programming with Data by John M. Chambers. See Appendix F
[References], page 94, for precise references.
There are now a number of books which describe how to use R for data analysis and statistics,
and documentation for S/S-Plus can typically be used with R, keeping the differences between
the S implementations in mind. See section “What documentation exists for R?” in The R
statistical system FAQ.

1.3 R and statistics

Our introduction to the R environment did not mention statistics, yet many people use R as a
statistics system. We prefer to think of it of an environment within which many classical and
modern statistical techniques have been implemented. A few of these are built into the base R
environment, but many are supplied as packages. There are about 25 packages supplied with
R (called “standard” and “recommended” packages) and many more are available through the
CRAN family of Internet sites (via http://CRAN.R-project.org) and elsewhere. More details
on packages are given later (see Chapter 13 [Packages], page 76).
Most classical statistics and much of the latest methodology is available for use with R, but
users may need to be prepared to do a little work to find it.
Chapter 1: Introduction and preliminaries 3

There is an important difference in philosophy between S (and hence R) and the other
main statistical systems. In S a statistical analysis is normally done as a series of steps, with
intermediate results being stored in objects. Thus whereas SAS and SPSS will give copious
output from a regression or discriminant analysis, R will give minimal output and store the
results in a fit object for subsequent interrogation by further R functions.

1.4 R and the window system

The most convenient way to use R is at a graphics workstation running a windowing system.
This guide is aimed at users who have this facility. In particular we will occasionally refer to
the use of R on an X window system although the vast bulk of what is said applies generally to
any implementation of the R environment.
Most users will find it necessary to interact directly with the operating system on their
computer from time to time. In this guide, we mainly discuss interaction with the operating
system on UNIX machines. If you are running R under Windows or MacOS you will need to
make some small adjustments.
Setting up a workstation to take full advantage of the customizable features of R is a straight-
forward if somewhat tedious procedure, and will not be considered further here. Users in diffi-
culty should seek local expert help.

1.5 Using R interactively

When you use the R program it issues a prompt when it expects input commands. The default
prompt is ‘>’, which on UNIX might be the same as the shell prompt, and so it may appear that
nothing is happening. However, as we shall see, it is easy to change to a different R prompt if
you wish. We will assume that the UNIX shell prompt is ‘$’.
In using R under UNIX the suggested procedure for the first occasion is as follows:
1. Create a separate sub-directory, say ‘work’, to hold data files on which you will use R for
this problem. This will be the working directory whenever you use R for this particular
problem.
$ mkdir work
$ cd work
2. Start the R program with the command
$ R
3. At this point R commands may be issued (see later).
4. To quit the R program the command is
> q()
At this point you will be asked whether you want to save the data from your R session. On
some systems this will bring up a dialog box, and on others you will receive a text prompt
to which you can respond yes, no or cancel (a single letter abbreviation will do) to save
the data before quitting, quit without saving, or return to the R session. Data which is
saved will be available in future R sessions.
Further R sessions are simple.
1. Make ‘work’ the working directory and start the program as before:
$ cd work
$ R
2. Use the R program, terminating with the q() command at the end of the session.
To use R under Windows the procedure to follow is basically the same. Create a folder as
the working directory, and set that in the ‘Start In’ field in your R shortcut. Then launch R
by double clicking on the icon.
Chapter 1: Introduction and preliminaries 4

1.6 An introductory session

Readers wishing to get a feel for R at a computer before proceeding are strongly advised to work
through the introductory session given in Appendix A [A sample session], page 78.

1.7 Getting help with functions and features

R has an inbuilt help facility similar to the man facility of UNIX. To get more information on
any specific named function, for example solve, the command is
> help(solve)
An alternative is
> ?solve
For a feature specified by special characters, the argument must be enclosed in double or single
quotes, making it a “character string”: This is also necessary for a few words with syntactic
meaning including if, for and function.
> help("[[")
Either form of quote mark may be used to escape the other, as in the string "It’s
important". Our convention is to use double quote marks for preference.
On most R installations help is available in HTML format by running
> help.start()
which will launch a Web browser that allows the help pages to be browsed with hyperlinks. On
UNIX, subsequent help requests are sent to the HTML-based help system. The ‘Search Engine
and Keywords’ link in the page loaded by help.start() is particularly useful as it is contains
a high-level concept list which searches though available functions. It can be a great way to get
your bearings quickly and to understand the breadth of what R has to offer.
The help.search command allows searching for help in various ways: try ?help.search for
details and examples.
The examples on a help topic can normally be run by
> example(topic )
Windows versions of R have other optional help systems: use
> ?help
for further details.

1.8 R commands, case sensitivity, etc.

Technically R is an expression language with a very simple syntax. It is case sensitive as are most
UNIX based packages, so A and a are different symbols and would refer to different variables.
The set of symbols which can be used in R names depends on the operating system and country
within which R is being run (technically on the locale in use). Normally all alphanumeric
symbols are allowed1 (and in some countries this includes accented letters) plus ‘.’ and ‘_’, with
the restriction that a name must start with ‘.’ or a letter, and if it starts with ‘.’ the second
character must not be a digit.
Elementary commands consist of either expressions or assignments. If an expression is given
as a command, it is evaluated, printed (unless specifically made invisible), and the value is lost.
An assignment also evaluates an expression and passes the value to a variable but the result is
not automatically printed.
Commands are separated either by a semi-colon (‘;’), or by a newline. Elementary commands
can be grouped together into one compound expression by braces (‘{’ and ‘}’). Comments can
1
For portable R code (including that to be used in R packages) only A–Za–z0–9 should be used.
Chapter 1: Introduction and preliminaries 5

be put almost2 anywhere, starting with a hashmark (‘#’), everything to the end of the line is a
comment.
If a command is not complete at the end of a line, R will give a different prompt, by default
+
on second and subsequent lines and continue to read input until the command is syntactically
complete. This prompt may be changed by the user. We will generally omit the continuation
prompt and indicate continuation by simple indenting.
Command lines entered at the console are limited3 to about 1024 bytes (not characters).

1.9 Recall and correction of previous commands

Under many versions of UNIX and on Windows, R provides a mechanism for recalling and re-
executing previous commands. The vertical arrow keys on the keyboard can be used to scroll
forward and backward through a command history. Once a command is located in this way, the
cursor can be moved within the command using the horizontal arrow keys, and characters can
be removed with the hDELi key or added with the other keys. More details are provided later:
see Appendix C [The command-line editor], page 87.
The recall and editing capabilities under UNIX are highly customizable. You can find out
how to do this by reading the manual entry for the readline library.
Alternatively, the Emacs text editor provides more general support mechanisms (via ESS,
Emacs Speaks Statistics) for working interactively with R. See section “R and Emacs” in The
R statistical system FAQ.

1.10 Executing commands from or diverting output to a file

If commands4 are stored in an external file, say ‘commands.R’ in the working directory ‘work’,
they may be executed at any time in an R session with the command
> source("commands.R")
For Windows Source is also available on the File menu. The function sink,
> sink("record.lis")
will divert all subsequent output from the console to an external file, ‘record.lis’. The com-
mand
> sink()
restores it to the console once again.

1.11 Data permanency and removing objects

The entities that R creates and manipulates are known as objects. These may be variables, arrays
of numbers, character strings, functions, or more general structures built from such components.
During an R session, objects are created and stored by name (we discuss this process in the
next session). The R command
> objects()
(alternatively, ls()) can be used to display the names of (most of) the objects which are currently
stored within R. The collection of objects currently stored is called the workspace.
To remove objects the function rm is available:
2
not inside strings, nor within the argument list of a function definition
3
some of the consoles will not allow you to enter more, and amongst those which do some will silently discard
the excess and some will use it as the start of the next line.
4
of unlimited length.
Chapter 1: Introduction and preliminaries 6

> rm(x, y, z, ink, junk, temp, foo, bar)

All objects created during an R sessions can be stored permanently in a file for use in future
R sessions. At the end of each R session you are given the opportunity to save all the currently
available objects. If you indicate that you want to do this, the objects are written to a file called
‘.RData’5 in the current directory, and the command lines used in the session are saved to a file
called ‘.Rhistory’.
When R is started at later time from the same directory it reloads the workspace from this
file. At the same time the associated commands history is reloaded.
It is recommended that you should use separate working directories for analyses conducted
with R. It is quite common for objects with names x and y to be created during an analysis.
Names like this are often meaningful in the context of a single analysis, but it can be quite
hard to decide what they might be when the several analyses have been conducted in the same
directory.

5
The leading “dot” in this file name makes it invisible in normal file listings in UNIX.
Chapter 2: Simple manipulations; numbers and vectors 7

2 Simple manipulations; numbers and vectors

2.1 Vectors and assignment

R operates on named data structures. The simplest such structure is the numeric vector, which
is a single entity consisting of an ordered collection of numbers. To set up a vector named x,
say, consisting of five numbers, namely 10.4, 5.6, 3.1, 6.4 and 21.7, use the R command
> x <- c(10.4, 5.6, 3.1, 6.4, 21.7)
This is an assignment statement using the function c() which in this context can take an
arbitrary number of vector arguments and whose value is a vector got by concatenating its
arguments end to end.1
A number occurring by itself in an expression is taken as a vector of length one.
Notice that the assignment operator (‘<-’), which consists of the two characters ‘<’ (“less
than”) and ‘-’ (“minus”) occurring strictly side-by-side and it ‘points’ to the object receiving
the value of the expression. In most contexts the ‘=’ operator can be used as a alternative.
Assignment can also be made using the function assign(). An equivalent way of making
the same assignment as above is with:
> assign("x", c(10.4, 5.6, 3.1, 6.4, 21.7))
The usual operator, <-, can be thought of as a syntactic short-cut to this.
Assignments can also be made in the other direction, using the obvious change in the assign-
ment operator. So the same assignment could be made using
> c(10.4, 5.6, 3.1, 6.4, 21.7) -> x
If an expression is used as a complete command, the value is printed and lost 2 . So now if we
were to use the command
> 1/x
the reciprocals of the five values would be printed at the terminal (and the value of x, of course,
unchanged).
The further assignment
> y <- c(x, 0, x)
would create a vector y with 11 entries consisting of two copies of x with a zero in the middle
place.

2.2 Vector arithmetic

Vectors can be used in arithmetic expressions, in which case the operations are performed element
by element. Vectors occurring in the same expression need not all be of the same length. If
they are not, the value of the expression is a vector with the same length as the longest vector
which occurs in the expression. Shorter vectors in the expression are recycled as often as need be
(perhaps fractionally) until they match the length of the longest vector. In particular a constant
is simply repeated. So with the above assignments the command
> v <- 2*x + y + 1
generates a new vector v of length 11 constructed by adding together, element by element, 2*x
repeated 2.2 times, y repeated just once, and 1 repeated 11 times.
The elementary arithmetic operators are the usual +, -, *, / and ^ for raising to a power. In
addition all of the common arithmetic functions are available. log, exp, sin, cos, tan, sqrt,
1
With other than vector types of argument, such as list mode arguments, the action of c() is rather different.
See Section 6.2.1 [Concatenating lists], page 27.
2
Actually, it is still available as .Last.value before any other statements are executed.
Chapter 2: Simple manipulations; numbers and vectors 8

and so on, all have their usual meaning. max and min select the largest and smallest elements of a
vector respectively. range is a function whose value is a vector of length two, namely c(min(x),
max(x)). length(x) is the number of elements in x, sum(x) gives the total of the elements in
x, and prod(x) their product.
Two statistical functions are mean(x) which calculates the sample mean, which is the same
as sum(x)/length(x), and var(x) which gives
sum((x-mean(x))^2)/(length(x)-1)
or sample variance. If the argument to var() is an n-by-p matrix the value is a p-by-p sample
covariance matrix got by regarding the rows as independent p-variate sample vectors.
sort(x) returns a vector of the same size as x with the elements arranged in increasing order;
however there are other more flexible sorting facilities available (see order() or sort.list()
which produce a permutation to do the sorting).
Note that max and min select the largest and smallest values in their arguments, even if they
are given several vectors. The parallel maximum and minimum functions pmax and pmin return
a vector (of length equal to their longest argument) that contains in each element the largest
(smallest) element in that position in any of the input vectors.
For most purposes the user will not be concerned if the “numbers” in a numeric vector
are integers, reals or even complex. Internally calculations are done as double precision real
numbers, or double precision complex numbers if the input data are complex.
To work with complex numbers, supply an explicit complex part. Thus
sqrt(-17)
will give NaN and a warning, but
sqrt(-17+0i)
will do the computations as complex numbers.

2.3 Generating regular sequences

R has a number of facilities for generating commonly used sequences of numbers. For example
1:30 is the vector c(1, 2, ..., 29, 30). The colon operator has high priority within an ex-
pression, so, for example 2*1:15 is the vector c(2, 4, ..., 28, 30). Put n <- 10 and compare
the sequences 1:n-1 and 1:(n-1).
The construction 30:1 may be used to generate a sequence backwards.
The function seq() is a more general facility for generating sequences. It has five arguments,
only some of which may be specified in any one call. The first two arguments, if given, specify
the beginning and end of the sequence, and if these are the only two arguments given the result
is the same as the colon operator. That is seq(2,10) is the same vector as 2:10.
Parameters to seq(), and to many other R functions, can also be given in named form, in
which case the order in which they appear is irrelevant. The first two parameters may be named
from=value and to=value ; thus seq(1,30), seq(from=1, to=30) and seq(to=30, from=1)
are all the same as 1:30. The next two parameters to seq() may be named by=value and
length=value , which specify a step size and a length for the sequence respectively. If neither
of these is given, the default by=1 is assumed.
For example
> seq(-5, 5, by=.2) -> s3
generates in s3 the vector c(-5.0, -4.8, -4.6, ..., 4.6, 4.8, 5.0). Similarly
> s4 <- seq(length=51, from=-5, by=.2)
generates the same vector in s4.
Chapter 2: Simple manipulations; numbers and vectors 9

The fifth parameter may be named along=vector , which if used must be the only parameter,
and creates a sequence 1, 2, ..., length(vector ), or the empty sequence if the vector is
empty (as it can be).
A related function is rep() which can be used for replicating an object in various complicated
ways. The simplest form is
> s5 <- rep(x, times=5)
which will put five copies of x end-to-end in s5. Another useful version is
> s6 <- rep(x, each=5)
which repeats each element of x five times before moving on to the next.

2.4 Logical vectors

As well as numerical vectors, R allows manipulation of logical quantities. The elements of a
logical vector can have the values TRUE, FALSE, and NA (for “not available”, see below). The
first two are often abbreviated as T and F, respectively. Note however that T and F are just
variables which are set to TRUE and FALSE by default, but are not reserved words and hence can
be overwritten by the user. Hence, you should always use TRUE and FALSE.
Logical vectors are generated by conditions. For example
> temp <- x > 13
sets temp as a vector of the same length as x with values FALSE corresponding to elements of x
where the condition is not met and TRUE where it is.
The logical operators are <, <=, >, >=, == for exact equality and != for inequality. In addition
if c1 and c2 are logical expressions, then c1 & c2 is their intersection (“and”), c1 | c2 is their
union (“or”), and !c1 is the negation of c1.
Logical vectors may be used in ordinary arithmetic, in which case they are coerced into
numeric vectors, FALSE becoming 0 and TRUE becoming 1. However there are situations where
logical vectors and their coerced numeric counterparts are not equivalent, for example see the
next subsection.

2.5 Missing values

In some cases the components of a vector may not be completely known. When an element
or value is “not available” or a “missing value” in the statistical sense, a place within a vector
may be reserved for it by assigning it the special value NA. In general any operation on an NA
becomes an NA. The motivation for this rule is simply that if the specification of an operation
is incomplete, the result cannot be known and hence is not available.
The function is.na(x) gives a logical vector of the same size as x with value TRUE if and
only if the corresponding element in x is NA.
> z <- c(1:3,NA); ind <- is.na(z)
Notice that the logical expression x == NA is quite different from is.na(x) since NA is not
really a value but a marker for a quantity that is not available. Thus x == NA is a vector of the
same length as x all of whose values are NA as the logical expression itself is incomplete and
hence undecidable.
Note that there is a second kind of “missing” values which are produced by numerical com-
putation, the so-called Not a Number, NaN, values. Examples are
> 0/0
or
Chapter 2: Simple manipulations; numbers and vectors 10

> Inf - Inf

which both give NaN since the result cannot be defined sensibly.
In summary, is.na(xx) is TRUE both for NA and NaN values. To differentiate these,
is.nan(xx) is only TRUE for NaNs.
Missing values are sometimes printed as <NA>, when character vectors are printed without
quotes.

2.6 Character vectors

Character quantities and character vectors are used frequently in R, for example as plot labels.
Where needed they are denoted by a sequence of characters delimited by the double quote
character, e.g., "x-values", "New iteration results".
Character strings are entered using either double (") or single (’) quotes, but are printed
using double quotes (or sometimes without quotes). They use C-style escape sequences, using \
as the escape character, so \\ is entered and printed as \\, and inside double quotes " is entered
as \". Other useful escape sequences are \n, newline, \t, tab and \b, backspace.
Character vectors may be concatenated into a vector by the c() function; examples of their
use will emerge frequently.
The paste() function takes an arbitrary number of arguments and concatenates them one by
one into character strings. Any numbers given among the arguments are coerced into character
strings in the evident way, that is, in the same way they would be if they were printed. The
arguments are by default separated in the result by a single blank character, but this can be
changed by the named parameter, sep=string , which changes it to string , possibly empty.
For example
> labs <- paste(c("X","Y"), 1:10, sep="")
makes labs into the character vector
c("X1", "Y2", "X3", "Y4", "X5", "Y6", "X7", "Y8", "X9", "Y10")
Note particularly that recycling of short lists takes place here too; thus c("X", "Y") is
repeated 5 times to match the sequence 1:10.3

2.7 Index vectors; selecting and modifying subsets of a data set

Subsets of the elements of a vector may be selected by appending to the name of the vector an
index vector in square brackets. More generally any expression that evaluates to a vector may
have subsets of its elements similarly selected by appending an index vector in square brackets
immediately after the expression.
Such index vectors can be any of four distinct types.
1. A logical vector. In this case the index vector must be of the same length as the vector
from which elements are to be selected. Values corresponding to TRUE in the index vector
are selected and those corresponding to FALSE are omitted. For example
> y <- x[!is.na(x)]
creates (or re-creates) an object y which will contain the non-missing values of x, in the
same order. Note that if x has missing values, y will be shorter than x. Also
> (x+1)[(!is.na(x)) & x>0] -> z
creates an object z and places in it the values of the vector x+1 for which the corresponding
value in x was both non-missing and positive.
3
paste(..., collapse=ss ) joins the arguments into a single character string putting ss in between. There are
more tools for character manipulation, see the help for sub and substring.
Chapter 2: Simple manipulations; numbers and vectors 11

2. A vector of positive integral quantities. In this case the values in the index vector must lie
in the set {1, 2, . . . , length(x)}. The corresponding elements of the vector are selected
and concatenated, in that order, in the result. The index vector can be of any length and the
result is of the same length as the index vector. For example x[6] is the sixth component
of x and
> x[1:10]
selects the first 10 elements of x (assuming length(x) is not less than 10). Also
> c("x","y")[rep(c(1,2,2,1), times=4)]
(an admittedly unlikely thing to do) produces a character vector of length 16 consisting of
"x", "y", "y", "x" repeated four times.
3. A vector of negative integral quantities. Such an index vector specifies the values to be
excluded rather than included. Thus
> y <- x[-(1:5)]
gives y all but the first five elements of x.
4. A vector of character strings. This possibility only applies where an object has a names
attribute to identify its components. In this case a sub-vector of the names vector may be
used in the same way as the positive integral labels in item 2 further above.
> fruit <- c(5, 10, 1, 20)
> names(fruit) <- c("orange", "banana", "apple", "peach")
> lunch <- fruit[c("apple","orange")]
The advantage is that alphanumeric names are often easier to remember than numeric
indices. This option is particularly useful in connection with data frames, as we shall see
later.
An indexed expression can also appear on the receiving end of an assignment, in which case
the assignment operation is performed only on those elements of the vector. The expression
must be of the form vector[index_vector ] as having an arbitrary expression in place of the
vector name does not make much sense here.
The vector assigned must match the length of the index vector, and in the case of a logical
index vector it must again be the same length as the vector it is indexing.
For example
> x[is.na(x)] <- 0
replaces any missing values in x by zeros and
> y[y < 0] <- -y[y < 0]
has the same effect as
> y <- abs(y)

2.8 Other types of objects

Vectors are the most important type of object in R, but there are several others which we will
meet more formally in later sections.
• matrices or more generally arrays are multi-dimensional generalizations of vectors. In fact,
they are vectors that can be indexed by two or more indices and will be printed in special
ways. See Chapter 5 [Arrays and matrices], page 18.
• factors provide compact ways to handle categorical data. See Chapter 4 [Factors], page 16.
• lists are a general form of vector in which the various elements need not be of the same
type, and are often themselves vectors or lists. Lists provide a convenient way to return the
results of a statistical computation. See Section 6.1 [Lists], page 26.
Chapter 2: Simple manipulations; numbers and vectors 12

• data frames are matrix-like structures, in which the columns can be of different types. Think
of data frames as ‘data matrices’ with one row per observational unit but with (possibly)
both numerical and categorical variables. Many experiments are best described by data
frames: the treatments are categorical but the response is numeric. See Section 6.3 [Data
frames], page 27.
• functions are themselves objects in R which can be stored in the project’s workspace. This
provides a simple and convenient way to extend R. See Chapter 10 [Writing your own
functions], page 42.
Chapter 3: Objects, their modes and attributes 13

3 Objects, their modes and attributes

3.1 Intrinsic attributes: mode and length

The entities R operates on are technically known as objects. Examples are vectors of numeric
(real) or complex values, vectors of logical values and vectors of character strings. These are
known as “atomic” structures since their components are all of the same type, or mode, namely
numeric 1 , complex, logical, character and raw.
Vectors must have their values all of the same mode. Thus any given vector must be un-
ambiguously either logical, numeric, complex, character or raw. (The only apparent exception
to this rule is the special “value” listed as NA for quantities not available, but in fact there are
several types of NA). Note that a vector can be empty and still have a mode. For example
the empty character string vector is listed as character(0) and the empty numeric vector as
numeric(0).
R also operates on objects called lists, which are of mode list. These are ordered sequences
of objects which individually can be of any mode. lists are known as “recursive” rather than
atomic structures since their components can themselves be lists in their own right.
The other recursive structures are those of mode function and expression. Functions are
the objects that form part of the R system along with similar user written functions, which we
discuss in some detail later. Expressions as objects form an advanced part of R which will not
be discussed in this guide, except indirectly when we discuss formulae used with modeling in R.
By the mode of an object we mean the basic type of its fundamental constituents. This is a
special case of a “property” of an object. Another property of every object is its length. The
functions mode(object ) and length(object ) can be used to find out the mode and length of
any defined structure2 .
Further properties of an object are usually provided by attributes(object ), see Section 3.3
[Getting and setting attributes], page 14. Because of this, mode and length are also called
“intrinsic attributes” of an object.
For example, if z is a complex vector of length 100, then in an expression mode(z) is the
character string "complex" and length(z) is 100.
R caters for changes of mode almost anywhere it could be considered sensible to do so, (and
a few where it might not be). For example with
> z <- 0:9
we could put
> digits <- as.character(z)
after which digits is the character vector c("0", "1", "2", ..., "9"). A further coercion, or
change of mode, reconstructs the numerical vector again:
> d <- as.integer(digits)
Now d and z are the same.3 There is a large collection of functions of the form as.something ()
for either coercion from one mode to another, or for investing an object with some other attribute
it may not already possess. The reader should consult the different help files to become familiar
with them.
1
numeric mode is actually an amalgam of two distinct modes, namely integer and double precision, as explained
in the manual.
2
Note however that length(object ) does not always contain intrinsic useful information, e.g., when object
is a function.
3
In general, coercion from numeric to character and back again will not be exactly reversible, because of
roundoff errors in the character representation.
Chapter 3: Objects, their modes and attributes 14

3.2 Changing the length of an object

An “empty” object may still have a mode. For example
> e <- numeric()
makes e an empty vector structure of mode numeric. Similarly character() is a empty character
vector, and so on. Once an object of any size has been created, new components may be added
to it simply by giving it an index value outside its previous range. Thus
> e[3] <- 17
now makes e a vector of length 3, (the first two components of which are at this point both NA).
This applies to any structure at all, provided the mode of the additional component(s) agrees
with the mode of the object in the first place.
This automatic adjustment of lengths of an object is used often, for example in the scan()
function for input. (see Section 7.2 [The scan() function], page 31.)
Conversely to truncate the size of an object requires only an assignment to do so. Hence if
alpha is an object of length 10, then
> alpha <- alpha[2 * 1:5]
makes it an object of length 5 consisting of just the former components with even index. (The
old indices are not retained, of course.) We can then retain just the first three values by
> length(alpha) <- 3
and vectors can be extended (by missing values) in the same way.

3.3 Getting and setting attributes

The function attributes(object ) returns a list of all the non-intrinsic attributes currently
defined for that object. The function attr(object, name ) can be used to select a specific
attribute. These functions are rarely used, except in rather special circumstances when some
new attribute is being created for some particular purpose, for example to associate a creation
date or an operator with an R object. The concept, however, is very important.
Some care should be exercised when assigning or deleting attributes since they are an integral
part of the object system used in R.
When it is used on the left hand side of an assignment it can be used either to associate a
new attribute with object or to change an existing one. For example
> attr(z, "dim") <- c(10,10)
allows R to treat z as if it were a 10-by-10 matrix.

3.4 The class of an object

All objects in R have a class, reported by the function class. For simple vectors this is just the
mode, for example "numeric", "logical", "character" or "list", but "matrix", "array",
"factor" and "data.frame" are other possible values.
A special attribute known as the class of the object is used to allow for an object-oriented
style4 of programming in R. For example if an object has class "data.frame", it will be printed
in a certain way, the plot() function will display it graphically in a certain way, and other
so-called generic functions such as summary() will react to it as an argument in a way sensitive
to its class.
To remove temporarily the effects of class, use the function unclass(). For example if winter
has the class "data.frame" then
4
A different style using ‘formal’ or ‘S4’ classes is provided in package methods.
Chapter 3: Objects, their modes and attributes 15

> winter
will print it in data frame form, which is rather like a matrix, whereas
> unclass(winter)
will print it as an ordinary list. Only in rather special situations do you need to use this facility,
but one is when you are learning to come to terms with the idea of class and generic functions.
Generic functions and classes will be discussed further in Section 10.9 [Object orientation],
page 48, but only briefly.
Chapter 4: Ordered and unordered factors 16

4 Ordered and unordered factors

A factor is a vector object used to specify a discrete classification (grouping) of the components
of other vectors of the same length. R provides both ordered and unordered factors. While the
“real” application of factors is with model formulae (see Section 11.1.1 [Contrasts], page 52), we
here look at a specific example.

4.1 A specific example

Suppose, for example, we have a sample of 30 tax accountants from all the states and territories
of Australia1 and their individual state of origin is specified by a character vector of state
mnemonics as
> state <- c("tas", "sa", "qld", "nsw", "nsw", "nt", "wa", "wa",
"qld", "vic", "nsw", "vic", "qld", "qld", "sa", "tas",
"sa", "nt", "wa", "vic", "qld", "nsw", "nsw", "wa",
"sa", "act", "nsw", "vic", "vic", "act")
Notice that in the case of a character vector, “sorted” means sorted in alphabetical order.
A factor is similarly created using the factor() function:
> statef <- factor(state)
The print() function handles factors slightly differently from other objects:
> statef
[1] tas sa qld nsw nsw nt wa wa qld vic nsw vic qld qld sa
[16] tas sa nt wa vic qld nsw nsw wa sa act nsw vic vic act
Levels: act nsw nt qld sa tas vic wa
To find out the levels of a factor the function levels() can be used.
> levels(statef)
[1] "act" "nsw" "nt" "qld" "sa" "tas" "vic" "wa"

4.2 The function tapply() and ragged arrays

To continue the previous example, suppose we have the incomes of the same tax accountants in
another vector (in suitably large units of money)
> incomes <- c(60, 49, 40, 61, 64, 60, 59, 54, 62, 69, 70, 42, 56,
61, 61, 61, 58, 51, 48, 65, 49, 49, 41, 48, 52, 46,
59, 46, 58, 43)
To calculate the sample mean income for each state we can now use the special function
tapply():
> incmeans <- tapply(incomes, statef, mean)
giving a means vector with the components labelled by the levels
act nsw nt qld sa tas vic wa
44.500 57.333 55.500 53.600 55.000 60.500 56.000 52.250
The function tapply() is used to apply a function, here mean(), to each group of components
of the first argument, here incomes, defined by the levels of the second component, here statef2 ,
1
Readers should note that there are eight states and territories in Australia, namely the Australian Capital
Territory, New South Wales, the Northern Territory, Queensland, South Australia, Tasmania, Victoria and
Western Australia.
2
Note that tapply() also works in this case when its second argument is not a factor, e.g., ‘tapply(incomes,
state)’, and this is true for quite a few other functions, since arguments are coerced to factors when necessary
(using as.factor()).
Chapter 4: Ordered and unordered factors 17

as if they were separate vector structures. The result is a structure of the same length as the
levels attribute of the factor containing the results. The reader should consult the help document
for more details.
Suppose further we needed to calculate the standard errors of the state income means. To do
this we need to write an R function to calculate the standard error for any given vector. Since
there is an builtin function var() to calculate the sample variance, such a function is a very
simple one liner, specified by the assignment:
> stderr <- function(x) sqrt(var(x)/length(x))
(Writing functions will be considered later in Chapter 10 [Writing your own functions], page 42,
and in this case was unnecessary as R also has a builtin function sd().) After this assignment,
the standard errors are calculated by
> incster <- tapply(incomes, statef, stderr)
and the values calculated are then
> incster
act nsw nt qld sa tas vic wa
1.5 4.3102 4.5 4.1061 2.7386 0.5 5.244 2.6575
As an exercise you may care to find the usual 95% confidence limits for the state mean
incomes. To do this you could use tapply() once more with the length() function to find
the sample sizes, and the qt() function to find the percentage points of the appropriate t-
distributions. (You could also investigate R’s facilities for t-tests.)
The function tapply() can also be used to handle more complicated indexing of a vector
by multiple categories. For example, we might wish to split the tax accountants by both state
and sex. However in this simple instance (just one factor) what happens can be thought of as
follows. The values in the vector are collected into groups corresponding to the distinct entries
in the factor. The function is then applied to each of these groups individually. The value is a
vector of function results, labelled by the levels attribute of the factor.
The combination of a vector and a labelling factor is an example of what is sometimes called
a ragged array, since the subclass sizes are possibly irregular. When the subclass sizes are all
the same the indexing may be done implicitly and much more efficiently, as we see in the next
section.

4.3 Ordered factors

The levels of factors are stored in alphabetical order, or in the order they were specified to
factor if they were specified explicitly.
Sometimes the levels will have a natural ordering that we want to record and want our
statistical analysis to make use of. The ordered() function creates such ordered factors but
is otherwise identical to factor. For most purposes the only difference between ordered and
unordered factors is that the former are printed showing the ordering of the levels, but the
contrasts generated for them in fitting linear models are different.
Chapter 5: Arrays and matrices 18

5 Arrays and matrices

5.1 Arrays
An array can be considered as a multiply subscripted collection of data entries, for example
numeric. R allows simple facilities for creating and handling arrays, and in particular the
special case of matrices.
A dimension vector is a vector of non-negative integers. If its length is k then the array is
k-dimensional, e.g. a matrix is a 2-dimensional array. The dimensions are indexed from one up
to the values given in the dimension vector.
A vector can be used by R as an array only if it has a dimension vector as its dim attribute.
Suppose, for example, z is a vector of 1500 elements. The assignment
> dim(z) <- c(3,5,100)
gives it the dim attribute that allows it to be treated as a 3 by 5 by 100 array.
Other functions such as matrix() and array() are available for simpler and more natural
looking assignments, as we shall see in Section 5.4 [The array() function], page 20.
The values in the data vector give the values in the array in the same order as they would
occur in FORTRAN, that is “column major order,” with the first subscript moving fastest and
the last subscript slowest.
For example if the dimension vector for an array, say a, is c(3,4,2) then there are 3 × 4 ×
2 = 24 entries in a and the data vector holds them in the order a[1,1,1], a[2,1,1], ...,
a[2,4,2], a[3,4,2].
Arrays can be one-dimensional: such arrays are usually treated in the same way as vectors
(including when printing), but the exceptions can cause confusion.

5.2 Array indexing. Subsections of an array

Individual elements of an array may be referenced by giving the name of the array followed by
the subscripts in square brackets, separated by commas.
More generally, subsections of an array may be specified by giving a sequence of index vectors
in place of subscripts; however if any index position is given an empty index vector, then the full
range of that subscript is taken.
Continuing the previous example, a[2,,] is a 4 × 2 array with dimension vector c(4,2) and
data vector containing the values
c(a[2,1,1], a[2,2,1], a[2,3,1], a[2,4,1],
a[2,1,2], a[2,2,2], a[2,3,2], a[2,4,2])
in that order. a[,,] stands for the entire array, which is the same as omitting the subscripts
entirely and using a alone.
For any array, say Z, the dimension vector may be referenced explicitly as dim(Z) (on either
side of an assignment).
Also, if an array name is given with just one subscript or index vector, then the corresponding
values of the data vector only are used; in this case the dimension vector is ignored. This is not
the case, however, if the single index is not a vector but itself an array, as we next discuss.
Chapter 5: Arrays and matrices 19

5.3 Index matrices

As well as an index vector in any subscript position, a matrix may be used with a single index
matrix in order either to assign a vector of quantities to an irregular collection of elements in
the array, or to extract an irregular collection as a vector.
A matrix example makes the process clear. In the case of a doubly indexed array, an index
matrix may be given consisting of two columns and as many rows as desired. The entries in the
index matrix are the row and column indices for the doubly indexed array. Suppose for example
we have a 4 by 5 array X and we wish to do the following:
• Extract elements X[1,3], X[2,2] and X[3,1] as a vector structure, and
• Replace these entries in the array X by zeroes.
In this case we need a 3 by 2 subscript array, as in the following example.
> x <- array(1:20, dim=c(4,5)) # Generate a 4 by 5 array.
> x
[,1] [,2] [,3] [,4] [,5]
[1,] 1 5 9 13 17
[2,] 2 6 10 14 18
[3,] 3 7 11 15 19
[4,] 4 8 12 16 20
> i <- array(c(1:3,3:1), dim=c(3,2))
> i # i is a 3 by 2 index array.
[,1] [,2]
[1,] 1 3
[2,] 2 2
[3,] 3 1
> x[i] # Extract those elements
[1] 9 6 3
> x[i] <- 0 # Replace those elements by zeros.
> x
[,1] [,2] [,3] [,4] [,5]
[1,] 1 5 0 13 17
[2,] 2 0 10 14 18
[3,] 0 7 11 15 19
[4,] 4 8 12 16 20
>
Negative indices are not allowed in index matrices. NA and zero values are allowed: rows in the
index matrix containing a zero are ignored, and rows containing an NA produce an NA in the
result.
As a less trivial example, suppose we wish to generate an (unreduced) design matrix for a
block design defined by factors blocks (b levels) and varieties (v levels). Further suppose
there are n plots in the experiment. We could proceed as follows:
> Xb <- matrix(0, n, b)
> Xv <- matrix(0, n, v)
> ib <- cbind(1:n, blocks)
> iv <- cbind(1:n, varieties)
> Xb[ib] <- 1
> Xv[iv] <- 1
> X <- cbind(Xb, Xv)
To construct the incidence matrix, N say, we could use
> N <- crossprod(Xb, Xv)
Chapter 5: Arrays and matrices 20

However a simpler direct way of producing this matrix is to use table():

> N <- table(blocks, varieties)
Index matrices must be numerical: any other form of matrix (e.g. a logical or character
matrix) supplied as a matrix is treated as an indexing vector.

5.4 The array() function

As well as giving a vector structure a dim attribute, arrays can be constructed from vectors by
the array function, which has the form
> Z <- array(data_vector, dim_vector )
For example, if the vector h contains 24 or fewer, numbers then the command
> Z <- array(h, dim=c(3,4,2))
would use h to set up 3 by 4 by 2 array in Z. If the size of h is exactly 24 the result is the same
as
> dim(Z) <- c(3,4,2)
However if h is shorter than 24, its values are recycled from the beginning again to make
it up to size 24 (see Section 5.4.1 [The recycling rule], page 20). As an extreme but common
example
> Z <- array(0, c(3,4,2))
makes Z an array of all zeros.
At this point dim(Z) stands for the dimension vector c(3,4,2), and Z[1:24] stands for the
data vector as it was in h, and Z[] with an empty subscript or Z with no subscript stands for
the entire array as an array.
Arrays may be used in arithmetic expressions and the result is an array formed by element-
by-element operations on the data vector. The dim attributes of operands generally need to be
the same, and this becomes the dimension vector of the result. So if A, B and C are all similar
arrays, then
> D <- 2*A*B + C + 1
makes D a similar array with its data vector being the result of the given element-by-element
operations. However the precise rule concerning mixed array and vector calculations has to be
considered a little more carefully.

5.4.1 Mixed vector and array arithmetic. The recycling rule

The precise rule affecting element by element mixed calculations with vectors and arrays is
somewhat quirky and hard to find in the references. From experience we have found the following
to be a reliable guide.
• The expression is scanned from left to right.
• Any short vector operands are extended by recycling their values until they match the size
of any other operands.
• As long as short vectors and arrays only are encountered, the arrays must all have the same
dim attribute or an error results.
• Any vector operand longer than a matrix or array operand generates an error.
• If array structures are present and no error or coercion to vector has been precipitated, the
result is an array structure with the common dim attribute of its array operands.
Chapter 5: Arrays and matrices 21

5.5 The outer product of two arrays

An important operation on arrays is the outer product. If a and b are two numeric arrays,
their outer product is an array whose dimension vector is obtained by concatenating their two
dimension vectors (order is important), and whose data vector is got by forming all possible
products of elements of the data vector of a with those of b. The outer product is formed by
the special operator %o%:
> ab <- a %o% b
An alternative is
> ab <- outer(a, b, "*")
The multiplication function can be replaced by an arbitrary function of two variables. For
example if we wished to evaluate the function f (x; y) = cos(y)/(1 + x2 ) over a regular grid of
values with x- and y-coordinates defined by the R vectors x and y respectively, we could proceed
as follows:
> f <- function(x, y) cos(y)/(1 + x^2)
> z <- outer(x, y, f)
In particular the outer product of two ordinary vectors is a doubly subscripted array (that
is a matrix, of rank at most 1). Notice that the outer product operator is of course non-
commutative. Defining your own R functions will be considered further in Chapter 10 [Writing
your own functions], page 42.

An example: Determinants of 2 by 2 single-digit matrices

As an artificial but cute example, consider the determinants of 2 by 2 matrices [a, b; c, d] where
each entry is a non-negative integer in the range 0, 1, . . . , 9, that is a digit.
The problem is to find the determinants, ad − bc, of all possible matrices of this form and
represent the frequency with which each value occurs as a high density plot. This amounts to
finding the probability distribution of the determinant if each digit is chosen independently and
uniformly at random.
A neat way of doing this uses the outer() function twice:
> d <- outer(0:9, 0:9)
> fr <- table(outer(d, d, "-"))
> plot(as.numeric(names(fr)), fr, type="h",
xlab="Determinant", ylab="Frequency")
Notice the coercion of the names attribute of the frequency table to numeric in order to
recover the range of the determinant values. The “obvious” way of doing this problem with for
loops, to be discussed in Chapter 9 [Loops and conditional execution], page 40, is so inefficient
as to be impractical.
It is also perhaps surprising that about 1 in 20 such matrices is singular.

5.6 Generalized transpose of an array

The function aperm(a, perm) may be used to permute an array, a. The argument perm must be
a permutation of the integers {1, . . . , k}, where k is the number of subscripts in a. The result of
the function is an array of the same size as a but with old dimension given by perm[j] becoming
the new j-th dimension. The easiest way to think of this operation is as a generalization of
transposition for matrices. Indeed if A is a matrix, (that is, a doubly subscripted array) then B
given by
> B <- aperm(A, c(2,1))
is just the transpose of A. For this special case a simpler function t() is available, so we could
have used B <- t(A).
Chapter 5: Arrays and matrices 22

5.7 Matrix facilities

As noted above, a matrix is just an array with two subscripts. However it is such an important
special case it needs a separate discussion. R contains many operators and functions that are
available only for matrices. For example t(X) is the matrix transpose function, as noted above.
The functions nrow(A) and ncol(A) give the number of rows and columns in the matrix A
respectively.

5.7.1 Matrix multiplication

The operator %*% is used for matrix multiplication. An n by 1 or 1 by n matrix may of course
be used as an n-vector if in the context such is appropriate. Conversely, vectors which occur in
matrix multiplication expressions are automatically promoted either to row or column vectors,
whichever is multiplicatively coherent, if possible, (although this is not always unambiguously
possible, as we see later).
If, for example, A and B are square matrices of the same size, then
> A * B
is the matrix of element by element products and
> A %*% B
is the matrix product. If x is a vector, then
> x %*% A %*% x
is a quadratic form.1
The function crossprod() forms “crossproducts”, meaning that crossprod(X, y) is the
same as t(X) %*% y but the operation is more efficient. If the second argument to crossprod()
is omitted it is taken to be the same as the first.
The meaning of diag() depends on its argument. diag(v), where v is a vector, gives a
diagonal matrix with elements of the vector as the diagonal entries. On the other hand diag(M),
where M is a matrix, gives the vector of main diagonal entries of M. This is the same convention
as that used for diag() in Matlab. Also, somewhat confusingly, if k is a single numeric value
then diag(k) is the k by k identity matrix!

5.7.2 Linear equations and inversion

Solving linear equations is the inverse of matrix multiplication. When after
> b <- A %*% x
only A and b are given, the vector x is the solution of that linear equation system. In R,
> solve(A,b)
solves the system, returning x (up to some accuracy loss). Note that in linear algebra, formally
x = A−1 b where A−1 denotes the inverse of A, which can be computed by
solve(A)
but rarely is needed. Numerically, it is both inefficient and potentially unstable to compute x
<- solve(A) %*% b instead of solve(A,b).
The quadratic form x0 A−1 x which is used in multivariate computations, should be computed
by something like2 x %*% solve(A,x), rather than computing the inverse of A.
1
Note that x %*% x is ambiguous, as it could mean either x0 x or xx0 , where x is the column form. In such
cases the smaller matrix seems implicitly to be the interpretation adopted, so the scalar x0 x is in this case
the result. The matrix xx0 may be calculated either by cbind(x) %*% x or x %*% rbind(x) since the result of
rbind() or cbind() is always a matrix. However, the best way to compute x0 x or xx0 is crossprod(x) or x
%o% x respectively.
2
Even better would be to form a matrix square root B with A = BB 0 and find the squared length of the
solution of By = x, perhaps using the Cholesky or eigendecomposition of A.
Chapter 5: Arrays and matrices 23

5.7.3 Eigenvalues and eigenvectors

The function eigen(Sm) calculates the eigenvalues and eigenvectors of a symmetric matrix
Sm. The result of this function is a list of two components named values and vectors. The
assignment
> ev <- eigen(Sm)
will assign this list to ev. Then ev$val is the vector of eigenvalues of Sm and ev$vec is the
matrix of corresponding eigenvectors. Had we only needed the eigenvalues we could have used
the assignment:
> evals <- eigen(Sm)$values
evals now holds the vector of eigenvalues and the second component is discarded. If the
expression
> eigen(Sm)
is used by itself as a command the two components are printed, with their names. For large
matrices it is better to avoid computing the eigenvectors if they are not needed by using the
expression
> evals <- eigen(Sm, only.values = TRUE)$values

5.7.4 Singular value decomposition and determinants

The function svd(M) takes an arbitrary matrix argument, M, and calculates the singular value
decomposition of M. This consists of a matrix of orthonormal columns U with the same column
space as M, a second matrix of orthonormal columns V whose column space is the row space
of M and a diagonal matrix of positive entries D such that M = U %*% D %*% t(V). D is actually
returned as a vector of the diagonal elements. The result of svd(M) is actually a list of three
components named d, u and v, with evident meanings.
If M is in fact square, then, it is not hard to see that
> absdetM <- prod(svd(M)$d)
calculates the absolute value of the determinant of M. If this calculation were needed often with
a variety of matrices it could be defined as an R function
> absdet <- function(M) prod(svd(M)$d)
after which we could use absdet() as just another R function. As a further trivial but potentially
useful example, you might like to consider writing a function, say tr(), to calculate the trace
of a square matrix. [Hint: You will not need to use an explicit loop. Look again at the diag()
function.]
R has a builtin function det to calculate a determinant, including the sign, and another,
determinant, to give the sign and modulus (optionally on log scale),

5.7.5 Least squares fitting and the QR decomposition

The function lsfit() returns a list giving results of a least squares fitting procedure. An
assignment such as
> ans <- lsfit(X, y)
gives the results of a least squares fit where y is the vector of observations and X is the design
matrix. See the help facility for more details, and also for the follow-up function ls.diag() for,
among other things, regression diagnostics. Note that a grand mean term is automatically in-
cluded and need not be included explicitly as a column of X. Further note that you almost always
will prefer using lm(.) (see Section 11.2 [Linear models], page 53) to lsfit() for regression
modelling.
Another closely related function is qr() and its allies. Consider the following assignments
Chapter 5: Arrays and matrices 24

> Xplus <- qr(X)

> b <- qr.coef(Xplus, y)
> fit <- qr.fitted(Xplus, y)
> res <- qr.resid(Xplus, y)
These compute the orthogonal projection of y onto the range of X in fit, the projection onto
the orthogonal complement in res and the coefficient vector for the projection in b, that is, b is
essentially the result of the Matlab ‘backslash’ operator.
It is not assumed that X has full column rank. Redundancies will be discovered and removed
as they are found.
This alternative is the older, low-level way to perform least squares calculations. Although
still useful in some contexts, it would now generally be replaced by the statistical models features,
as will be discussed in Chapter 11 [Statistical models in R], page 50.

5.8 Forming partitioned matrices, cbind() and rbind()

As we have already seen informally, matrices can be built up from other vectors and matrices
by the functions cbind() and rbind(). Roughly cbind() forms matrices by binding together
matrices horizontally, or column-wise, and rbind() vertically, or row-wise.
In the assignment
> X <- cbind(arg_1, arg_2, arg_3, ...)
the arguments to cbind() must be either vectors of any length, or matrices with the same
column size, that is the same number of rows. The result is a matrix with the concatenated
arguments arg 1, arg 2, . . . forming the columns.
If some of the arguments to cbind() are vectors they may be shorter than the column size
of any matrices present, in which case they are cyclically extended to match the matrix column
size (or the length of the longest vector if no matrices are given).
The function rbind() does the corresponding operation for rows. In this case any vector
argument, possibly cyclically extended, are of course taken as row vectors.
Suppose X1 and X2 have the same number of rows. To combine these by columns into a
matrix X, together with an initial column of 1s we can use
> X <- cbind(1, X1, X2)
The result of rbind() or cbind() always has matrix status. Hence cbind(x) and rbind(x)
are possibly the simplest ways explicitly to allow the vector x to be treated as a column or row
matrix respectively.

5.9 The concatenation function, c(), with arrays

It should be noted that whereas cbind() and rbind() are concatenation functions that respect
dim attributes, the basic c() function does not, but rather clears numeric objects of all dim and
dimnames attributes. This is occasionally useful in its own right.
The official way to coerce an array back to a simple vector object is to use as.vector()
> vec <- as.vector(X)
However a similar result can be achieved by using c() with just one argument, simply for
this side-effect:
> vec <- c(X)
There are slight differences between the two, but ultimately the choice between them is
largely a matter of style (with the former being preferable).
Chapter 5: Arrays and matrices 25

5.10 Frequency tables from factors

Recall that a factor defines a partition into groups. Similarly a pair of factors defines a two
way cross classification, and so on. The function table() allows frequency tables to be calcu-
lated from equal length factors. If there are k factor arguments, the result is a k-way array of
frequencies.
Suppose, for example, that statef is a factor giving the state code for each entry in a data
vector. The assignment
> statefr <- table(statef)
gives in statefr a table of frequencies of each state in the sample. The frequencies are ordered
and labelled by the levels attribute of the factor. This simple case is equivalent to, but more
convenient than,
> statefr <- tapply(statef, statef, length)
Further suppose that incomef is a factor giving a suitably defined “income class” for each
entry in the data vector, for example with the cut() function:
> factor(cut(incomes, breaks = 35+10*(0:7))) -> incomef
Then to calculate a two-way table of frequencies:
> table(incomef,statef)
statef
incomef act nsw nt qld sa tas vic wa
(35,45] 1 1 0 1 0 0 1 0
(45,55] 1 1 1 1 2 0 1 3
(55,65] 0 3 1 3 2 2 2 1
(65,75] 0 1 0 0 0 0 1 0
Extension to higher-way frequency tables is immediate.
Chapter 6: Lists and data frames 26

6 Lists and data frames

6.1 Lists
An R list is an object consisting of an ordered collection of objects known as its components.
There is no particular need for the components to be of the same mode or type, and, for
example, a list could consist of a numeric vector, a logical value, a matrix, a complex vector, a
character array, a function, and so on. Here is a simple example of how to make a list:
> Lst <- list(name="Fred", wife="Mary", no.children=3,
child.ages=c(4,7,9))
Components are always numbered and may always be referred to as such. Thus if Lst is
the name of a list with four components, these may be individually referred to as Lst[[1]],
Lst[[2]], Lst[[3]] and Lst[[4]]. If, further, Lst[[4]] is a vector subscripted array then
Lst[[4]][1] is its first entry.
If Lst is a list, then the function length(Lst) gives the number of (top level) components
it has.
Components of lists may also be named, and in this case the component may be referred to
either by giving the component name as a character string in place of the number in double
square brackets, or, more conveniently, by giving an expression of the form
> name $component_name
for the same thing.
This is a very useful convention as it makes it easier to get the right component if you forget
the number.
So in the simple example given above:
Lst$name is the same as Lst[[1]] and is the string "Fred",
Lst$wife is the same as Lst[[2]] and is the string "Mary",
Lst$child.ages[1] is the same as Lst[[4]][1] and is the number 4.
Additionally, one can also use the names of the list components in double square brackets,
i.e., Lst[["name"]] is the same as Lst$name. This is especially useful, when the name of the
component to be extracted is stored in another variable as in
> x <- "name"; Lst[[x]]
It is very important to distinguish Lst[[1]] from Lst[1]. ‘[[...]]’ is the operator used
to select a single element, whereas ‘[...]’ is a general subscripting operator. Thus the former
is the first object in the list Lst, and if it is a named list the name is not included. The latter
is a sublist of the list Lst consisting of the first entry only. If it is a named list, the names are
transferred to the sublist.
The names of components may be abbreviated down to the minimum number of letters needed
to identify them uniquely. Thus Lst$coefficients may be minimally specified as Lst$coe and
Lst$covariance as Lst$cov.
The vector of names is in fact simply an attribute of the list like any other and may be handled
as such. Other structures besides lists may, of course, similarly be given a names attribute also.

6.2 Constructing and modifying lists

New lists may be formed from existing objects by the function list(). An assignment of the
form
Chapter 6: Lists and data frames 27

> Lst <- list(name_1 =object_1, ..., name_m =object_m )

sets up a list Lst of m components using object 1, . . . , object m for the components and giving
them names as specified by the argument names, (which can be freely chosen). If these names
are omitted, the components are numbered only. The components used to form the list are
copied when forming the new list and the originals are not affected.
Lists, like any subscripted object, can be extended by specifying additional components. For
example
> Lst[5] <- list(matrix=Mat)

6.2.1 Concatenating lists

When the concatenation function c() is given list arguments, the result is an object of mode
list also, whose components are those of the argument lists joined together in sequence.
> list.ABC <- c(list.A, list.B, list.C)
Recall that with vector objects as arguments the concatenation function similarly joined
together all arguments into a single vector structure. In this case all other attributes, such as
dim attributes, are discarded.

6.3 Data frames

A data frame is a list with class "data.frame". There are restrictions on lists that may be made
into data frames, namely
• The components must be vectors (numeric, character, or logical), factors, numeric matrices,
lists, or other data frames.
• Matrices, lists, and data frames provide as many variables to the new data frame as they
have columns, elements, or variables, respectively.
• Numeric vectors, logicals and factors are included as is, and character vectors are coerced
to be factors, whose levels are the unique values appearing in the vector.
• Vector structures appearing as variables of the data frame must all have the same length,
and matrix structures must all have the same row size.
A data frame may for many purposes be regarded as a matrix with columns possibly of
differing modes and attributes. It may be displayed in matrix form, and its rows and columns
extracted using matrix indexing conventions.

6.3.1 Making data frames

Objects satisfying the restrictions placed on the columns (components) of a data frame may be
used to form one using the function data.frame:
> accountants <- data.frame(home=statef, loot=incomes, shot=incomef)
A list whose components conform to the restrictions of a data frame may be coerced into a
data frame using the function as.data.frame()
The simplest way to construct a data frame from scratch is to use the read.table() function
to read an entire data frame from an external file. This is discussed further in Chapter 7 [Reading
data from files], page 30.

6.3.2 attach() and detach()

The $ notation, such as accountants$statef, for list components is not always very convenient.
A useful facility would be somehow to make the components of a list or data frame temporarily
visible as variables under their component name, without the need to quote the list name
explicitly each time.
Chapter 6: Lists and data frames 28

The attach() function takes a ‘database’ such as a list or data frame as its argument. Thus
suppose lentils is a data frame with three variables lentils$u, lentils$v, lentils$w. The
attach
> attach(lentils)
places the data frame in the search path at position 2, and provided there are no variables u, v
or w in position 1, u, v and w are available as variables from the data frame in their own right.
At this point an assignment such as
> u <- v+w
does not replace the component u of the data frame, but rather masks it with another variable
u in the working directory at position 1 on the search path. To make a permanent change to
the data frame itself, the simplest way is to resort once again to the $ notation:
> lentils$u <- v+w
However the new value of component u is not visible until the data frame is detached and
attached again.
To detach a data frame, use the function
> detach()
More precisely, this statement detaches from the search path the entity currently at
position 2. Thus in the present context the variables u, v and w would be no longer visible,
except under the list notation as lentils$u and so on. Entities at positions greater than 2
on the search path can be detached by giving their number to detach, but it is much safer to
always use a name, for example by detach(lentils) or detach("lentils")
Note: In R lists and data frames can only be attached at position 2 or above, and
what is attached is a copy of the original object. You can alter the attached values
via assign, but the original list or data frame is unchanged.

6.3.3 Working with data frames

A useful convention that allows you to work with many different problems comfortably together
in the same working directory is
• gather together all variables for any well defined and separate problem in a data frame
under a suitably informative name;
• when working with a problem attach the appropriate data frame at position 2, and use the
working directory at level 1 for operational quantities and temporary variables;
• before leaving a problem, add any variables you wish to keep for future reference to the
data frame using the $ form of assignment, and then detach();
• finally remove all unwanted variables from the working directory and keep it as clean of
left-over temporary variables as possible.
In this way it is quite simple to work with many problems in the same directory, all of which
have variables named x, y and z, for example.

6.3.4 Attaching arbitrary lists

attach() is a generic function that allows not only directories and data frames to be attached
to the search path, but other classes of object as well. In particular any object of mode "list"
may be attached in the same way:
> attach(any.old.list)
Anything that has been attached can be detached by detach, by position number or, prefer-
ably, by name.
Chapter 6: Lists and data frames 29

6.3.5 Managing the search path

The function search shows the current search path and so is a very useful way to keep track of
which data frames and lists (and packages) have been attached and detached. Initially it gives
> search()
[1] ".GlobalEnv" "Autoloads" "package:base"
where .GlobalEnv is the workspace.1
After lentils is attached we have
> search()
[1] ".GlobalEnv" "lentils" "Autoloads" "package:base"
> ls(2)
[1] "u" "v" "w"
and as we see ls (or objects) can be used to examine the contents of any position on the search
path.
Finally, we detach the data frame and confirm it has been removed from the search path.
> detach("lentils")
> search()
[1] ".GlobalEnv" "Autoloads" "package:base"

1
See the on-line help for autoload for the meaning of the second term.
Chapter 7: Reading data from files 30

7 Reading data from files

Large data objects will usually be read as values from external files rather than entered during
an R session at the keyboard. R input facilities are simple and their requirements are fairly
strict and even rather inflexible. There is a clear presumption by the designers of R that you
will be able to modify your input files using other tools, such as file editors or Perl1 to fit in
with the requirements of R. Generally this is very simple.
If variables are to be held mainly in data frames, as we strongly suggest they should be, an
entire data frame can be read directly with the read.table() function. There is also a more
primitive input function, scan(), that can be called directly.
For more details on importing data into R and also exporting data, see the R Data Im-
port/Export manual.

7.1 The read.table() function

To read an entire data frame directly, the external file will normally have a special form.
• The first line of the file should have a name for each variable in the data frame.
• Each additional line of the file has as its first item a row label and the values for each
variable.
If the file has one fewer item in its first line than in its second, this arrangement is presumed
to be in force. So the first few lines of a file to be read as a data frame might look as follows.

Input file form with names and row labels:

Price Floor Area Rooms Age Cent.heat

01 52.00 111.0 830 5 6.2 no
02 54.75 128.0 710 5 7.5 no
03 57.50 101.0 1000 5 4.2 no
04 57.50 131.0 690 6 8.8 no
05 59.75 93.0 900 5 1.9 yes
...

By default numeric items (except row labels) are read as numeric variables and non-numeric
variables, such as Cent.heat in the example, as factors. This can be changed if necessary.
The function read.table() can then be used to read the data frame directly
> HousePrice <- read.table("houses.data")
Often you will want to omit including the row labels directly and use the default labels. In
this case the file may omit the row label column as in the following.

Input file form without row labels:

Price Floor Area Rooms Age Cent.heat

52.00 111.0 830 5 6.2 no
54.75 128.0 710 5 7.5 no
57.50 101.0 1000 5 4.2 no
57.50 131.0 690 6 8.8 no
59.75 93.0 900 5 1.9 yes
...

1
Under UNIX, the utilities Sed or Awk can be used.
Chapter 7: Reading data from files 31

The data frame may then be read as

> HousePrice <- read.table("houses.data", header=TRUE)
where the header=TRUE option specifies that the first line is a line of headings, and hence, by
implication from the form of the file, that no explicit row labels are given.

7.2 The scan() function

Suppose the data vectors are of equal length and are to be read in parallel. Further suppose
that there are three vectors, the first of mode character and the remaining two of mode numeric,
and the file is ‘input.dat’. The first step is to use scan() to read in the three vectors as a list,
as follows
> inp <- scan("input.dat", list("",0,0))
The second argument is a dummy list structure that establishes the mode of the three vectors
to be read. The result, held in inp, is a list whose components are the three vectors read in. To
separate the data items into three separate vectors, use assignments like
> label <- inp[[1]]; x <- inp[[2]]; y <- inp[[3]]
More conveniently, the dummy list can have named components, in which case the names
can be used to access the vectors read in. For example
> inp <- scan("input.dat", list(id="", x=0, y=0))
If you wish to access the variables separately they may either be re-assigned to variables in
the working frame:
> label <- inp$id; x <- inp$x; y <- inp$y
or the list may be attached at position 2 of the search path (see Section 6.3.4 [Attaching arbitrary
lists], page 28).
If the second argument is a single value and not a list, a single vector is read in, all components
of which must be of the same mode as the dummy value.
> X <- matrix(scan("light.dat", 0), ncol=5, byrow=TRUE)
There are more elaborate input facilities available and these are detailed in the manuals.

7.3 Accessing builtin datasets

Around 100 datasets are supplied with R (in package datasets), and others are available in
packages (including the recommended packages supplied with R). To see the list of datasets
currently available use
data()
As from R version 2.0.0 all the datasets suppied with R are available directly by name. However,
many packages still use the earlier convention in which data was also used to load datasets into
R, for example
data(infert)
and this can still be used with the standard packages (as in this example). In most cases this
will load an R object of the same name. However, in a few cases it loads several objects, so see
the on-line help for the object to see what to expect.

7.3.1 Loading data from other R packages

To access data from a particular package, use the package argument, for example
data(package="rpart")
data(Puromycin, package="datasets")
If a package has been attached by library, its datasets are automatically included in the
search.
User-contributed packages can be a rich source of datasets.
Chapter 7: Reading data from files 32

7.4 Editing data

When invoked on a data frame or matrix, edit brings up a separate spreadsheet-like environment
for editing. This is useful for making small changes once a data set has been read. The command
> xnew <- edit(xold)
will allow you to edit your data set xold, and on completion the changed object is assigned
to xnew. If you want to alter the original dataset xold, the simplest way is to use fix(xold),
which is equivalent to xold <- edit(xold).
Use
> xnew <- edit(data.frame())
to enter new data via the spreadsheet interface.
Chapter 8: Probability distributions 33

8 Probability distributions

8.1 R as a set of statistical tables

One convenient use of R is to provide a comprehensive set of statistical tables. Functions are
provided to evaluate the cumulative distribution function P (X ≤ x), the probability density
function and the quantile function (given q, the smallest x such that P (X ≤ x) > q), and to
simulate from the distribution.

Distribution R name additional arguments

beta beta shape1, shape2, ncp
binomial binom size, prob
Cauchy cauchy location, scale
chi-squared chisq df, ncp
exponential exp rate
F f df1, df2, ncp
gamma gamma shape, scale
geometric geom prob
hypergeometric hyper m, n, k
log-normal lnorm meanlog, sdlog
logistic logis location, scale
negative binomial nbinom size, prob
normal norm mean, sd
Poisson pois lambda
Student’s t t df, ncp
uniform unif min, max
Weibull weibull shape, scale
Wilcoxon wilcox m, n
Prefix the name given here by ‘d’ for the density, ‘p’ for the CDF, ‘q’ for the quantile function
and ‘r’ for simulation (r andom deviates). The first argument is x for dxxx , q for pxxx , p for
qxxx and n for rxxx (except for rhyper and rwilcox, for which it is nn). In not quite all cases
is the non-centrality parameter ncp are currently available: see the on-line help for details.
The pxxx and qxxx functions all have logical arguments lower.tail and log.p and the
dxxx ones have log. This allows, e.g., getting the cumulative (or “integrated”) hazard function,
H(t) = − log(1 − F (t)), by
- pxxx (t, ..., lower.tail = FALSE, log.p = TRUE)
or more accurate log-likelihoods (by dxxx (..., log = TRUE)), directly.
In addition there are functions ptukey and qtukey for the distribution of the studentized
range of samples from a normal distribution.
Here are some examples
> ## 2-tailed p-value for t distribution
> 2*pt(-2.43, df = 13)
> ## upper 1% point for an F(2, 7) distribution
> qf(0.01, 2, 7, lower.tail = FALSE)

8.2 Examining the distribution of a set of data

Given a (univariate) set of data we can examine its distribution in a large number of ways. The
simplest is to examine the numbers. Two slightly different summaries are given by summary and
fivenum and a display of the numbers by stem (a “stem and leaf” plot).
Chapter 8: Probability distributions 34

> attach(faithful)
> summary(eruptions)
Min. 1st Qu. Median Mean 3rd Qu. Max.
1.600 2.163 4.000 3.488 4.454 5.100
> fivenum(eruptions)
[1] 1.6000 2.1585 4.0000 4.4585 5.1000
> stem(eruptions)

The decimal point is 1 digit(s) to the left of the |

16 | 070355555588
18 | 000022233333335577777777888822335777888
20 | 00002223378800035778
22 | 0002335578023578
24 | 00228
26 | 23
28 | 080
30 | 7
32 | 2337
34 | 250077
36 | 0000823577
38 | 2333335582225577
40 | 0000003357788888002233555577778
42 | 03335555778800233333555577778
44 | 02222335557780000000023333357778888
46 | 0000233357700000023578
48 | 00000022335800333
50 | 0370

A stem-and-leaf plot is like a histogram, and R has a function hist to plot histograms.

> hist(eruptions)
## make the bins smaller, make a plot of density
> hist(eruptions, seq(1.6, 5.2, 0.2), prob=TRUE)
> lines(density(eruptions, bw=0.1))
> rug(eruptions) # show the actual data points

More elegant density plots can be made by density, and we added a line produced by
density in this example. The bandwidth bw was chosen by trial-and-error as the default gives
Chapter 8: Probability distributions 35

too much smoothing (it usually does for “interesting” densities). (Better automated methods of
bandwidth choice are available, and in this example bw = "SJ" gives a good result.)

Histogram of eruptions
0.7
0.6
0.5
Relative Frequency

0.4
0.3
0.2
0.1
0.0

1.5 2.0 2.5 3.0 3.5 4.0 4.5 5.0

eruptions

We can plot the empirical cumulative distribution function by using the function ecdf.
> plot(ecdf(eruptions), do.points=FALSE, verticals=TRUE)
This distribution is obviously far from any standard distribution. How about the right-hand
mode, say eruptions of longer than 3 minutes? Let us fit a normal distribution and overlay the
fitted CDF.
> long <- eruptions[eruptions > 3]
> plot(ecdf(long), do.points=FALSE, verticals=TRUE)
> x <- seq(3, 5.4, 0.01)
> lines(x, pnorm(x, mean=mean(long), sd=sqrt(var(long))), lty=3)

ecdf(long)
1.0
0.8
0.6
Fn(x)

0.4
0.2
0.0

3.0 3.5 4.0 4.5 5.0

Quantile-quantile (Q-Q) plots can help us examine this more carefully.

par(pty="s") # arrange for a square figure region
qqnorm(long); qqline(long)
Chapter 8: Probability distributions 36

which shows a reasonable fit but a shorter right tail than one would expect from a normal
distribution. Let us compare this with some simulated data from a t distribution

Normal Q−Q Plot

5.0
4.5
Sample Quantiles

4.0
3.5
3.0

−2 −1 0 1 2

Theoretical Quantiles

x <- rt(250, df = 5)
qqnorm(x); qqline(x)
which will usually (if it is a random sample) show longer tails than expected for a normal. We
can make a Q-Q plot against the generating distribution by
qqplot(qt(ppoints(250), df = 5), x, xlab = "Q-Q plot for t dsn")
qqline(x)
Finally, we might want a more formal test of agreement with normality (or not). R provides
the Shapiro-Wilk test
> shapiro.test(long)

Shapiro-Wilk normality test

data: long
W = 0.9793, p-value = 0.01052
and the Kolmogorov-Smirnov test
> ks.test(long, "pnorm", mean = mean(long), sd = sqrt(var(long)))

One-sample Kolmogorov-Smirnov test

data: long
D = 0.0661, p-value = 0.4284
alternative hypothesis: two.sided
(Note that the distribution theory is not valid here as we have estimated the parameters of the
normal distribution from the same sample.)

8.3 One- and two-sample tests

So far we have compared a single sample to a normal distribution. A much more common
operation is to compare aspects of two samples. Note that in R, all “classical” tests including
the ones used below are in package stats which is normally loaded.
Consider the following sets of data on the latent heat of the fusion of ice (cal/gm) from Rice
(1995, p.490)
Chapter 8: Probability distributions 37

Method A: 79.98 80.04 80.02 80.04 80.03 80.03 80.04 79.97

80.05 80.03 80.02 80.00 80.02
Method B: 80.02 79.94 79.98 79.97 79.97 80.03 79.95 79.97
Boxplots provide a simple graphical comparison of the two samples.
A <- scan()
79.98 80.04 80.02 80.04 80.03 80.03 80.04 79.97
80.05 80.03 80.02 80.00 80.02

B <- scan()
80.02 79.94 79.98 79.97 79.97 80.03 79.95 79.97

boxplot(A, B)
which indicates that the first group tends to give higher results than the second.
80.04
80.02
80.00
79.98
79.96
79.94

1 2

To test for the equality of the means of the two examples, we can use an unpaired t-test by
> t.test(A, B)

Welch Two Sample t-test

data: A and B
t = 3.2499, df = 12.027, p-value = 0.00694
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
0.01385526 0.07018320
sample estimates:
mean of x mean of y
80.02077 79.97875
which does indicate a significant difference, assuming normality. By default the R function does
not assume equality of variances in the two samples (in contrast to the similar S-Plus t.test
function). We can use the F test to test for equality in the variances, provided that the two
samples are from normal populations.
> var.test(A, B)

F test to compare two variances

Chapter 8: Probability distributions 38

data: A and B
F = 0.5837, num df = 12, denom df = 7, p-value = 0.3938
alternative hypothesis: true ratio of variances is not equal to 1
95 percent confidence interval:
0.1251097 2.1052687
sample estimates:
ratio of variances
0.5837405
which shows no evidence of a significant difference, and so we can use the classical t-test that
assumes equality of the variances.
> t.test(A, B, var.equal=TRUE)

Two Sample t-test

data: A and B
t = 3.4722, df = 19, p-value = 0.002551
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
0.01669058 0.06734788
sample estimates:
mean of x mean of y
80.02077 79.97875
All these tests assume normality of the two samples. The two-sample Wilcoxon (or Mann-
Whitney) test only assumes a common continuous distribution under the null hypothesis.
> wilcox.test(A, B)

Wilcoxon rank sum test with continuity correction

data: A and B
W = 89, p-value = 0.007497
alternative hypothesis: true location shift is not equal to 0

Warning message:
Cannot compute exact p-value with ties in: wilcox.test(A, B)
Note the warning: there are several ties in each sample, which suggests strongly that these data
are from a discrete distribution (probably due to rounding).
There are several ways to compare graphically the two samples. We have already seen a pair
of boxplots. The following
> plot(ecdf(A), do.points=FALSE, verticals=TRUE, xlim=range(A, B))
> plot(ecdf(B), do.points=FALSE, verticals=TRUE, add=TRUE)
will show the two empirical CDFs, and qqplot will perform a Q-Q plot of the two samples. The
Kolmogorov-Smirnov test is of the maximal vertical distance between the two ecdf’s, assuming
a common continuous distribution:
> ks.test(A, B)

Two-sample Kolmogorov-Smirnov test

data: A and B
D = 0.5962, p-value = 0.05919
Chapter 8: Probability distributions 39

alternative hypothesis: two-sided

Warning message:
cannot compute correct p-values with ties in: ks.test(A, B)
Chapter 9: Grouping, loops and conditional execution 40

9 Grouping, loops and conditional execution

9.1 Grouped expressions

R is an expression language in the sense that its only command type is a function or expression
which returns a result. Even an assignment is an expression whose result is the value assigned,
and it may be used wherever any expression may be used; in particular multiple assignments
are possible.
Commands may be grouped together in braces, {expr_1 ; ...; expr_m }, in which case the
value of the group is the result of the last expression in the group evaluated. Since such a group
is also an expression it may, for example, be itself included in parentheses and used a part of an
even larger expression, and so on.

9.2 Control statements

9.2.1 Conditional execution: if statements
The language has available a conditional construction of the form
> if (expr_1 ) expr_2 else expr_3
where expr 1 must evaluate to a single logical value and the result of the entire expression is
then evident.
The “short-circuit” operators && and || are often used as part of the condition in an if
statement. Whereas & and | apply element-wise to vectors, && and || apply to vectors of length
one, and only evaluate their second argument if necessary.
There is a vectorized version of the if/else construct, the ifelse function. This has the
form ifelse(condition, a, b) and returns a vector of the length of its longest argument, with
elements a[i] if condition[i] is true, otherwise b[i].

9.2.2 Repetitive execution: for loops, repeat and while

There is also a for loop construction which has the form
> for (name in expr_1 ) expr_2
where name is the loop variable. expr 1 is a vector expression, (often a sequence like 1:20), and
expr 2 is often a grouped expression with its sub-expressions written in terms of the dummy
name. expr 2 is repeatedly evaluated as name ranges through the values in the vector result of
expr 1.
As an example, suppose ind is a vector of class indicators and we wish to produce separate
plots of y versus x within classes. One possibility here is to use coplot(),1 which will produce
an array of plots corresponding to each level of the factor. Another way to do this, now putting
all plots on the one display, is as follows:
> xc <- split(x, ind)
> yc <- split(y, ind)
> for (i in 1:length(yc)) {
plot(xc[[i]], yc[[i]]);
abline(lsfit(xc[[i]], yc[[i]]))
}
(Note the function split() which produces a list of vectors obtained by splitting a larger
vector according to the classes specified by a factor. This is a useful function, mostly used in
connection with boxplots. See the help facility for further details.)
1
to be discussed later, or use xyplot from package lattice.
Chapter 9: Grouping, loops and conditional execution 41

Warning: for() loops are used in R code much less often than in compiled languages.
Code that takes a ‘whole object’ view is likely to be both clearer and faster in R.
Other looping facilities include the
> repeat expr
statement and the
> while (condition ) expr
statement.
The break statement can be used to terminate any loop, possibly abnormally. This is the
only way to terminate repeat loops.
The next statement can be used to discontinue one particular cycle and skip to the “next”.
Control statements are most often used in connection with functions which are discussed in
Chapter 10 [Writing your own functions], page 42, and where more examples will emerge.
Chapter 10: Writing your own functions 42

10 Writing your own functions

As we have seen informally along the way, the R language allows the user to create objects of
mode function. These are true R functions that are stored in a special internal form and may be
used in further expressions and so on. In the process, the language gains enormously in power,
convenience and elegance, and learning to write useful functions is one of the main ways to make
your use of R comfortable and productive.
It should be emphasized that most of the functions supplied as part of the R system, such
as mean(), var(), postscript() and so on, are themselves written in R and thus do not differ
materially from user written functions.
A function is defined by an assignment of the form
> name <- function(arg_1, arg_2, ...) expression
The expression is an R expression, (usually a grouped expression), that uses the arguments,
arg i, to calculate a value. The value of the expression is the value returned for the function.
A call to the function then usually takes the form name (expr_1, expr_2, ...) and may
occur anywhere a function call is legitimate.

10.1 Simple examples

As a first example, consider a function to calculate the two sample t-statistic, showing “all the
steps”. This is an artificial example, of course, since there are other, simpler ways of achieving
the same end.
The function is defined as follows:
> twosam <- function(y1, y2) {
n1 <- length(y1); n2 <- length(y2)
yb1 <- mean(y1); yb2 <- mean(y2)
s1 <- var(y1); s2 <- var(y2)
s <- ((n1-1)*s1 + (n2-1)*s2)/(n1+n2-2)
tst <- (yb1 - yb2)/sqrt(s*(1/n1 + 1/n2))
tst
}
With this function defined, you could perform two sample t-tests using a call such as
> tstat <- twosam(data$male, data$female); tstat
As a second example, consider a function to emulate directly the Matlab backslash com-
mand, which returns the coefficients of the orthogonal projection of the vector y onto the column
space of the matrix, X. (This is ordinarily called the least squares estimate of the regression
coefficients.) This would ordinarily be done with the qr() function; however this is sometimes
a bit tricky to use directly and it pays to have a simple function such as the following to use it
safely.
Thus given a n by 1 vector y and an n by p matrix X then X y is defined as (X 0 X)− X 0 y,
where (X 0 X)− is a generalized inverse of X 0 X.
> bslash <- function(X, y) {
X <- qr(X)
qr.coef(X, y)
}
After this object is created it may be used in statements such as
> regcoeff <- bslash(Xmat, yvar)
and so on.
Chapter 10: Writing your own functions 43

The classical R function lsfit() does this job quite well, and more1 . It in turn uses the
functions qr() and qr.coef() in the slightly counterintuitive way above to do this part of the
calculation. Hence there is probably some value in having just this part isolated in a simple to
use function if it is going to be in frequent use. If so, we may wish to make it a matrix binary
operator for even more convenient use.

10.2 Defining new binary operators

Had we given the bslash() function a different name, namely one of the form
%anything %
it could have been used as a binary operator in expressions rather than in function form. Suppose,
for example, we choose ! for the internal character. The function definition would then start as
> "%!%" <- function(X, y) { ... }
(Note the use of quote marks.) The function could then be used as X %!% y. (The backslash
symbol itself is not a convenient choice as it presents special problems in this context.)
The matrix multiplication operator, %*%, and the outer product matrix operator %o% are
other examples of binary operators defined in this way.

10.3 Named arguments and defaults

As first noted in Section 2.3 [Generating regular sequences], page 8, if arguments to called
functions are given in the “name =object ” form, they may be given in any order. Furthermore
the argument sequence may begin in the unnamed, positional form, and specify named arguments
after the positional arguments.
Thus if there is a function fun1 defined by
> fun1 <- function(data, data.frame, graph, limit) {
[function body omitted]
}
then the function may be invoked in several ways, for example
> ans <- fun1(d, df, TRUE, 20)
> ans <- fun1(d, df, graph=TRUE, limit=20)
> ans <- fun1(data=d, limit=20, graph=TRUE, data.frame=df)
are all equivalent.
In many cases arguments can be given commonly appropriate default values, in which case
they may be omitted altogether from the call when the defaults are appropriate. For example,
if fun1 were defined as
> fun1 <- function(data, data.frame, graph=TRUE, limit=20) { ... }
it could be called as
> ans <- fun1(d, df)
which is now equivalent to the three cases above, or as
> ans <- fun1(d, df, limit=10)
which changes one of the defaults.
It is important to note that defaults may be arbitrary expressions, even involving other
arguments to the same function; they are not restricted to be constants as in our simple example
here.
1
See also the methods described in Chapter 11 [Statistical models in R], page 50
Chapter 10: Writing your own functions 44

10.4 The ‘...’ argument

Another frequent requirement is to allow one function to pass on argument settings to another.
For example many graphics functions use the function par() and functions like plot() allow the
user to pass on graphical parameters to par() to control the graphical output. (See Section 12.4.1
[The par() function], page 67, for more details on the par() function.) This can be done by
including an extra argument, literally ‘...’, of the function, which may then be passed on. An
outline example is given below.
fun1 <- function(data, data.frame, graph=TRUE, limit=20, ...) {
[omitted statements]
if (graph)
par(pch="*", ...)
[more omissions]
}

10.5 Assignments within functions

Note that any ordinary assignments done within the function are local and temporary and are
lost after exit from the function. Thus the assignment X <- qr(X) does not affect the value of
the argument in the calling program.
To understand completely the rules governing the scope of R assignments the reader needs
to be familiar with the notion of an evaluation frame. This is a somewhat advanced, though
hardly difficult, topic and is not covered further here.
If global and permanent assignments are intended within a function, then either the “su-
perassignment” operator, <<- or the function assign() can be used. See the help document for
details. S-Plus users should be aware that <<- has different semantics in R. These are discussed
further in Section 10.7 [Scope], page 46.

10.6 More advanced examples

10.6.1 Efficiency factors in block designs
As a more complete, if a little pedestrian, example of a function, consider finding the efficiency
factors for a block design. (Some aspects of this problem have already been discussed in Sec-
tion 5.3 [Index matrices], page 19.)
A block design is defined by two factors, say blocks (b levels) and varieties (v levels). If R
and K are the v by v and b by b replications and block size matrices, respectively, and N is the
b by v incidence matrix, then the efficiency factors are defined as the eigenvalues of the matrix

E = Iv − R−1/2 N 0 K −1 N R−1/2 = Iv − A0 A,

where A = K −1/2 N R−1/2 . One way to write the function is given below.
> bdeff <- function(blocks, varieties) {
blocks <- as.factor(blocks) # minor safety move
b <- length(levels(blocks))
varieties <- as.factor(varieties) # minor safety move
v <- length(levels(varieties))
K <- as.vector(table(blocks)) # remove dim attr
R <- as.vector(table(varieties)) # remove dim attr
N <- table(blocks, varieties)
A <- 1/sqrt(K) * N * rep(1/sqrt(R), rep(b, v))
sv <- svd(A)
list(eff=1 - sv$d^2, blockcv=sv$u, varietycv=sv$v)
Chapter 10: Writing your own functions 45

}
It is numerically slightly better to work with the singular value decomposition on this occasion
rather than the eigenvalue routines.
The result of the function is a list giving not only the efficiency factors as the first component,
but also the block and variety canonical contrasts, since sometimes these give additional useful
qualitative information.

10.6.2 Dropping all names in a printed array

For printing purposes with large matrices or arrays, it is often useful to print them in close block
form without the array names or numbers. Removing the dimnames attribute will not achieve
this effect, but rather the array must be given a dimnames attribute consisting of empty strings.
For example to print a matrix, X
> temp <- X
> dimnames(temp) <- list(rep("", nrow(X)), rep("", ncol(X)))
> temp; rm(temp)
This can be much more conveniently done using a function, no.dimnames(), shown below,
as a “wrap around” to achieve the same result. It also illustrates how some effective and useful
user functions can be quite short.
no.dimnames <- function(a) {
## Remove all dimension names from an array for compact printing.
d <- list()
l <- 0
for(i in dim(a)) {
d[[l <- l + 1]] <- rep("", i)
}
dimnames(a) <- d
a
}
With this function defined, an array may be printed in close format using
> no.dimnames(X)
This is particularly useful for large integer arrays, where patterns are the real interest rather
than the values.

10.6.3 Recursive numerical integration

Functions may be recursive, and may themselves define functions within themselves. Note,
however, that such functions, or indeed variables, are not inherited by called functions in higher
evaluation frames as they would be if they were on the search path.
The example below shows a naive way of performing one-dimensional numerical integration.
The integrand is evaluated at the end points of the range and in the middle. If the one-panel
trapezium rule answer is close enough to the two panel, then the latter is returned as the value.
Otherwise the same process is recursively applied to each panel. The result is an adaptive
integration process that concentrates function evaluations in regions where the integrand is
farthest from linear. There is, however, a heavy overhead, and the function is only competitive
with other algorithms when the integrand is both smooth and very difficult to evaluate.
The example is also given partly as a little puzzle in R programming.
area <- function(f, a, b, eps = 1.0e-06, lim = 10) {
fun1 <- function(f, a, b, fa, fb, a0, eps, lim, fun) {
## function ‘fun1’ is only visible inside ‘area’
d <- (a + b)/2
Chapter 10: Writing your own functions 46

h <- (b - a)/4
fd <- f(d)
a1 <- h * (fa + fd)
a2 <- h * (fd + fb)
if(abs(a0 - a1 - a2) < eps || lim == 0)
return(a1 + a2)
else {
return(fun(f, a, d, fa, fd, a1, eps, lim - 1, fun) +
fun(f, d, b, fd, fb, a2, eps, lim - 1, fun))
}
}
fa <- f(a)
fb <- f(b)
a0 <- ((fa + fb) * (b - a))/2
fun1(f, a, b, fa, fb, a0, eps, lim, fun1)
}

10.7 Scope
The discussion in this section is somewhat more technical than in other parts of this document.
However, it details one of the major differences between S-Plus and R.
The symbols which occur in the body of a function can be divided into three classes; formal
parameters, local variables and free variables. The formal parameters of a function are those
occurring in the argument list of the function. Their values are determined by the process of
binding the actual function arguments to the formal parameters. Local variables are those whose
values are determined by the evaluation of expressions in the body of the functions. Variables
which are not formal parameters or local variables are called free variables. Free variables become
local variables if they are assigned to. Consider the following function definition.
f <- function(x) {
y <- 2*x
print(x)
print(y)
print(z)
}
In this function, x is a formal parameter, y is a local variable and z is a free variable.
In R the free variable bindings are resolved by first looking in the environment in which the
function was created. This is called lexical scope. First we define a function called cube.
cube <- function(n) {
sq <- function() n*n
n*sq()
}
The variable n in the function sq is not an argument to that function. Therefore it is a free
variable and the scoping rules must be used to ascertain the value that is to be associated with
it. Under static scope (S-Plus) the value is that associated with a global variable named n.
Under lexical scope (R) it is the parameter to the function cube since that is the active binding
for the variable n at the time the function sq was defined. The difference between evaluation
in R and evaluation in S-Plus is that S-Plus looks for a global variable called n while R first
looks for a variable called n in the environment created when cube was invoked.
## first evaluation in S
S> cube(2)
Error in sq(): Object "n" not found
Chapter 10: Writing your own functions 47

Dumped
S> n <- 3
S> cube(2)
[1] 18
## then the same function evaluated in R
R> cube(2)
[1] 8
Lexical scope can also be used to give functions mutable state. In the following example
we show how R can be used to mimic a bank account. A functioning bank account needs to
have a balance or total, a function for making withdrawals, a function for making deposits and
a function for stating the current balance. We achieve this by creating the three functions
within account and then returning a list containing them. When account is invoked it takes
a numerical argument total and returns a list containing the three functions. Because these
functions are defined in an environment which contains total, they will have access to its value.
The special assignment operator, <<-, is used to change the value associated with total.
This operator looks back in enclosing environments for an environment that contains the symbol
total and when it finds such an environment it replaces the value, in that environment, with
the value of right hand side. If the global or top-level environment is reached without finding
the symbol total then that variable is created and assigned to there. For most users <<- creates
a global variable and assigns the value of the right hand side to it2 . Only when <<- has been
used in a function that was returned as the value of another function will the special behavior
described here occur.
open.account <- function(total) {
list(
deposit = function(amount) {
if(amount <= 0)
stop("Deposits must be positive!\n")
total <<- total + amount
cat(amount, "deposited. Your balance is", total, "\n\n")
},
withdraw = function(amount) {
if(amount > total)
stop("You don’t have that much money!\n")
total <<- total - amount
cat(amount, "withdrawn. Your balance is", total, "\n\n")
},
balance = function() {
cat("Your balance is", total, "\n\n")
}
)
}

ross <- open.account(100)

robert <- open.account(200)

ross$withdraw(30)
ross$balance()
robert$balance()

2
In some sense this mimics the behavior in S-Plus since in S-Plus this operator always creates or assigns to
a global variable.
Chapter 10: Writing your own functions 48

ross$deposit(50)
ross$balance()
ross$withdraw(500)

10.8 Customizing the environment

Users can customize their environment in several different ways. There is a site initialization
file and every directory can have its own special initialization file. Finally, the special functions
.First and .Last can be used.
The location of the site initialization file is taken from the value of the R_PROFILE environment
variable. If that variable is unset, the file ‘Rprofile.site’ in the R home subdirectory ‘etc’
is used. This file should contain the commands that you want to execute every time R is
started under your system. A second, personal, profile file named ‘.Rprofile’3 can be placed
in any directory. If R is invoked in that directory then that file will be sourced. This file
gives individual users control over their workspace and allows for different startup procedures
in different working directories. If no ‘.Rprofile’ file is found in the startup directory, then R
looks for a ‘.Rprofile’ file in the user’s home directory and uses that (if it exists).
Any function named .First() in either of the two profile files or in the ‘.RData’ image has
a special status. It is automatically performed at the beginning of an R session and may be
used to initialize the environment. For example, the definition in the example below alters the
prompt to $ and sets up various other useful things that can then be taken for granted in the
rest of the session.
Thus, the sequence in which files are executed is, ‘Rprofile.site’, ‘.Rprofile’, ‘.RData’
and then .First(). A definition in later files will mask definitions in earlier files.
> .First <- function() {
options(prompt="$ ", continue="+\t") # $ is the prompt
options(digits=5, length=999) # custom numbers and printout
x11() # for graphics
par(pch = "+") # plotting character
source(file.path(Sys.getenv("HOME"), "R", "mystuff.R"))
# my personal functions
library(MASS) # attach a package
}
Similarly a function .Last(), if defined, is (normally) executed at the very end of the session.
An example is given below.
> .Last <- function() {
graphics.off() # a small safety measure.
cat(paste(date(),"\nAdios\n")) # Is it time for lunch?
}

10.9 Classes, generic functions and object orientation

The class of an object determines how it will be treated by what are known as generic functions.
Put the other way round, a generic function performs a task or action on its arguments specific
to the class of the argument itself. If the argument lacks any class attribute, or has a class
not catered for specifically by the generic function in question, there is always a default action
provided.
An example makes things clearer. The class mechanism offers the user the facility of designing
and writing generic functions for special purposes. Among the other generic functions are plot()
3
So it is hidden under UNIX.
Chapter 10: Writing your own functions 49

for displaying objects graphically, summary() for summarizing analyses of various types, and
anova() for comparing statistical models.
The number of generic functions that can treat a class in a specific way can be quite large.
For example, the functions that can accommodate in some fashion objects of class "data.frame"
include
[ [[<- any as.matrix
[<- mean plot summary
A currently complete list can be got by using the methods() function:
> methods(class="data.frame")
Conversely the number of classes a generic function can handle can also be quite large.
For example the plot() function has a default method and variants for objects of classes
"data.frame", "density", "factor", and more. A complete list can be got again by using
the methods() function:
> methods(plot)
For many generic functions the function body is quite short, for example
> coef
function (object, ...)
UseMethod("coef")
The presence of UseMethod indicates this is a generic function. To see what methods are available
we can use methods()
> methods(coef)
[1] coef.aov* coef.Arima* coef.default* coef.listof*
[5] coef.nls* coef.summary.nls*

Non-visible functions are asterisked

In this example there are six methods, none of which can be seen by typing its name. We can
read these by either of
> getAnywhere("coef.aov")
A single object matching ’coef.aov’ was found
It was found in the following places
registered S3 method for coef from namespace stats
namespace:stats
with value

function (object, ...)

{
z <- object$coef
z[!is.na(z)]
}

> getS3method("coef", "aov")

function (object, ...)
{
z <- object$coef
z[!is.na(z)]
}
The reader is referred to the R Language Definition for a more complete discussion of this
mechanism.
Chapter 11: Statistical models in R 50

11 Statistical models in R
This section presumes the reader has some familiarity with statistical methodology, in particular
with regression analysis and the analysis of variance. Later we make some rather more ambitious
presumptions, namely that something is known about generalized linear models and nonlinear
regression.
The requirements for fitting statistical models are sufficiently well defined to make it possible
to construct general tools that apply in a broad spectrum of problems.
R provides an interlocking suite of facilities that make fitting statistical models very simple.
As we mention in the introduction, the basic output is minimal, and one needs to ask for the
details by calling extractor functions.

11.1 Defining statistical models; formulae

The template for a statistical model is a linear regression model with independent, homoscedastic
errors
p
X
yi = βj xij + ei , ei ∼ NID(0, σ 2 ), i = 1, . . . , n
j=0

In matrix terms this would be written

y = Xβ + e

where the y is the response vector, X is the model matrix or design matrix and has columns
x0 , x1 , . . . , xp , the determining variables. Very often x0 will be a column of ones defining an
intercept term.

Examples
Before giving a formal specification, a few examples may usefully set the picture.
Suppose y, x, x0, x1, x2, . . . are numeric variables, X is a matrix and A, B, C, . . . are factors.
The following formulae on the left side below specify statistical models as described on the right.
y~x
y~1+x Both imply the same simple linear regression model of y on x. The first has an
implicit intercept term, and the second an explicit one.
y~0+x
y ~ -1 + x
y ~ x - 1 Simple linear regression of y on x through the origin (that is, without an intercept
term).
log(y) ~ x1 + x2
Multiple regression of the transformed variable, log(y), on x1 and x2 (with an
implicit intercept term).
y ~ poly(x,2)
y ~ 1 + x + I(x^2)
Polynomial regression of y on x of degree 2. The first form uses orthogonal polyno-
mials, and the second uses explicit powers, as basis.
y ~ X + poly(x,2)
Multiple regression y with model matrix consisting of the matrix X as well as
polynomial terms in x to degree 2.
Chapter 11: Statistical models in R 51

y~A Single classification analysis of variance model of y, with classes determined by A.

y~A+x Single classification analysis of covariance model of y, with classes determined by
A, and with covariate x.
y ~ A*B
y ~ A + B + A:B
y ~ B %in% A
y ~ A/B Two factor non-additive model of y on A and B. The first two specify the same
crossed classification and the second two specify the same nested classification. In
abstract terms all four specify the same model subspace.
y ~ (A + B + C)^2
y ~ A*B*C - A:B:C
Three factor experiment but with a model containing main effects and two factor
interactions only. Both formulae specify the same model.
y~A*x
y ~ A/x
y ~ A/(1 + x) - 1
Separate simple linear regression models of y on x within the levels of A, with
different codings. The last form produces explicit estimates of as many different
intercepts and slopes as there are levels in A.
y ~ A*B + Error(C)
An experiment with two treatment factors, A and B, and error strata determined
by factor C. For example a split plot experiment, with whole plots (and hence also
subplots), determined by factor C.
The operator ~ is used to define a model formula in R. The form, for an ordinary linear
model, is
response ~ op_1 term_1 op_2 term_2 op_3 term_3 ...
where
response is a vector or matrix, (or expression evaluating to a vector or matrix) defining the
response variable(s).
op i is an operator, either + or -, implying the inclusion or exclusion of a term in the
model, (the first is optional).
term i is either
• a vector or matrix expression, or 1,
• a factor, or
• a formula expression consisting of factors, vectors or matrices connected by
formula operators.
In all cases each term defines a collection of columns either to be added to or
removed from the model matrix. A 1 stands for an intercept column and is by
default included in the model matrix unless explicitly removed.
The formula operators are similar in effect to the Wilkinson and Rogers notation used by
such programs as Glim and Genstat. One inevitable change is that the operator ‘.’ becomes ‘:’
since the period is a valid name character in R.
The notation is summarized below (based on Chambers & Hastie, 1992, p.29):
Y ~M Y is modeled as M.
M_1 + M_2 Include M 1 and M 2.
Chapter 11: Statistical models in R 52

M_1 - M_2 Include M 1 leaving out terms of M 2.

M_1 : M_2 The tensor product of M 1 and M 2. If both terms are factors, then the “subclasses”
factor.
M_1 %in% M_2
Similar to M_1 :M_2 , but with a different coding.
M_1 * M_2 M_1 + M_2 + M_1 :M_2 .
M_1 / M_2 M_1 + M_2 %in% M_1 .
M ^n All terms in M together with “interactions” up to order n
I(M ) Insulate M. Inside M all operators have their normal arithmetic meaning, and that
term appears in the model matrix.
Note that inside the parentheses that usually enclose function arguments all operators have
their normal arithmetic meaning. The function I() is an identity function used to allow terms
in model formulae to be defined using arithmetic operators.
Note particularly that the model formulae specify the columns of the model matrix, the
specification of the parameters being implicit. This is not the case in other contexts, for example
in specifying nonlinear models.

11.1.1 Contrasts
We need at least some idea how the model formulae specify the columns of the model matrix.
This is easy if we have continuous variables, as each provides one column of the model matrix
(and the intercept will provide a column of ones if included in the model).
What about a k-level factor A? The answer differs for unordered and ordered factors. For
unordered factors k − 1 columns are generated for the indicators of the second, . . . , kth levels
of the factor. (Thus the implicit parameterization is to contrast the response at each level with
that at the first.) For ordered factors the k − 1 columns are the orthogonal polynomials on
1, . . . , k, omitting the constant term.
Although the answer is already complicated, it is not the whole story. First, if the intercept
is omitted in a model that contains a factor term, the first such term is encoded into k columns
giving the indicators for all the levels. Second, the whole behavior can be changed by the
options setting for contrasts. The default setting in R is
options(contrasts = c("contr.treatment", "contr.poly"))
The main reason for mentioning this is that R and S have different defaults for unordered factors,
S using Helmert contrasts. So if you need to compare your results to those of a textbook or
paper which used S-Plus, you will need to set
options(contrasts = c("contr.helmert", "contr.poly"))
This is a deliberate difference, as treatment contrasts (R’s default) are thought easier for new-
comers to interpret.
We have still not finished, as the contrast scheme to be used can be set for each term in the
model using the functions contrasts and C.
We have not yet considered interaction terms: these generate the products of the columns
introduced for their component terms.
Although the details are complicated, model formulae in R will normally generate the models
that an expert statistician would expect, provided that marginality is preserved. Fitting, for
example, a model with an interaction but not the corresponding main effects will in general lead
to surprising results, and is for experts only.
Chapter 11: Statistical models in R 53

11.2 Linear models

The basic function for fitting ordinary multiple models is lm(), and a streamlined version of the
call is as follows:
> fitted.model <- lm(formula, data = data.frame )
For example
> fm2 <- lm(y ~ x1 + x2, data = production)
would fit a multiple regression model of y on x1 and x2 (with implicit intercept term).
The important (but technically optional) parameter data = production specifies that any
variables needed to construct the model should come first from the production data frame.
This is the case regardless of whether data frame production has been attached on the search
path or not.

11.3 Generic functions for extracting model information

The value of lm() is a fitted model object; technically a list of results of class "lm". Information
about the fitted model can then be displayed, extracted, plotted and so on by using generic
functions that orient themselves to objects of class "lm". These include
add1 deviance formula predict step
alias drop1 kappa print summary
anova effects labels proj vcov
coef family plot residuals
A brief description of the most commonly used ones is given below.
anova(object_1, object_2 )
Compare a submodel with an outer model and produce an analysis of variance table.
coef(object )
Extract the regression coefficient (matrix).
Long form: coefficients(object ).
deviance(object )
Residual sum of squares, weighted if appropriate.
formula(object )
Extract the model formula.
plot(object )
Produce four plots, showing residuals, fitted values and some diagnostics.
predict(object, newdata=data.frame )
The data frame supplied must have variables specified with the same labels as the
original. The value is a vector or matrix of predicted values corresponding to the
determining variable values in data.frame.
print(object )
Print a concise version of the object. Most often used implicitly.
residuals(object )
Extract the (matrix of) residuals, weighted as appropriate.
Short form: resid(object ).
step(object )
Select a suitable model by adding or dropping terms and preserving hierarchies. The
model with the smallest value of AIC (Akaike’s An Information Criterion) discovered
in the stepwise search is returned.
Chapter 11: Statistical models in R 54

summary(object )
Print a comprehensive summary of the results of the regression analysis.
vcov(object )
Returns the variance-covariance matrix of the main parameters of a fitted model
object.

11.4 Analysis of variance and model comparison

The model fitting function aov(formula, data=data.frame ) operates at the simplest level in
a very similar way to the function lm(), and most of the generic functions listed in the table in
Section 11.3 [Generic functions for extracting model information], page 53 apply.
It should be noted that in addition aov() allows an analysis of models with multiple error
strata such as split plot experiments, or balanced incomplete block designs with recovery of
inter-block information. The model formula
response ~ mean.formula + Error(strata.formula )
specifies a multi-stratum experiment with error strata defined by the strata.formula. In the
simplest case, strata.formula is simply a factor, when it defines a two strata experiment, namely
between and within the levels of the factor.
For example, with all determining variables factors, a model formula such as that in:
> fm <- aov(yield ~ v + n*p*k + Error(farms/blocks), data=farm.data)
would typically be used to describe an experiment with mean model v + n*p*k and three error
strata, namely “between farms”, “within farms, between blocks” and “within blocks”.

11.4.1 ANOVA tables

Note also that the analysis of variance table (or tables) are for a sequence of fitted models.
The sums of squares shown are the decrease in the residual sums of squares resulting from an
inclusion of that term in the model at that place in the sequence. Hence only for orthogonal
experiments will the order of inclusion be inconsequential.
For multistratum experiments the procedure is first to project the response onto the error
strata, again in sequence, and to fit the mean model to each projection. For further details, see
Chambers & Hastie (1992).
A more flexible alternative to the default full ANOVA table is to compare two or more models
directly using the anova() function.
> anova(fitted.model.1, fitted.model.2, ...)
The display is then an ANOVA table showing the differences between the fitted models when
fitted in sequence. The fitted models being compared would usually be an hierarchical sequence,
of course. This does not give different information to the default, but rather makes it easier to
comprehend and control.

11.5 Updating fitted models

The update() function is largely a convenience function that allows a model to be fitted that
differs from one previously fitted usually by just a few additional or removed terms. Its form is
> new.model <- update(old.model, new.formula )
In the new.formula the special name consisting of a period, ‘.’, only, can be used to stand
for “the corresponding part of the old model formula”. For example,
> fm05 <- lm(y ~ x1 + x2 + x3 + x4 + x5, data = production)
> fm6 <- update(fm05, . ~ . + x6)
> smf6 <- update(fm6, sqrt(.) ~ .)
Chapter 11: Statistical models in R 55

would fit a five variate multiple regression with variables (presumably) from the data frame
production, fit an additional model including a sixth regressor variable, and fit a variant on
the model where the response had a square root transform applied.
Note especially that if the data= argument is specified on the original call to the model
fitting function, this information is passed on through the fitted model object to update() and
its allies.
The name ‘.’ can also be used in other contexts, but with slightly different meaning. For
example
> fmfull <- lm(y ~ . , data = production)
would fit a model with response y and regressor variables all other variables in the data frame
production.
Other functions for exploring incremental sequences of models are add1(), drop1() and
step(). The names of these give a good clue to their purpose, but for full details see the on-line
help.

11.6 Generalized linear models

Generalized linear modeling is a development of linear models to accommodate both non-normal
response distributions and transformations to linearity in a clean and straightforward way. A
generalized linear model may be described in terms of the following sequence of assumptions:
• There is a response, y, of interest and stimulus variables x1 , x2 , . . . , whose values influence
the distribution of the response.
• The stimulus variables influence the distribution of y through a single linear function, only.
This linear function is called the linear predictor, and is usually written

η = β1 x1 + β2 x2 + · · · + βp xp ,

hence xi has no influence on the distribution of y if and only if βi = 0.

• The distribution of y is of the form

A
 
fY (y; µ, ϕ) = exp {yλ(µ) − γ (λ(µ))} + τ (y, ϕ)
ϕ

where ϕ is a scale parameter (possibly known), and is constant for all observations, A
represents a prior weight, assumed known but possibly varying with the observations, and
µ is the mean of y. So it is assumed that the distribution of y is determined by its mean
and possibly a scale parameter as well.
• The mean, µ, is a smooth invertible function of the linear predictor:

µ = m(η), η = m−1 (µ) = `(µ)

and this inverse function, `(), is called the link function.

These assumptions are loose enough to encompass a wide class of models useful in statistical
practice, but tight enough to allow the development of a unified methodology of estimation and
inference, at least approximately. The reader is referred to any of the current reference works
on the subject for full details, such as McCullagh & Nelder (1989) or Dobson (1990).
Chapter 11: Statistical models in R 56

11.6.1 Families
The class of generalized linear models handled by facilities supplied in R includes gaussian,
binomial, poisson, inverse gaussian and gamma response distributions and also quasi-likelihood
models where the response distribution is not explicitly specified. In the latter case the variance
function must be specified as a function of the mean, but in other cases this function is implied
by the response distribution.
Each response distribution admits a variety of link functions to connect the mean with the
linear predictor. Those automatically available are shown in the following table:

Family name Link functions

binomial logit, probit, log, cloglog
gaussian identity, log, inverse
Gamma identity, inverse, log
inverse.gaussian 1/mu^2, identity, inverse, log
poisson identity, log, sqrt
quasi logit, probit, cloglog, identity, inverse,
log, 1/mu^2, sqrt
The combination of a response distribution, a link function and various other pieces of infor-
mation that are needed to carry out the modeling exercise is called the family of the generalized
linear model.

11.6.2 The glm() function

Since the distribution of the response depends on the stimulus variables through a single linear
function only, the same mechanism as was used for linear models can still be used to specify the
linear part of a generalized model. The family has to be specified in a different way.
The R function to fit a generalized linear model is glm() which uses the form
> fitted.model <- glm(formula, family=family.generator, data=data.frame )
The only new feature is the family.generator, which is the instrument by which the family is
described. It is the name of a function that generates a list of functions and expressions that
together define and control the model and estimation process. Although this may seem a little
complicated at first sight, its use is quite simple.
The names of the standard, supplied family generators are given under “Family Name” in
the table in Section 11.6.1 [Families], page 56. Where there is a choice of links, the name of the
link may also be supplied with the family name, in parentheses as a parameter. In the case of
the quasi family, the variance function may also be specified in this way.
Some examples make the process clear.

The gaussian family

A call such as
> fm <- glm(y ~ x1 + x2, family = gaussian, data = sales)
achieves the same result as
> fm <- lm(y ~ x1+x2, data=sales)
but much less efficiently. Note how the gaussian family is not automatically provided with a
choice of links, so no parameter is allowed. If a problem requires a gaussian family with a
nonstandard link, this can usually be achieved through the quasi family, as we shall see later.

The binomial family

Consider a small, artificial example, from Silvey (1970).
Chapter 11: Statistical models in R 57

On the Aegean island of Kalythos the male inhabitants suffer from a congenital eye disease,
the effects of which become more marked with increasing age. Samples of islander males of
various ages were tested for blindness and the results recorded. The data is shown below:
Age: 20 35 45 55 70
No. tested: 50 50 50 50 50
No. blind: 6 17 26 37 44
The problem we consider is to fit both logistic and probit models to this data, and to estimate
for each model the LD50, that is the age at which the chance of blindness for a male inhabitant
is 50%.
If y is the number of blind at age x and n the number tested, both models have the form
y ∼ B(n, F (β0 + β1 x))
where for the probit case, F (z) = Φ(z) is the standard normal distribution function, and in the
logit case (the default), F (z) = ez /(1 + ez ). In both cases the LD50 is
LD50 = −β0 /β1
that is, the point at which the argument of the distribution function is zero.
The first step is to set the data up as a data frame
> kalythos <- data.frame(x = c(20,35,45,55,70), n = rep(50,5),
y = c(6,17,26,37,44))
To fit a binomial model using glm() there are three possibilities for the response:
• If the response is a vector it is assumed to hold binary data, and so must be a 0/1 vector.
• If the response is a two-column matrix it is assumed that the first column holds the number
of successes for the trial and the second holds the number of failures.
• If the response is a factor, its first level is taken as failure (0) and all other levels as ‘success’
(1).
Here we need the second of these conventions, so we add a matrix to our data frame:
> kalythos$Ymat <- cbind(kalythos$y, kalythos$n - kalythos$y)
To fit the models we use
> fmp <- glm(Ymat ~ x, family = binomial(link=probit), data = kalythos)
> fml <- glm(Ymat ~ x, family = binomial, data = kalythos)
Since the logit link is the default the parameter may be omitted on the second call. To see
the results of each fit we could use
> summary(fmp)
> summary(fml)
Both models fit (all too) well. To find the LD50 estimate we can use a simple function:
> ld50 <- function(b) -b[1]/b[2]
> ldp <- ld50(coef(fmp)); ldl <- ld50(coef(fml)); c(ldp, ldl)
The actual estimates from this data are 43.663 years and 43.601 years respectively.

Poisson models
With the Poisson family the default link is the log, and in practice the major use of this family
is to fit surrogate Poisson log-linear models to frequency data, whose actual distribution is often
multinomial. This is a large and important subject we will not discuss further here. It even
forms a major part of the use of non-gaussian generalized models overall.
Occasionally genuinely Poisson data arises in practice and in the past it was often analyzed
as gaussian data after either a log or a square-root transformation. As a graceful alternative to
the latter, a Poisson generalized linear model may be fitted as in the following example:
Chapter 11: Statistical models in R 58

> fmod <- glm(y ~ A + B + x, family = poisson(link=sqrt),

data = worm.counts)

Quasi-likelihood models
For all families the variance of the response will depend on the mean and will have the scale
parameter as a multiplier. The form of dependence of the variance on the mean is a characteristic
of the response distribution; for example for the poisson distribution Var[y] = µ.
For quasi-likelihood estimation and inference the precise response distribution is not specified,
but rather only a link function and the form of the variance function as it depends on the
mean. Since quasi-likelihood estimation uses formally identical techniques to those for the
gaussian distribution, this family provides a way of fitting gaussian models with non-standard
link functions or variance functions, incidentally.
For example, consider fitting the non-linear regression

θ 1 z1
y= +e
z2 − θ 2

which may be written alternatively as

1
y= +e
β1 x1 + β2 x2

where x1 = z2 /z1 , x2 = −1/z1 , β1 = 1/θ1 and β2 = θ2 /θ1 . Supposing a suitable data frame to
be set up we could fit this non-linear regression as
> nlfit <- glm(y ~ x1 + x2 - 1,
family = quasi(link=inverse, variance=constant),
data = biochem)
The reader is referred to the manual and the help document for further information, as
needed.

11.7 Nonlinear least squares and maximum likelihood models

Certain forms of nonlinear model can be fitted by Generalized Linear Models (glm()). But
in the majority of cases we have to approach the nonlinear curve fitting problem as one of
nonlinear optimization. R’s nonlinear optimization routines are optim(), nlm() and (from R
2.2.0) nlminb(), which provide the functionality (and more) of S-Plus’s ms() and nlminb().
We seek the parameter values that minimize some index of lack-of-fit, and they do this by
trying out various parameter values iteratively. Unlike linear regression for example, there is no
guarantee that the procedure will converge on satisfactory estimates. All the methods require
initial guesses about what parameter values to try, and convergence may depend critically upon
the quality of the starting values.

11.7.1 Least squares

One way to fit a nonlinear model is by minimizing the sum of the squared errors (SSE) or
residuals. This method makes sense if the observed errors could have plausibly arisen from a
normal distribution.
Here is an example from Bates & Watts (1988), page 51. The data are:
> x <- c(0.02, 0.02, 0.06, 0.06, 0.11, 0.11, 0.22, 0.22, 0.56, 0.56,
1.10, 1.10)
> y <- c(76, 47, 97, 107, 123, 139, 159, 152, 191, 201, 207, 200)
The model to be fitted is:
Chapter 11: Statistical models in R 59

> fn <- function(p) sum((y - (p[1] * x)/(p[2] + x))^2)

In order to do the fit we need initial estimates of the parameters. One way to find sensible
starting values is to plot the data, guess some parameter values, and superimpose the model
curve using those values.
> plot(x, y)
> xfit <- seq(.02, 1.1, .05)
> yfit <- 200 * xfit/(0.1 + xfit)
> lines(spline(xfit, yfit))
We could do better, but these starting values of 200 and 0.1 seem adequate. Now do the fit:
> out <- nlm(fn, p = c(200, 0.1), hessian = TRUE)
After the fitting, out$minimum is the SSE, and out$estimate are the least squares estimates
of the parameters. To obtain the approximate standard errors (SE) of the estimates we do:
> sqrt(diag(2*out$minimum/(length(y) - 2) * solve(out$hessian)))
The 2 in the line above represents the number of parameters. A 95% confidence interval
would be the parameter estimate ± 1.96 SE. We can superimpose the least squares fit on a new
plot:
> plot(x, y)
> xfit <- seq(.02, 1.1, .05)
> yfit <- 212.68384222 * xfit/(0.06412146 + xfit)
> lines(spline(xfit, yfit))
The standard package stats provides much more extensive facilities for fitting non-linear
models by least squares. The model we have just fitted is the Michaelis-Menten model, so we
can use
> df <- data.frame(x=x, y=y)
> fit <- nls(y ~ SSmicmen(x, Vm, K), df)
> fit
Nonlinear regression model
model: y ~ SSmicmen(x, Vm, K)
data: df
Vm K
212.68370711 0.06412123
residual sum-of-squares: 1195.449
> summary(fit)

Formula: y ~ SSmicmen(x, Vm, K)

Parameters:
Estimate Std. Error t value Pr(>|t|)
Vm 2.127e+02 6.947e+00 30.615 3.24e-11
K 6.412e-02 8.281e-03 7.743 1.57e-05

Residual standard error: 10.93 on 10 degrees of freedom

Correlation of Parameter Estimates:

Vm
K 0.7651

11.7.2 Maximum likelihood

Maximum likelihood is a method of nonlinear model fitting that applies even if the errors are
not normal. The method finds the parameter values which maximize the log likelihood, or
Chapter 11: Statistical models in R 60

equivalently which minimize the negative log-likelihood. Here is an example from Dobson (1990),
pp. 108–111. This example fits a logistic model to dose-response data, which clearly could also
be fit by glm(). The data are:
> x <- c(1.6907, 1.7242, 1.7552, 1.7842, 1.8113,
1.8369, 1.8610, 1.8839)
> y <- c( 6, 13, 18, 28, 52, 53, 61, 60)
> n <- c(59, 60, 62, 56, 63, 59, 62, 60)
The negative log-likelihood to minimize is:
> fn <- function(p)
sum( - (y*(p[1]+p[2]*x) - n*log(1+exp(p[1]+p[2]*x))
+ log(choose(n, y)) ))
We pick sensible starting values and do the fit:
> out <- nlm(fn, p = c(-50,20), hessian = TRUE)
After the fitting, out$minimum is the negative log-likelihood, and out$estimate are the maxi-
mum likelihood estimates of the parameters. To obtain the approximate SEs of the estimates
we do:
> sqrt(diag(solve(out$hessian)))
A 95% confidence interval would be the parameter estimate ± 1.96 SE.

11.8 Some non-standard models

We conclude this chapter with just a brief mention of some of the other facilities available in R
for special regression and data analysis problems.
• Mixed models. The recommended nlme package provides functions lme() and nlme() for
linear and non-linear mixed-effects models, that is linear and non-linear regressions in which
some of the coefficients correspond to random effects. These functions make heavy use of
formulae to specify the models.
• Local approximating regressions. The loess() function fits a nonparametric regression by
using a locally weighted regression. Such regressions are useful for highlighting a trend in
messy data or for data reduction to give some insight into a large data set.
Function loess is in the standard package stats, together with code for projection pursuit
regression.
• Robust regression. There are several functions available for fitting regression models in a
way resistant to the influence of extreme outliers in the data. Function lqs in the rec-
ommended package MASS provides state-of-art algorithms for highly-resistant fits. Less
resistant but statistically more efficient methods are available in packages, for example
function rlm in package MASS.
• Additive models. This technique aims to construct a regression function from smooth
additive functions of the determining variables, usually one for each determining variable.
Functions avas and ace in package acepack and functions bruto and mars in package mda
provide some examples of these techniques in user-contributed packages to R. An extension
is Generalized Additive Models, implemented in user-contributed packages gam and mgcv.
• Tree-based models. Rather than seek an explicit global linear model for prediction or
interpretation, tree-based models seek to bifurcate the data, recursively, at critical points
of the determining variables in order to partition the data ultimately into groups that are
as homogeneous as possible within, and as heterogeneous as possible between. The results
often lead to insights that other data analysis methods tend not to yield.
Models are again specified in the ordinary linear model form. The model fitting function is
tree(), but many other generic functions such as plot() and text() are well adapted to
displaying the results of a tree-based model fit in a graphical way.
Chapter 11: Statistical models in R 61

Tree models are available in R via the user-contributed packages rpart and tree.
Chapter 12: Graphical procedures 62

12 Graphical procedures
Graphical facilities are an important and extremely versatile component of the R environment.
It is possible to use the facilities to display a wide variety of statistical graphs and also to build
entirely new types of graph.
The graphics facilities can be used in both interactive and batch modes, but in most cases,
interactive use is more productive. Interactive use is also easy because at startup time R initiates
a graphics device driver which opens a special graphics window for the display of interactive
graphics. Although this is done automatically, it is useful to know that the command used is
X11() under UNIX and windows() under Windows.
Once the device driver is running, R plotting commands can be used to produce a variety of
graphical displays and to create entirely new kinds of display.
Plotting commands are divided into three basic groups:
• High-level plotting functions create a new plot on the graphics device, possibly with axes,
labels, titles and so on.
• Low-level plotting functions add more information to an existing plot, such as extra points,
lines and labels.
• Interactive graphics functions allow you interactively add information to, or extract infor-
mation from, an existing plot, using a pointing device such as a mouse.
In addition, R maintains a list of graphical parameters which can be manipulated to customize
your plots.
This manual only describes what are known as ‘base’ graphics. A separate graphics sub-
system in package grid coexists with base – it is more powerful but harder to use. There is a
recommended package lattice which builds on grid and provides ways to produce multi-panel
plots akin to those in the Trellis system in S.

12.1 High-level plotting commands

High-level plotting functions are designed to generate a complete plot of the data passed as ar-
guments to the function. Where appropriate, axes, labels and titles are automatically generated
(unless you request otherwise.) High-level plotting commands always start a new plot, erasing
the current plot if necessary.

12.1.1 The plot() function

One of the most frequently used plotting functions in R is the plot() function. This is a generic
function: the type of plot produced is dependent on the type or class of the first argument.
plot(x, y )
plot(xy ) If x and y are vectors, plot(x, y ) produces a scatterplot of y against x. The same
effect can be produced by supplying one argument (second form) as either a list
containing two elements x and y or a two-column matrix.
plot(x ) If x is a time series, this produces a time-series plot. If x is a numeric vector, it
produces a plot of the values in the vector against their index in the vector. If x
is a complex vector, it produces a plot of imaginary versus real parts of the vector
elements.
plot(f )
plot(f, y )
f is a factor object, y is a numeric vector. The first form generates a bar plot of f ;
the second form produces boxplots of y for each level of f.
Chapter 12: Graphical procedures 63

plot(df )
plot(~ expr )
plot(y ~ expr )
df is a data frame, y is any object, expr is a list of object names separated by ‘+’
(e.g., a + b + c). The first two forms produce distributional plots of the variables in
a data frame (first form) or of a number of named objects (second form). The third
form plots y against every object named in expr.

12.1.2 Displaying multivariate data

R provides two very useful functions for representing multivariate data. If X is a numeric matrix
or data frame, the command
> pairs(X)
produces a pairwise scatterplot matrix of the variables defined by the columns of X, that is,
every column of X is plotted against every other column of X and the resulting n(n − 1) plots
are arranged in a matrix with plot scales constant over the rows and columns of the matrix.
When three or four variables are involved a coplot may be more enlightening. If a and b are
numeric vectors and c is a numeric vector or factor object (all of the same length), then the
command
> coplot(a ~ b | c)
produces a number of scatterplots of a against b for given values of c. If c is a factor, this
simply means that a is plotted against b for every level of c. When c is numeric, it is divided
into a number of conditioning intervals and for each interval a is plotted against b for values of c
within the interval. The number and position of intervals can be controlled with given.values=
argument to coplot()—the function co.intervals() is useful for selecting intervals. You can
also use two given variables with a command like
> coplot(a ~ b | c + d)
which produces scatterplots of a against b for every joint conditioning interval of c and d.
The coplot() and pairs() function both take an argument panel= which can be used to
customize the type of plot which appears in each panel. The default is points() to produce a
scatterplot but by supplying some other low-level graphics function of two vectors x and y as
the value of panel= you can produce any type of plot you wish. An example panel function
useful for coplots is panel.smooth().

12.1.3 Display graphics

Other high-level graphics functions produce different types of plots. Some examples are:
qqnorm(x)
qqline(x)
qqplot(x, y)
Distribution-comparison plots. The first form plots the numeric vector x against the
expected Normal order scores (a normal scores plot) and the second adds a straight
line to such a plot by drawing a line through the distribution and data quartiles.
The third form plots the quantiles of x against those of y to compare their respective
distributions.
hist(x)
hist(x, nclass=n )
hist(x, breaks=b, ...)
Produces a histogram of the numeric vector x. A sensible number of classes is
usually chosen, but a recommendation can be given with the nclass= argument.
Alternatively, the breakpoints can be specified exactly with the breaks= argument.
Chapter 12: Graphical procedures 64

If the probability=TRUE argument is given, the bars represent relative frequencies

instead of counts.
dotchart(x, ...)
Constructs a dotchart of the data in x. In a dotchart the y-axis gives a labelling
of the data in x and the x-axis gives its value. For example it allows easy visual
selection of all data entries with values lying in specified ranges.
image(x, y, z, ...)
contour(x, y, z, ...)
persp(x, y, z, ...)
Plots of three variables. The image plot draws a grid of rectangles using different
colours to represent the value of z, the contour plot draws contour lines to represent
the value of z, and the persp plot draws a 3D surface.

12.1.4 Arguments to high-level plotting functions

There are a number of arguments which may be passed to high-level graphics functions, as
follows:
add=TRUE Forces the function to act as a low-level graphics function, superimposing the plot
on the current plot (some functions only).
axes=FALSE
Suppresses generation of axes—useful for adding your own custom axes with the
axis() function. The default, axes=TRUE, means include axes.
log="x"
log="y"
log="xy" Causes the x, y or both axes to be logarithmic. This will work for many, but not
all, types of plot.
type= The type= argument controls the type of plot produced, as follows:
type="p" Plot individual points (the default)
type="l" Plot lines
type="b" Plot points connected by lines (both)
type="o" Plot points overlaid by lines
type="h" Plot vertical lines from points to the zero axis (high-density)
type="s"
type="S" Step-function plots. In the first form, the top of the vertical defines the
point; in the second, the bottom.
type="n" No plotting at all. However axes are still drawn (by default) and the
coordinate system is set up according to the data. Ideal for creating
plots with subsequent low-level graphics functions.
xlab=string
ylab=string
Axis labels for the x and y axes. Use these arguments to change the default labels,
usually the names of the objects used in the call to the high-level plotting function.
main=string
Figure title, placed at the top of the plot in a large font.
sub=string
Sub-title, placed just below the x-axis in a smaller font.
Chapter 12: Graphical procedures 65

12.2 Low-level plotting commands

Sometimes the high-level plotting functions don’t produce exactly the kind of plot you desire.
In this case, low-level plotting commands can be used to add extra information (such as points,
lines or text) to the current plot.
Some of the more useful low-level plotting functions are:
points(x, y)
lines(x, y)
Adds points or connected lines to the current plot. plot()’s type= argument can
also be passed to these functions (and defaults to "p" for points() and "l" for
lines().)
text(x, y, labels, ...)
Add text to a plot at points given by x, y. Normally labels is an integer or
character vector in which case labels[i] is plotted at point (x[i], y[i]). The
default is 1:length(x).
Note: This function is often used in the sequence
> plot(x, y, type="n"); text(x, y, names)
The graphics parameter type="n" suppresses the points but sets up the axes, and
the text() function supplies special characters, as specified by the character vector
names for the points.
abline(a, b)
abline(h=y )
abline(v=x )
abline(lm.obj )
Adds a line of slope b and intercept a to the current plot. h=y may be used to
specify y-coordinates for the heights of horizontal lines to go across a plot, and
v=x similarly for the x-coordinates for vertical lines. Also lm.obj may be list with a
coefficients component of length 2 (such as the result of model-fitting functions,)
which are taken as an intercept and slope, in that order.
polygon(x, y, ...)
Draws a polygon defined by the ordered vertices in (x, y) and (optionally) shade it
in with hatch lines, or fill it if the graphics device allows the filling of figures.
legend(x, y, legend, ...)
Adds a legend to the current plot at the specified position. Plotting characters, line
styles, colors etc., are identified with the labels in the character vector legend. At
least one other argument v (a vector the same length as legend) with the corre-
sponding values of the plotting unit must also be given, as follows:
legend( , fill=v )
Colors for filled boxes
legend( , col=v )
Colors in which points or lines will be drawn
legend( , lty=v )
Line styles
legend( , lwd=v )
Line widths
legend( , pch=v )
Plotting characters (character vector)
Chapter 12: Graphical procedures 66

title(main, sub)
Adds a title main to the top of the current plot in a large font and (optionally) a
sub-title sub at the bottom in a smaller font.
axis(side, ...)
Adds an axis to the current plot on the side given by the first argument (1 to 4,
counting clockwise from the bottom.) Other arguments control the positioning of
the axis within or beside the plot, and tick positions and labels. Useful for adding
custom axes after calling plot() with the axes=FALSE argument.
Low-level plotting functions usually require some positioning information (e.g., x and y co-
ordinates) to determine where to place the new plot elements. Coordinates are given in terms of
user coordinates which are defined by the previous high-level graphics command and are chosen
based on the supplied data.
Where x and y arguments are required, it is also sufficient to supply a single argument being
a list with elements named x and y. Similarly a matrix with two columns is also valid input.
In this way functions such as locator() (see below) may be used to specify positions on a plot
interactively.

12.2.1 Mathematical annotation

In some cases, it is useful to add mathematical symbols and formulae to a plot. This can be
achieved in R by specifying an expression rather than a character string in any one of text,
mtext, axis, or title. For example, the following code draws the formula for the Binomial
probability function:
> text(x, y, expression(paste(bgroup("(", atop(n, x), ")"), p^x, q^{n-x})))
More information, including a full listing of the features available can obtained from within
R using the commands:
> help(plotmath)
> example(plotmath)
> demo(plotmath)

12.2.2 Hershey vector fonts

It is possible to specify Hershey vector fonts for rendering text when using the text and contour
functions. There are three reasons for using the Hershey fonts:
• Hershey fonts can produce better output, especially on a computer screen, for rotated
and/or small text.
• Hershey fonts provide certain symbols that may not be available in the standard fonts. In
particular, there are zodiac signs, cartographic symbols and astronomical symbols.
• Hershey fonts provide cyrillic and japanese (Kana and Kanji) characters.
More information, including tables of Hershey characters can be obtained from within R
using the commands:
> help(Hershey)
> demo(Hershey)
> help(Japanese)
> demo(Japanese)

12.3 Interacting with graphics

R also provides functions which allow users to extract or add information to a plot using a
mouse. The simplest of these is the locator() function:
Chapter 12: Graphical procedures 67

locator(n, type)
Waits for the user to select locations on the current plot using the left mouse button.
This continues until n (default 512) points have been selected, or another mouse
button is pressed. The type argument allows for plotting at the selected points and
has the same effect as for high-level graphics commands; the default is no plotting.
locator() returns the locations of the points selected as a list with two components
x and y.
locator() is usually called with no arguments. It is particularly useful for interactively
selecting positions for graphic elements such as legends or labels when it is difficult to calculate
in advance where the graphic should be placed. For example, to place some informative text
near an outlying point, the command
> text(locator(1), "Outlier", adj=0)
may be useful. (locator() will be ignored if the current device, such as postscript does not
support interactive pointing.)
identify(x, y, labels)
Allow the user to highlight any of the points defined by x and y (using the left mouse
button) by plotting the corresponding component of labels nearby (or the index
number of the point if labels is absent). Returns the indices of the selected points
when another button is pressed.
Sometimes we want to identify particular points on a plot, rather than their positions. For
example, we may wish the user to select some observation of interest from a graphical display
and then manipulate that observation in some way. Given a number of (x, y) coordinates in two
numeric vectors x and y, we could use the identify() function as follows:
> plot(x, y)
> identify(x, y)
The identify() functions performs no plotting itself, but simply allows the user to move
the mouse pointer and click the left mouse button near a point. If there is a point near the
mouse pointer it will be marked with its index number (that is, its position in the x/y vectors)
plotted nearby. Alternatively, you could use some informative string (such as a case name) as a
highlight by using the labels argument to identify(), or disable marking altogether with the
plot = FALSE argument. When the process is terminated (see above), identify() returns the
indices of the selected points; you can use these indices to extract the selected points from the
original vectors x and y.

12.4 Using graphics parameters

When creating graphics, particularly for presentation or publication purposes, R’s defaults do
not always produce exactly that which is required. You can, however, customize almost every
aspect of the display using graphics parameters. R maintains a list of a large number of graphics
parameters which control things such as line style, colors, figure arrangement and text justifica-
tion among many others. Every graphics parameter has a name (such as ‘col’, which controls
colors,) and a value (a color number, for example.)
A separate list of graphics parameters is maintained for each active device, and each device has
a default set of parameters when initialized. Graphics parameters can be set in two ways: either
permanently, affecting all graphics functions which access the current device; or temporarily,
affecting only a single graphics function call.

12.4.1 Permanent changes: The par() function

The par() function is used to access and modify the list of graphics parameters for the current
graphics device.
Chapter 12: Graphical procedures 68

par() Without arguments, returns a list of all graphics parameters and their values for
the current device.
par(c("col", "lty"))
With a character vector argument, returns only the named graphics parameters
(again, as a list.)
par(col=4, lty=2)
With named arguments (or a single list argument), sets the values of the named
graphics parameters, and returns the original values of the parameters as a list.
Setting graphics parameters with the par() function changes the value of the parameters
permanently, in the sense that all future calls to graphics functions (on the current device) will
be affected by the new value. You can think of setting graphics parameters in this way as
setting “default” values for the parameters, which will be used by all graphics functions unless
an alternative value is given.
Note that calls to par() always affect the global values of graphics parameters, even when
par() is called from within a function. This is often undesirable behavior—usually we want to
set some graphics parameters, do some plotting, and then restore the original values so as not
to affect the user’s R session. You can restore the initial values by saving the result of par()
when making changes, and restoring the initial values when plotting is complete.
> oldpar <- par(col=4, lty=2)
. . . plotting commands . . .
> par(oldpar)
To save and restore all settable1 graphical parameters use
> oldpar <- par(no.readonly=TRUE)
. . . plotting commands . . .
> par(oldpar)

12.4.2 Temporary changes: Arguments to graphics functions

Graphics parameters may also be passed to (almost) any graphics function as named arguments.
This has the same effect as passing the arguments to the par() function, except that the changes
only last for the duration of the function call. For example:
> plot(x, y, pch="+")
produces a scatterplot using a plus sign as the plotting character, without changing the default
plotting character for future plots.
Unfortunately, this is not implemented entirely consistently and it is sometimes necessary to
set and reset graphics parameters using par().

12.5 Graphics parameters list

The following sections detail many of the commonly-used graphical parameters. The R help
documentation for the par() function provides a more concise summary; this is provided as a
somewhat more detailed alternative.
Graphics parameters will be presented in the following form:
name =value
A description of the parameter’s effect. name is the name of the parameter, that
is, the argument name to use in calls to par() or a graphics function. value is a
typical value you might use when setting the parameter.
Note that axes is not a graphics parameter but an argument to a few plot methods: see
xaxt and yaxt.
1
Some graphics parameters such as the size of the current device are for information only.
Chapter 12: Graphical procedures 69

12.5.1 Graphical elements

R plots are made up of points, lines, text and polygons (filled regions.) Graphical parameters
exist which control how these graphical elements are drawn, as follows:

pch="+" Character to be used for plotting points. The default varies with graphics drivers,
but it is usually ‘◦’. Plotted points tend to appear slightly above or below the
appropriate position unless you use "." as the plotting character, which produces
centered points.

pch=4 When pch is given as an integer between 0 and 25 inclusive, a specialized plotting
symbol is produced. To see what the symbols are, use the command
> legend(locator(1), as.character(0:25), pch = 0:25)
Those from 21 to 25 may appear to duplicate earlier symbols, but can be coloured
in different ways: see the help on points and its examples.
In addition, pch can be a character or a number in the range 32:255 representing
a character in the current font.

lty=2 Line types. Alternative line styles are not supported on all graphics devices (and
vary on those that do) but line type 1 is always a solid line, line type 0 is always invis-
ible, and line types 2 and onwards are dotted or dashed lines, or some combination
of both.

lwd=2 Line widths. Desired width of lines, in multiples of the “standard” line width.
Affects axis lines as well as lines drawn with lines(), etc. Not all devices support
this, and some have restrictions on the widths that can be used.

col=2 Colors to be used for points, lines, text, filled regions and images. A number from
the current palette (see ?palette) or a named colour.

col.axis
col.lab
col.main
col.sub The color to be used for axis annotation, x and y labels, main and sub-titles, re-
spectively.

font=2 An integer which specifies which font to use for text. If possible, device drivers
arrange so that 1 corresponds to plain text, 2 to bold face, 3 to italic, 4 to bold
italic and 5 to a symbol font (which include Greek letters).

font.axis
font.lab
font.main
font.sub The font to be used for axis annotation, x and y labels, main and sub-titles, respec-
tively.

adj=-0.1 Justification of text relative to the plotting position. 0 means left justify, 1 means
right justify and 0.5 means to center horizontally about the plotting position. The
actual value is the proportion of text that appears to the left of the plotting position,
so a value of -0.1 leaves a gap of 10% of the text width between the text and the
plotting position.

cex=1.5 Character expansion. The value is the desired size of text characters (including
plotting characters) relative to the default text size.
Chapter 12: Graphical procedures 70

cex.axis
cex.lab
cex.main
cex.sub The character expansion to be used for axis annotation, x and y labels, main and
sub-titles, respectively.

12.5.2 Axes and tick marks

Many of R’s high-level plots have axes, and you can construct axes yourself with the low-level
axis() graphics function. Axes have three main components: the axis line (line style controlled
by the lty graphics parameter), the tick marks (which mark off unit divisions along the axis
line) and the tick labels (which mark the units.) These components can be customized with the
following graphics parameters.

lab=c(5, 7, 12)
The first two numbers are the desired number of tick intervals on the x and y axes
respectively. The third number is the desired length of axis labels, in characters
(including the decimal point.) Choosing a too-small value for this parameter may
result in all tick labels being rounded to the same number!

las=1 Orientation of axis labels. 0 means always parallel to axis, 1 means always horizon-
tal, and 2 means always perpendicular to the axis.

mgp=c(3, 1, 0)
Positions of axis components. The first component is the distance from the axis
label to the axis position, in text lines. The second component is the distance to
the tick labels, and the final component is the distance from the axis position to the
axis line (usually zero). Positive numbers measure outside the plot region, negative
numbers inside.

tck=0.01 Length of tick marks, as a fraction of the size of the plotting region. When tck
is small (less than 0.5) the tick marks on the x and y axes are forced to be the
same size. A value of 1 gives grid lines. Negative values give tick marks outside the
plotting region. Use tck=0.01 and mgp=c(1,-1.5,0) for internal tick marks.

xaxs="r"
yaxs="i" Axis styles for the x and y axes, respectively. With styles "i" (internal) and "r"
(the default) tick marks always fall within the range of the data, however style "r"
leaves a small amount of space at the edges. (S has other styles not implemented in
R.)

12.5.3 Figure margins

A single plot in R is known as a figure and comprises a plot region surrounded by margins
(possibly containing axis labels, titles, etc.) and (usually) bounded by the axes themselves.
Chapter 12: Graphical procedures 71

A typical figure is

−−−−−−−−−−−−−−−−−−
−−−−−−−−−−−−−−−−−−
−−−−−−−−−−−−−−−−−−
−−−−−−−−−−−−−−−−−− mar[3]
−−−−−−−−−−−−−−−−−−
−−−−−−−−−−−−−−−−−−
3.0

Plot region
1.5
0.0
y

mai[2]
−1.5
−3.0

−3.0 −1.5 0.0 1.5 3.0

mai[1] x
Margin

Graphics parameters controlling figure layout include:

mai=c(1, 0.5, 0.5, 0)

Widths of the bottom, left, top and right margins, respectively, measured in inches.

mar=c(4, 2, 2, 1)
Similar to mai, except the measurement unit is text lines.

mar and mai are equivalent in the sense that setting one changes the value of the other. The
default values chosen for this parameter are often too large; the right-hand margin is rarely
needed, and neither is the top margin if no title is being used. The bottom and left margins
must be large enough to accommodate the axis and tick labels. Furthermore, the default is
chosen without regard to the size of the device surface: for example, using the postscript()
driver with the height=4 argument will result in a plot which is about 50% margin unless mar
or mai are set explicitly. When multiple figures are in use (see below) the margins are reduced,
however this may not be enough when many figures share the same page.
Chapter 12: Graphical procedures 72

12.5.4 Multiple figure environment

R allows you to create an n by m array of figures on a single page. Each figure has its own
margins, and the array of figures is optionally surrounded by an outer margin, as shown in the
following figure.

−−−−−−−−−−−−−−−
−−−−−−−−−−−−−−−
−−−−−−−−−−−−−−− oma[3]
−−−−−−−−−−−−−−−
−−−−−−−−−−−−−−−

omi[4]
mfg=c(3,2,3,2)

omi[1]
mfrow=c(3,2)

The graphical parameters relating to multiple figures are as follows:

mfcol=c(3, 2)
mfrow=c(2, 4)
Set the size of a multiple figure array. The first value is the number of rows; the
second is the number of columns. The only difference between these two parameters
is that setting mfcol causes figures to be filled by column; mfrow fills by rows.
The layout in the Figure could have been created by setting mfrow=c(3,2); the
figure shows the page after four plots have been drawn.
Setting either of these can reduce the base size of symbols and text (controlled by
par("cex") and the pointsize of the device). In a layout with exactly two rows and
columns the base size is reduced by a factor of 0.83: if there are three or more of
either rows or columns, the reduction factor is 0.66.

mfg=c(2, 2, 3, 2)
Position of the current figure in a multiple figure environment. The first two numbers
are the row and column of the current figure; the last two are the number of rows
and columns in the multiple figure array. Set this parameter to jump between figures
in the array. You can even use different values for the last two numbers than the
true values for unequally-sized figures on the same page.

fig=c(4, 9, 1, 4)/10
Position of the current figure on the page. Values are the positions of the left, right,
bottom and top edges respectively, as a percentage of the page measured from the
bottom left corner. The example value would be for a figure in the bottom right of
the page. Set this parameter for arbitrary positioning of figures within a page. If
you want to add a figure to a current page, use new=TRUE as well (unlike S).
Chapter 12: Graphical procedures 73

oma=c(2, 0, 3, 0)
omi=c(0, 0, 0.8, 0)
Size of outer margins. Like mar and mai, the first measures in text lines and the
second in inches, starting with the bottom margin and working clockwise.
Outer margins are particularly useful for page-wise titles, etc. Text can be added to the outer
margins with the mtext() function with argument outer=TRUE. There are no outer margins by
default, however, so you must create them explicitly using oma or omi.
More complicated arrangements of multiple figures can be produced by the split.screen()
and layout() functions, as well as by the grid and lattice packages.

12.6 Device drivers

R can generate graphics (of varying levels of quality) on almost any type of display or printing
device. Before this can begin, however, R needs to be informed what type of device it is dealing
with. This is done by starting a device driver. The purpose of a device driver is to convert
graphical instructions from R (“draw a line,” for example) into a form that the particular device
can understand.
Device drivers are started by calling a device driver function. There is one such function
for every device driver: type help(Devices) for a list of them all. For example, issuing the
command
> postscript()
causes all future graphics output to be sent to the printer in PostScript format. Some commonly-
used device drivers are:
X11() For use with the X11 window system on Unix-alikes
windows()
For use on Windows
quartz() For use on MacOS X
postscript()
For printing on PostScript printers, or creating PostScript graphics files.
pdf() Produces a PDF file, which can also be included into PDF files.
png() Produces a bitmap PNG file. (Not always available: see its help page.)
jpeg() Produces a bitmap JPEG file, best used for image plots. (Not always available: see
its help page.)
When you have finished with a device, be sure to terminate the device driver by issuing the
command
> dev.off()
This ensures that the device finishes cleanly; for example in the case of hardcopy devices
this ensures that every page is completed and has been sent to the printer. (This will happen
automatically at the normal end of a session.)

12.6.1 PostScript diagrams for typeset documents

By passing the file argument to the postscript() device driver function, you may store the
graphics in PostScript format in a file of your choice. The plot will be in landscape orientation
unless the horizontal=FALSE argument is given, and you can control the size of the graphic with
the width and height arguments (the plot will be scaled as appropriate to fit these dimensions.)
For example, the command
Chapter 12: Graphical procedures 74

> postscript("file.ps", horizontal=FALSE, height=5, pointsize=10)

will produce a file containing PostScript code for a figure five inches high, perhaps for inclusion
in a document. It is important to note that if the file named in the command already exists,
it will be overwritten. This is the case even if the file was only created earlier in the same R
session.
Many usages of PostScript output will be to incorporate the figure in another document. This
works best when encapsulated PostScript is produced: R always produces conformant output,
but only marks the output as such when the onefile=FALSE argument is supplied. This unusual
notation stems from S-compatibility: it really means that the output will be a single page (which
is part of the EPSF specification). Thus to produce a plot for inclusion use something like
> postscript("plot1.eps", horizontal=FALSE, onefile=FALSE,
height=8, width=6, pointsize=10)

12.6.2 Multiple graphics devices

In advanced use of R it is often useful to have several graphics devices in use at the same time.
Of course only one graphics device can accept graphics commands at any one time, and this is
known as the current device. When multiple devices are open, they form a numbered sequence
with names giving the kind of device at any position.
The main commands used for operating with multiple devices, and their meanings are as
follows:

X11() [UNIX]
windows()
win.printer()
win.metafile()
[Windows]
quartz() [MacOS X]
postscript()
pdf()
... Each new call to a device driver function opens a new graphics device, thus extending
by one the device list. This device becomes the current device, to which graphics
output will be sent. (Some platforms may have further devices available.)
dev.list()
Returns the number and name of all active devices. The device at position 1 on the
list is always the null device which does not accept graphics commands at all.
dev.next()
dev.prev()
Returns the number and name of the graphics device next to, or previous to the
current device, respectively.
dev.set(which=k )
Can be used to change the current graphics device to the one at position k of the
device list. Returns the number and label of the device.
dev.off(k )
Terminate the graphics device at point k of the device list. For some devices, such as
postscript devices, this will either print the file immediately or correctly complete
the file for later printing, depending on how the device was initiated.
Chapter 12: Graphical procedures 75

dev.copy(device, ..., which=k )

dev.print(device, ..., which=k )
Make a copy of the device k. Here device is a device function, such as postscript,
with extra arguments, if needed, specified by ‘...’. dev.print is similar, but the
copied device is immediately closed, so that end actions, such as printing hardcopies,
are immediately performed.
graphics.off()
Terminate all graphics devices on the list, except the null device.

12.7 Dynamic graphics

R does not have builtin capabilities for dynamic or interactive graphics, e.g. rotating point
clouds or to “brushing” (interactively highlighting) points. However, extensive dynamic graphics
facilities are available in the system GGobi by Swayne, Cook and Buja available from
http://www.ggobi.org/
and these can be accessed from R via the package rggobi, described at
http://www.ggobi.org/rggobi.
Also, package rgl provides ways to interact with 3D plots, for example of surfaces.
Chapter 13: Packages 76

13 Packages
All R functions and datasets are stored in packages. Only when a package is loaded are its
contents available. This is done both for efficiency (the full list would take more memory and
would take longer to search than a subset), and to aid package developers, who are protected
from name clashes with other code. The process of developing packages is described in section
“Creating R packages” in Writing R Extensions. Here, we will describe them from a user’s point
of view.
To see which packages are installed at your site, issue the command
> library()
with no arguments. To load a particular package (e.g., the boot package containing functions
from Davison & Hinkley (1997)), use a command like
> library(boot)
Users connected to the Internet can use the install.packages() and update.packages()
functions (available through the Packages menu in the Windows and RAqua GUIs, see section
“Installing packages” in R Installation and Adminstration) to install and update packages.
To see which packages are currently loaded, use
> search()
to display the search list. Some packages may be loaded but not available on the search list (see
Section 13.3 [Namespaces], page 76): these will be included in the list given by
> loadedNamespaces()
To see a list of all available help topics in an installed package, use
> help.start()
to start the HTML help system, and then navigate to the package listing in the Reference
section.

13.1 Standard packages

The standard (or base) packages are considered part of the R source code. They contain the
basic functions that allow R to work, and the datasets and standard statistical and graphical
functions that are described in this manual. They should be automatically available in any R
installation. See section “R packages” in R FAQ, for a complete list.

13.2 Contributed packages and CRAN

There are hundreds of contributed packages for R, written by many different authors. Some of
these packages implement specialized statistical methods, others give access to data or hard-
ware, and others are designed to complement textbooks. Some (the recommended packages) are
distributed with every binary distribution of R. Most are available for download from CRAN
(http://CRAN.R-project.org/ and its mirrors), and other repositories such as Bioconductor
(http://www.bioconductor.org/). The R FAQ contains a list that was current at the time of
release, but the collection of available packages changes frequently.

13.3 Namespaces
Packages can have namespaces, and currently all of the base and recommended packages do
expect the datasets package. Namespaces do three things: they allow the package writer
to hide functions and data that are meant only for internal use, they prevent functions from
breaking when a user (or other package writer) picks a name that clashes with one in the package,
and they provide a way to refer to an object within a particular package.
Chapter 13: Packages 77

For example, t() is the transpose function in R, but users might define their own function
named t. Namespaces prevent the user’s definition from taking precedence, and breaking every
function that tries to transpose a matrix.
There are two operators that work with namespaces. The double-colon operator :: selects
definitions from a particular namespace. In the example above, the transpose function will
always be available as base::t, because it is defined in the base package. Only functions that
are exported from the package can be retrieved in this way.
The triple-colon operator ::: may be seen in a few places in R code: it acts like the
double-colon operator but also allows access to hidden objects. Users are more likely to use
the getAnywhere() function, which searches multiple packages.
Packages are often inter-dependent, and loading one may cause others to be automatically
loaded. The colon operators described above will also cause automatic loading of the associated
package. When packages with namespaces are loaded automatically they are not added to the
search list.
Appendix A: A sample session 78

Appendix A A sample session

The following session is intended to introduce to you some features of the R environment by
using them. Many features of the system will be unfamiliar and puzzling at first, but this
puzzlement will soon disappear.
Login, start your windowing system.
$R Start R as appropriate for your platform.
The R program begins, with a banner.
(Within R, the prompt on the left hand side will not be shown to avoid confusion.)
help.start()
Start the HTML interface to on-line help (using a web browser available at your
machine). You should briefly explore the features of this facility with the mouse.
Iconify the help window and move on to the next part.
x <- rnorm(50)
y <- rnorm(x)
Generate two pseudo-random normal vectors of x- and y-coordinates.
plot(x, y)
Plot the points in the plane. A graphics window will appear automatically.
ls() See which R objects are now in the R workspace.
rm(x, y) Remove objects no longer needed. (Clean up).
x <- 1:20 Make x = (1, 2, . . . , 20).
w <- 1 + sqrt(x)/2
A ‘weight’ vector of standard deviations.
dummy <- data.frame(x=x, y= x + rnorm(x)*w)
dummy Make a data frame of two columns, x and y, and look at it.
fm <- lm(y ~ x, data=dummy)
summary(fm)
Fit a simple linear regression of y on x and look at the analysis.
fm1 <- lm(y ~ x, data=dummy, weight=1/w^2)
summary(fm1)
Since we know the standard deviations, we can do a weighted regression.
attach(dummy)
Make the columns in the data frame visible as variables.
lrf <- lowess(x, y)
Make a nonparametric local regression function.
plot(x, y)
Standard point plot.
lines(x, lrf$y)
Add in the local regression.
abline(0, 1, lty=3)
The true regression line: (intercept 0, slope 1).
abline(coef(fm))
Unweighted regression line.
Appendix A: A sample session 79

abline(coef(fm1), col = "red")

Weighted regression line.
detach() Remove data frame from the search path.
plot(fitted(fm), resid(fm),
xlab="Fitted values",
ylab="Residuals",
main="Residuals vs Fitted")
A standard regression diagnostic plot to check for heteroscedasticity. Can you see
it?
qqnorm(resid(fm), main="Residuals Rankit Plot")
A normal scores plot to check for skewness, kurtosis and outliers. (Not very useful
here.)
rm(fm, fm1, lrf, x, dummy)
Clean up again.
The next section will look at data from the classical experiment of Michaelson and Morley
to measure the speed of light. This dataset is available in the morley object, but we will read
it to illustrate the read.table function.
filepath <- system.file("data", "morley.tab" , package="datasets")
filepath Get the path to the data file.
file.show(filepath)
Optional. Look at the file.
mm <- read.table(filepath)
mm Read in the Michaelson and Morley data as a data frame, and look at it. There are
five experiments (column Expt) and each has 20 runs (column Run) and sl is the
recorded speed of light, suitably coded.
mm$Expt <- factor(mm$Expt)
mm$Run <- factor(mm$Run)
Change Expt and Run into factors.
attach(mm)
Make the data frame visible at position 3 (the default).
plot(Expt, Speed, main="Speed of Light Data", xlab="Experiment No.")
Compare the five experiments with simple boxplots.
fm <- aov(Speed ~ Run + Expt, data=mm)
summary(fm)
Analyze as a randomized block, with ‘runs’ and ‘experiments’ as factors.
fm0 <- update(fm, . ~ . - Run)
anova(fm0, fm)
Fit the sub-model omitting ‘runs’, and compare using a formal analysis of variance.
detach()
rm(fm, fm0)
Clean up before moving on.
We now look at some more graphical features: contour and image plots.
x <- seq(-pi, pi, len=50)
y <- x x is a vector of 50 equally spaced values in −π ≤ x ≤ π. y is the same.
Appendix A: A sample session 80

f <- outer(x, y, function(x, y) cos(y)/(1 + x^2))

f is a square matrix, with rows and columns indexed by x and y respectively, of
values of the function cos(y)/(1 + x2 ).
oldpar <- par(no.readonly = TRUE)
par(pty="s")
Save the plotting parameters and set the plotting region to “square”.
contour(x, y, f)
contour(x, y, f, nlevels=15, add=TRUE)
Make a contour map of f ; add in more lines for more detail.
fa <- (f-t(f))/2
fa is the “asymmetric part” of f . (t() is transpose).
contour(x, y, fa, nlevels=15)
Make a contour plot, . . .
par(oldpar)
. . . and restore the old graphics parameters.
image(x, y, f)
image(x, y, fa)
Make some high density image plots, (of which you can get hardcopies if you wish),
...
objects(); rm(x, y, f, fa)
. . . and clean up before moving on.
R can do complex arithmetic, also.
th <- seq(-pi, pi, len=100)
z <- exp(1i*th)
1i is used for the complex number i.
par(pty="s")
plot(z, type="l")
Plotting complex arguments means plot imaginary versus real parts. This should
be a circle.
w <- rnorm(100) + rnorm(100)*1i
Suppose we want to sample points within the unit circle. One method would be to
take complex numbers with standard normal real and imaginary parts . . .
w <- ifelse(Mod(w) > 1, 1/w, w)
. . . and to map any outside the circle onto their reciprocal.
plot(w, xlim=c(-1,1), ylim=c(-1,1), pch="+",xlab="x", ylab="y")
lines(z)
All points are inside the unit circle, but the distribution is not uniform.
w <- sqrt(runif(100))*exp(2*pi*runif(100)*1i)
plot(w, xlim=c(-1,1), ylim=c(-1,1), pch="+", xlab="x", ylab="y")
lines(z)
The second method uses the uniform distribution. The points should now look more
evenly spaced over the disc.
rm(th, w, z)
Clean up again.
q() Quit the R program. You will be asked if you want to save the R workspace, and
for an exploratory session like this, you probably do not want to save it.
Appendix B: Invoking R 81

Appendix B Invoking R

B.1 Invoking R from the command line

When working in UNIX or at a command line in Windows, the command ‘R’ can be used both
for starting the main R program in the form
R [options] [<infile] [>outfile],
or, via the R CMD interface, as a wrapper to various R tools (e.g., for processing files in R
documentation format or manipulating add-on packages) which are not intended to be called
“directly”.
You need to ensure that either the environment variable TMPDIR is unset or it points to a
valid place to create temporary files and directories.
Most options control what happens at the beginning and at the end of an R session. The
startup mechanism is as follows (see also the on-line help for topic ‘Startup’ for more informa-
tion, and the section below for some Windows-specific details).
• Unless ‘--no-environ’ was given, R searches for user and site files to process for setting
environment variables. The name of the site file is the one pointed to by the environment
variable R_ENVIRON; if this is unset, ‘$R_HOME/etc/Renviron.site’ is used (if it exists).
The user file searched for is ‘.Renviron’ in the current or in the user’s home directory (in
that order). These files should contain lines of the form ‘name =value ’. (See help(Startup)
for a precise description.) Variables you might want to set include R_PAPERSIZE (the default
paper size), R_PRINTCMD (the default print command) and R_LIBS (specifies the list of R
library trees searched for add-on packages).
• Then R searches for the site-wide startup profile unless the command line option
‘--no-site-file’ was given. The name of this file is taken from the value
of the R_PROFILE environment variable. If that variable is unset, the default
‘$R_HOME/etc/Rprofile.site’ is used if this exists.
• Then, unless ‘--no-init-file’ was given, R searches for a file called ‘.Rprofile’ in the
current directory or in the user’s home directory (in that order) and sources it.
• It also loads a saved image from ‘.RData’ if there is one (unless ‘--no-restore’ or
‘--no-restore-data’ was specified).
• Finally, if a function .First exists, it is executed. This function (as well as .Last which is
executed at the end of the R session) can be defined in the appropriate startup profiles, or
reside in ‘.RData’.
In addition, there are options for controlling the memory available to the R process (see the
on-line help for topic ‘Memory’ for more information). Users will not normally need to use these
unless they are trying to limit the amount of memory used by R.
R accepts the following command-line options.
‘--help’
‘-h’ Print short help message to standard output and exit successfully.
‘--version’
Print version information to standard output and exit successfully.
‘--encoding=enc ’
Specify the encoding to be assumed for input from the console or stdin. This needs
to be an encoding known to iconv: see its help page.
‘RHOME’ Print the path to the R “home directory” to standard output and exit success-
fully. Apart from the front-end shell script and the man page, R installation puts
everything (executables, packages, etc.) into this directory.
Appendix B: Invoking R 82

‘--save’
‘--no-save’
Control whether data sets should be saved or not at the end of the R session. If
neither is given in an interactive session, the user is asked for the desired behavior
when ending the session with q(); in non-interactive use one of these must be
specified or implied by some other option (see below).
‘--no-environ’
Do not read any user file to set environment variables.
‘--no-site-file’
Do not read the site-wide profile at startup.
‘--no-init-file’
Do not read the user’s profile at startup.
‘--restore’
‘--no-restore’
‘--no-restore-data’
Control whether saved images (file ‘.RData’ in the directory where R was started)
should be restored at startup or not. The default is to restore. (‘--no-restore’
implies all the specific ‘--no-restore-*’ options.)
‘--no-restore-history’
Control whether the history file (normally file ‘.Rhistory’ in the directory where
R was started, but can be set by the environment variable R_HISTFILE) should be
restored at startup or not. The default is to restore.
‘--no-Rconsole’
(Windows only) Prevent loading the ‘Rconsole’ file at startup.
‘--vanilla’
Combine ‘--no-save’, ‘--no-environ’, ‘--no-site-file’, ‘--no-init-file’ and
‘--no-restore’. Under Windows, this also includes ‘--no-Rconsole’.
‘-f file ’
‘--file=file ’
Take input from file: ‘-’ means stdin. Implies ‘--no-save’ unless ‘--save’ has
been set.
‘-e expression ’
Use expression as an input line. One or more ‘-e’ options can be used, but not
together with ‘-f’ or ‘--file’. Implies ‘--no-save’ unless ‘--save’ has been set.
(There is a limit of 10,000 bytes on the total length of expressions used in this way.)
‘--no-readline’
(UNIX only) Turn off command-line editing via readline. This is useful when run-
ning R from within Emacs using the ESS (“Emacs Speaks Statistics”) package. See
Appendix C [The command-line editor], page 87, for more information.
‘--ess’ (Windows only) Set Rterm up for use by R-inferior-mode in ESS.
‘--min-vsize=N ’
‘--max-vsize=N ’
Specify the minimum or maximum amount of memory used for variable size objects
by setting the “vector heap” size to N bytes. Here, N must either be an integer
or an integer ending with ‘G’, ‘M’, ‘K’, or ‘k’, meaning ‘Giga’ (2^30), ‘Mega’ (2^20),
(computer) ‘Kilo’ (2^10), or regular ‘kilo’ (1000).
Appendix B: Invoking R 83

‘--min-nsize=N ’
‘--max-nsize=N ’
Specify the amount of memory used for fixed size objects by setting the number of
“cons cells” to N. See the previous option for details on N. A cons cell takes 28 bytes
on a 32-bit machine, and usually 56 bytes on a 64-bit machine.
‘--max-ppsize=N ’
Specify the maximum size of the pointer protection stack as N locations. This
defaults to 10000, but can be increased to allow large and complicated calculations
to be done. Currently the maximum value accepted is 100000.
‘--max-mem-size=N ’
(Windows only) Specify a limit for the amount of memory to be used both for R
objects and working areas. This is set by default to the smaller of 1.5Gb1 and the
amount of physical RAM in the machine, and must be between 32Mb and 3Gb.
‘--quiet’
‘--silent’
‘-q’ Do not print out the initial copyright and welcome messages.
‘--slave’ Make R run as quietly as possible. This option is intended to support programs
which use R to compute results for them. It implies ‘--quiet’ and ‘--no-save’.
‘--verbose’
Print more information about progress, and in particular set R’s option verbose to
TRUE. R code uses this option to control the printing of diagnostic messages.
‘--debugger=name ’
‘-d name ’ (UNIX only) Run R through debugger name. For most debuggers (the exceptions are
valgrind and recent versions of gdb), further command line options are disregarded,
and should instead be given when starting the R executable from inside the debugger.
‘--gui=type ’
‘-g type ’ (UNIX only) Use type as graphical user interface (note that this also includes in-
teractive graphics). Currently, possible values for type are ‘X11’ (the default), pro-
vided that ‘Tcl/Tk’ support is available, ‘Tk’ and ‘gnome’ provided that package
gnomeGUI is installed. (For back-compatibility, ‘x11’, ‘tk’ and ‘GNOME’ are ac-
cepted.)
‘--args’ This flag does nothing except cause the rest of the command line to be skipped:
this can be useful to retrieve values from it with commandArgs(TRUE).
Note that input and output can be redirected in the usual way (using ‘<’ and ‘>’), but the
line length limit of 1024 bytes still applies. Warning and error messages are sent to the error
channel (stderr) except on Windows 9X/ME.
The command R CMD allows the invocation of various tools which are useful in conjunction
with R, but not intended to be called “directly”. The general form is
R CMD command args
where command is the name of the tool and args the arguments passed on to it.
Currently, the following tools are available.
BATCH Run R in batch mode.
COMPILE (UNIX only) Compile files for use with R.
1
2.5Gb on versions of Windows that support 3Gb per process and have the support enabled: see the ‘rw-FAQ’
Q2.9.
Appendix B: Invoking R 84

SHLIB Build shared library for dynamic loading.

INSTALL Install add-on packages.
REMOVE Remove add-on packages.
build Build (that is, package) add-on packages.
check Check add-on packages.
LINK (UNIX only) Front-end for creating executable programs.
Rprof Post-process R profiling files.
Rdconv Convert Rd format to various other formats, including HTML, Nroff, LATEX, plain
text, and S documentation format.
Rd2dvi Convert Rd format to DVI/PDF.
Rd2txt Convert Rd format to text.
Sd2Rd Convert S documentation to Rd format.
config Obtain configuration information.
Use
R CMD command --help
to obtain usage information for each of the tools accessible via the R CMD interface.

B.2 Invoking R under Windows

There are two ways to run R under Windows. Within a terminal window (e.g. cmd.exe or
command.com or a more capable shell), the methods described in the previous section may be
used, invoking by R.exe or more directly by Rterm.exe. (These are principally intended for
batch use.) For interactive use, there is a console-based GUI (Rgui.exe).
The startup procedure under Windows is very similar to that under UNIX, but references
to the ‘home directory’ need to be clarified, as this is not always defined on Windows. If the
environment variable R_USER is defined, that gives the home directory. Next, if the environment
variable HOME is defined, that gives the home directory. After those two user-controllable settings,
R tries to find system defined home directories. It first tries to use the Windows "personal"
directory (typically C:\Documents and Settings\username\My Documents in Windows XP). If
that fails, and environment variables HOMEDRIVE and HOMEPATH are defined (and they normally
are under Windows NT/2000/XP) these define the home directory. Failing all those, the home
directory is taken to be the starting directory.
You need to ensure that either the environment variables TMPDIR, TMP and TEMP are either
unset or one of them points to a valid place to create temporary files and directories.
Environment variables can be supplied as ‘name =value ’ pairs at the end of the command
line.
The following additional command-line options are available when invoking RGui.exe.
‘--mdi’
‘--sdi’
‘--no-mdi’
Control whether Rgui will operate as an MDI program (with multiple child windows
within one main window) or an SDI application (with multiple top-level windows for
the console, graphics and pager). The command-line setting overrides the setting in
the user’s ‘Rconsole’ file.
Appendix B: Invoking R 85

‘--debug’ Enable the “Break to debugger” menu item in Rgui, and trigger a break to the
debugger during command line processing.
In Windows with R CMD you may also specify your own ‘*.bat’ or ‘*.exe’ file instead of one of
the built-in commands. It will be run with the following environment variables set appropriately:
R_HOME, R_VERSION, R_CMD, R_OSTYPE, PATH, PERL5LIB, and TEXINPUTS. For example, if you
already have ‘latex.exe’ on your path, then
R CMD latex.exe mydoc
will run LATEX on ‘mydoc.tex’, with the path to R’s ‘share/texmf’ macros added to TEXINPUTS.

B.3 Invoking R under Mac OS X

There are two ways to run R under Mac OS X. Within a Terminal.app window by invoking R,
the methods described in the previous sections apply. There is also console-based GUI (R.app)
that by default is installed in the Applications folder on your system. It is a standard double-
clickable Mac OS X application.
The startup procedure under Mac OS X is very similar to that under UNIX. The ‘home
directory’ is the one inside the R.framework, but the startup and current working directory are
set as the user’s home directory unless a different startup directory is given in the Preferences
window accessible from within the GUI.

B.4 Scripting with R

If you just want to run a file ‘foo.R’ of R commands, the recommended way is to use R CMD
BATCH foo.R. If you want to run this in the background or as a batch job use OS-specific
facilities to do so: for example in most shells on Unix-alike OSes R CMD BATCH foo.R & runs a
background job.
You can pass parameters to scripts via additional arguments on the command line: for
example
R CMD BATCH --args arg1 arg2 foo.R &
will pass arguments to a script which can be retrieved as a character vector by
args <- commandArgs(TRUE)
This is made simpler by the alternative front-end Rscript, which can be invoked by
Rscript foo.R arg1 arg2
and this can also be used to write executable script files like (at least on Unix-alikes, and in
some Windows shells)
#! /path/to/Rscript
args <- commandArgs(TRUE)
...
q(status=<exit status code>)
If this is entered into a text file ‘runfoo’ and this is made executable (by chmod 755 runfoo),
it can be invoked for different arguments by
runfoo arg1 arg2
For further options see help("Rscript"). If you do not wish to hardcode the path to Rscript
but have it in your path (which is normally the case for an installed R), use
#! /usr/bin/env Rscript
...
At least in Bourne and bash shells, the #! mechanism does not allow extra arguments like #!
/usr/bin/env Rscript --vanilla.
Appendix B: Invoking R 86

One thing to consider is what stdin() refers to. It is commonplace to write R scripts with
segments like
chem <- scan(n=24)
2.90 3.10 3.40 3.40 3.70 3.70 2.80 2.50 2.40 2.40 2.70 2.20
5.28 3.37 3.03 3.03 28.95 3.77 3.40 2.20 3.50 3.60 3.70 3.70
and stdin() refers to the script file to allow such traditional usage. If you want to refer to the
process’s ‘stdin’, use "stdin" as a file connection, e.g. scan("stdin", ...).
Another way to write executable script files (suggested by François Pinard) is to use a here
document like
#!/bin/sh
[environment variables can be set here]
R --slave [other options] <<EOF

R program goes here...

EOF
but here stdin() refers to the program source and "stdin" will not be usable.
Appendix C: The command-line editor 87

Appendix C The command-line editor

C.1 Preliminaries
When the GNU readline library is available at the time R is configured for compilation un-
der UNIX, an inbuilt command line editor allowing recall, editing and re-submission of prior
commands is used.
It can be disabled (useful for usage with ESS1 ) using the startup option ‘--no-readline’.
Windows versions of R have somewhat simpler command-line editing: see ‘Console’ under the
‘Help’ menu of the GUI, and the file ‘README.Rterm’ for command-line editing under Rterm.exe.
When using R with readline capabilities, the functions described below are available.
Many of these use either Control or Meta characters. Control characters, such as Control-m,
are obtained by holding the hCTRLi down while you press the hmi key, and are written as C-m
below. Meta characters, such as Meta-b, are typed by holding down hMETAi2 and pressing hbi,
and written as M-b in the following. If your terminal does not have a hMETAi key, you can still
type Meta characters using two-character sequences starting with ESC. Thus, to enter M-b, you
could type hESCihbi. The ESC character sequences are also allowed on terminals with real Meta
keys. Note that case is significant for Meta characters.

C.2 Editing actions

The R program keeps a history of the command lines you type, including the erroneous lines,
and commands in your history may be recalled, changed if necessary, and re-submitted as new
commands. In Emacs-style command-line editing any straight typing you do while in this
editing phase causes the characters to be inserted in the command you are editing, displacing
any characters to the right of the cursor. In vi mode character insertion mode is started by M-i
or M-a, characters are typed and insertion mode is finished by typing a further hESCi.
Pressing the hRETi command at any time causes the command to be re-submitted.
Other editing actions are summarized in the following table.

C.3 Command-line editor summary

Command recall and vertical motion
C-p Go to the previous command (backwards in the history).
C-n Go to the next command (forwards in the history).
C-r text Find the last command with the text string in it.
On most terminals, you can also use the up and down arrow keys instead of C-p and C-n,
respectively.

Horizontal motion of the cursor

C-a Go to the beginning of the command.
C-e Go to the end of the line.
M-b Go back one word.
M-f Go forward one word.
1
The ‘Emacs Speaks Statistics’ package; see the URL http://ESS.R-project.org
2
On a PC keyboard this is usually the Alt key, occasionally the ‘Windows’ key.
Appendix C: The command-line editor 88

C-b Go back one character.

C-f Go forward one character.
On most terminals, you can also use the left and right arrow keys instead of C-b and C-f,
respectively.

Editing and re-submission

text Insert text at the cursor.
C-f text Append text after the cursor.
hDELi Delete the previous character (left of the cursor).
C-d Delete the character under the cursor.
M-d Delete the rest of the word under the cursor, and “save” it.
C-k Delete from cursor to end of command, and “save” it.
C-y Insert (yank) the last “saved” text here.
C-t Transpose the character under the cursor with the next.
M-l Change the rest of the word to lower case.
M-c Change the rest of the word to upper case.
hRETi Re-submit the command to R.
The final hRETi terminates the command line editing sequence.
Appendix D: Function and variable index 89

Appendix D Function and variable index

! ^
!. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 ^. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
!= . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

|
% |. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
%*% . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22 || . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
%o% . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
~
& ~ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
&. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
&& . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
A
abline . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
* ace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
*. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 add1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
anova . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53, 54
aov . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
+ aperm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
+. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 array . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
as.data.frame. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
as.vector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
- attach . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
-. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 attr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
attributes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
avas . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
. axis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
.First . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
.Last . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48 B
boxplot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
break . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
/ bruto . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
/. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
C
: c . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7, 10, 24, 27
:. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 C . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
:: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76 cbind . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
::: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76 coef . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
coefficients . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
contour . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
< contrasts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
<. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 coplot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
<<- . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47 cos . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
<= . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 crossprod . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19, 22
cut . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
=
== . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 D
data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
data.frame . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
> density . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
>. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 det . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
>= . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 detach . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
determinant . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
dev.list . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
? dev.next . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
?. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 dev.off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
Appendix D: Function and variable index 90

dev.prev . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74 list . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
dev.set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74 lm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
deviance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53 lme . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
diag . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22 locator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
dim . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18 loess . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
dotchart . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64 log . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
drop1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55 lqs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
lsfit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
E
ecdf . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35 M
edit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32 mars . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
eigen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23 max . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
else . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40 mean . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Error . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54 methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
example . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 min . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
exp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

F N
F. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
NA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
factor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
NaN . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
FALSE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
ncol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
fivenum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
next . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
for . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
formula . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53 nlm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58, 59, 60
function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42 nlme . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
nlminb . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
nrow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
G
getAnywhere . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
getS3method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
O
glm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56 optim . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
order . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
ordered . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
H outer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
help . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
help.search . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
help.start . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 P
hist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34, 63 pairs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
par . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
paste . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
I pdf . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
identify . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67 persp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
if . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40 plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53, 62
ifelse . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40 pmax . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
image . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64 pmin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
is.na . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 png . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
is.nan . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10 points . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
polygon . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
J postscript . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
predict . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
jpeg . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73 print . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
prod . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
K
ks.test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36 Q
qqline . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35, 63
L qqnorm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35, 63
legend . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65 qqplot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
length . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8, 13 qr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
levels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16 quartz . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
lines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
Appendix D: Function and variable index 91

R T
range . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 t . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
rbind . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24 T. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
read.table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30 t.test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
rep . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20, 25
repeat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41 tan . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
resid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53 tapply . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
residuals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53 text . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
title . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
rlm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
tree . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
rm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
TRUE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

S U
scan . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31 unclass . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
sd . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17 update . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
search . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
seq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
shapiro.test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36 V
sin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 var . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8, 17
sink . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 var.test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
solve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22 vcov . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
sort . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 vector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
source . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
split . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
sqrt . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
W
stem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33 while . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
step . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53, 55 wilcox.test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
sum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 windows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33, 53
svd . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23 X
X11 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
Appendix E: Concept index 92

Appendix E Concept index

A K
Accessing builtin datasets . . . . . . . . . . . . . . . . . . . . . . . 31 Kolmogorov-Smirnov test . . . . . . . . . . . . . . . . . . . . . . . 36
Additive models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
Analysis of variance . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
Arithmetic functions and operators . . . . . . . . . . . . . . . 7 L
Arrays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18 Least squares fitting . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Assignment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 Linear equations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Attributes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13 Linear models. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
Lists . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Local approximating regressions . . . . . . . . . . . . . . . . . 60
B Loops and conditional execution. . . . . . . . . . . . . . . . . 40
Binary operators . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Box plots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
M
Matrices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
C Matrix multiplication . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Character vectors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10 Maximum likelihood . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
Classes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14, 48 Missing values . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Concatenating lists . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27 Mixed models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
Contrasts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
Control statements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40 N
CRAN . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
Customizing the environment . . . . . . . . . . . . . . . . . . . 48 Named arguments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Namespace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
Nonlinear least squares . . . . . . . . . . . . . . . . . . . . . . . . . 58
D
Data frames . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27 O
Default values . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Object orientation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
Density estimation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Objects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Determinants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
One- and two-sample tests . . . . . . . . . . . . . . . . . . . . . . 36
Diverting input and output . . . . . . . . . . . . . . . . . . . . . . 5
Ordered factors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16, 52
Dynamic graphics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
Outer products of arrays . . . . . . . . . . . . . . . . . . . . . . . . 21

E P
Eigenvalues and eigenvectors . . . . . . . . . . . . . . . . . . . . 23 Packages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2, 76
Empirical CDFs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35 Probability distributions . . . . . . . . . . . . . . . . . . . . . . . . 33

F Q
Factors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16, 52 QR decomposition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Families . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56 Quantile-quantile plots . . . . . . . . . . . . . . . . . . . . . . . . . 35
Formulae . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50

R
G Reading data from files . . . . . . . . . . . . . . . . . . . . . . . . . 30
Generalized linear models . . . . . . . . . . . . . . . . . . . . . . . 55 Recycling rule . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7, 20
Generalized transpose of an array . . . . . . . . . . . . . . . 21 Regular sequences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Generic functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48 Removing objects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Graphics device drivers . . . . . . . . . . . . . . . . . . . . . . . . . 73 Robust regression . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
Graphics parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
Grouped expressions . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
S
Scope . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
I Search path . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Indexing of and by arrays . . . . . . . . . . . . . . . . . . . . . . . 18 Shapiro-Wilk test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
Indexing vectors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10 Singular value decomposition. . . . . . . . . . . . . . . . . . . . 23
Statistical models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Appendix E: Concept index 93

Student’s t test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37 V
Vectors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
T
Tabulation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Tree-based models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60 W
Wilcoxon test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
U Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Updating fitted models . . . . . . . . . . . . . . . . . . . . . . . . . 54 Writing functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
Appendix F: References 94

Appendix F References
D. M. Bates and D. G. Watts (1988), Nonlinear Regression Analysis and Its Applications. John
Wiley & Sons, New York.
Richard A. Becker, John M. Chambers and Allan R. Wilks (1988), The New S Language. Chap-
man & Hall, New York. This book is often called the “Blue Book ”.
John M. Chambers and Trevor J. Hastie eds. (1992), Statistical Models in S. Chapman & Hall,
New York. This is also called the “White Book ”.
John M. Chambers (1998) Programming with Data. Springer, New York. This is also called the
“Green Book ”.
A. C. Davison and D. V. Hinkley (1997), Bootstrap Methods and Their Applications, Cambridge
University Press.
Annette J. Dobson (1990), An Introduction to Generalized Linear Models, Chapman and Hall,
London.
Peter McCullagh and John A. Nelder (1989), Generalized Linear Models. Second edition, Chap-
man and Hall, London.
John A. Rice (1995), Mathematical Statistics and Data Analysis. Second edition. Duxbury
Press, Belmont, CA.
S. D. Silvey (1970), Statistical Inference. Penguin, London.
R for Beginners

Emmanuel Paradis

Institut des Sciences de l’Évolution

Université Montpellier II
F-34095 Montpellier cédex 05
France

E-mail: [email protected]
 I thank Julien Claude, Christophe Declercq, Élodie Gazave, Friedrich Leisch,
Louis Luangkesron, François Pinard, and Mathieu Ros for their comments and
suggestions on earlier versions of this document. I am also grateful to all the
members of the R Development Core Team for their considerable efforts in
developing R and animating the discussion list ‘rhelp’. Thanks also to the
R users whose questions or comments helped me to write “R for Beginners”.
Special thanks to Jorge Ahumada for the Spanish translation.

c 2002, 2005, Emmanuel Paradis (12th September 2005)

Permission is granted to make and distribute copies, either in part or in

full and in any language, of this document on any support provided the above
copyright notice is included in all copies. Permission is granted to translate
this document, either in part or in full, in any language provided the above
copyright notice is included.
 Contents

1 Preamble 1

2 A few concepts before starting 3

2.1 How R works . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
2.2 Creating, listing and deleting the objects in memory . . . . . . 5
2.3 The on-line help . . . . . . . . . . . . . . . . . . . . . . . . . . 7

3 Data with R 9
3.1 Objects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
3.2 Reading data in a file . . . . . . . . . . . . . . . . . . . . . . . 11
3.3 Saving data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
3.4 Generating data . . . . . . . . . . . . . . . . . . . . . . . . . . 15
3.4.1 Regular sequences . . . . . . . . . . . . . . . . . . . . . 15
3.4.2 Random sequences . . . . . . . . . . . . . . . . . . . . . 17
3.5 Manipulating objects . . . . . . . . . . . . . . . . . . . . . . . . 18
3.5.1 Creating objects . . . . . . . . . . . . . . . . . . . . . . 18
3.5.2 Converting objects . . . . . . . . . . . . . . . . . . . . . 23
3.5.3 Operators . . . . . . . . . . . . . . . . . . . . . . . . . . 25
3.5.4 Accessing the values of an object: the indexing system . 26
3.5.5 Accessing the values of an object with names . . . . . . 29
3.5.6 The data editor . . . . . . . . . . . . . . . . . . . . . . . 31
3.5.7 Arithmetics and simple functions . . . . . . . . . . . . . 31
3.5.8 Matrix computation . . . . . . . . . . . . . . . . . . . . 33

4 Graphics with R 36
4.1 Managing graphics . . . . . . . . . . . . . . . . . . . . . . . . . 36
4.1.1 Opening several graphical devices . . . . . . . . . . . . . 36
4.1.2 Partitioning a graphic . . . . . . . . . . . . . . . . . . . 37
4.2 Graphical functions . . . . . . . . . . . . . . . . . . . . . . . . . 40
4.3 Low-level plotting commands . . . . . . . . . . . . . . . . . . . 41
4.4 Graphical parameters . . . . . . . . . . . . . . . . . . . . . . . 43
4.5 A practical example . . . . . . . . . . . . . . . . . . . . . . . . 44
4.6 The grid and lattice packages . . . . . . . . . . . . . . . . . . . 48

5 Statistical analyses with R 55

5.1 A simple example of analysis of variance . . . . . . . . . . . . . 55
5.2 Formulae . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
5.3 Generic functions . . . . . . . . . . . . . . . . . . . . . . . . . . 58
5.4 Packages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
6 Programming with R in pratice 64
6.1 Loops and vectorization . . . . . . . . . . . . . . . . . . . . . . 64
6.2 Writing a program in R . . . . . . . . . . . . . . . . . . . . . . 66
6.3 Writing your own functions . . . . . . . . . . . . . . . . . . . . 67

7 Literature on R 71
 1 Preamble

The goal of the present document is to give a starting point for people newly
interested in R. I chose to emphasize on the understanding of how R works,
with the aim of a beginner, rather than expert, use. Given that the possibilities
offered by R are vast, it is useful to a beginner to get some notions and
concepts in order to progress easily. I tried to simplify the explanations as
much as I could to make them understandable by all, while giving useful
details, sometimes with tables.
R is a system for statistical analyses and graphics created by Ross Ihaka
and Robert Gentleman1 . R is both a software and a language considered as a
dialect of the S language created by the AT&T Bell Laboratories. S is available
as the software S-PLUS commercialized by Insightful 2 . There are important
differences in the designs of R and of S: those who want to know more on this
point can read the paper by Ihaka & Gentleman (1996) or the R-FAQ 3 , a copy
of which is also distributed with R.
R is freely distributed under the terms of the GNU General Public Licence 4 ;
its development and distribution are carried out by several statisticians known
as the R Development Core Team.
R is available in several forms: the sources (written mainly in C and
some routines in Fortran), essentially for Unix and Linux machines, or some
pre-compiled binaries for Windows, Linux, and Macintosh. The files needed
to install R, either from the sources or from the pre-compiled binaries, are
distributed from the internet site of the Comprehensive R Archive Network
(CRAN)5 where the instructions for the installation are also available. Re-
garding the distributions of Linux (Debian, . . . ), the binaries are generally
available for the most recent versions; look at the CRAN site if necessary.
R has many functions for statistical analyses and graphics; the latter are
visualized immediately in their own window and can be saved in various for-
mats (jpg, png, bmp, ps, pdf, emf, pictex, xfig; the available formats may
depend on the operating system). The results from a statistical analysis are
displayed on the screen, some intermediate results (P-values, regression coef-
ficients, residuals, . . . ) can be saved, written in a file, or used in subsequent
analyses.
The R language allows the user, for instance, to program loops to suc-
cessively analyse several data sets. It is also possible to combine in a single
program different statistical functions to perform more complex analyses. The
1
Ihaka R. & Gentleman R. 1996. R: a language for data analysis and graphics. Journal
of Computational and Graphical Statistics 5: 299–314.
2
See http://www.insightful.com/products/splus/default.asp for more information
3
http://cran.r-project.org/doc/FAQ/R-FAQ.html
4
For more information: http://www.gnu.org/
5
http://cran.r-project.org/

1
R users may benefit from a large number of programs written for S and avail-
able on the internet6 , most of these programs can be used directly with R.
At first, R could seem too complex for a non-specialist. This may not
be true actually. In fact, a prominent feature of R is its flexibility. Whereas
a classical software displays immediately the results of an analysis, R stores
these results in an “object”, so that an analysis can be done with no result
displayed. The user may be surprised by this, but such a feature is very useful.
Indeed, the user can extract only the part of the results which is of interest.
For example, if one runs a series of 20 regressions and wants to compare the
different regression coefficients, R can display only the estimated coefficients:
thus the results may take a single line, whereas a classical software could well
open 20 results windows. We will see other examples illustrating the flexibility
of a system such as R compared to traditional softwares.

6
For example: http://stat.cmu.edu/S/

2
 2 A few concepts before starting

Once R is installed on your computer, the software is executed by launching

the corresponding executable. The prompt, by default ‘>’, indicates that R
is waiting for your commands. Under Windows using the program Rgui.exe,
some commands (accessing the on-line help, opening files, . . . ) can be executed
via the pull-down menus. At this stage, a new user is likely to wonder “What
do I do now?” It is indeed very useful to have a few ideas on how R works
when it is used for the first time, and this is what we will see now.
We shall see first briefly how R works. Then, I will describe the “assign”
operator which allows creating objects, how to manage objects in memory,
and finally how to use the on-line help which is very useful when running R.

2.1 How R works

The fact that R is a language may deter some users who think “I can’t pro-
gram”. This should not be the case for two reasons. First, R is an interpreted
language, not a compiled one, meaning that all commands typed on the key-
board are directly executed without requiring to build a complete program
like in most computer languages (C, Fortran, Pascal, . . . ).
Second, R’s syntax is very simple and intuitive. For instance, a linear
regression can be done with the command lm(y ~ x) which means “fitting
a linear model with y as response and x as predictor”. In R, in order to
be executed, a function always needs to be written with parentheses, even
if there is nothing within them (e.g., ls()). If one just types the name of a
function without parentheses, R will display the content of the function. In this
document, the names of the functions are generally written with parentheses in
order to distinguish them from other objects, unless the text indicates clearly
so.
When R is running, variables, data, functions, results, etc, are stored in
the active memory of the computer in the form of objects which have a name.
The user can do actions on these objects with operators (arithmetic, logical,
comparison, . . . ) and functions (which are themselves objects). The use of
operators is relatively intuitive, we will see the details later (p. 25). An R
function may be sketched as follows:

arguments −→ function
↑ =⇒result
options −→ default arguments

The arguments can be objects (“data”, formulae, expressions, . . . ), some

3
 of which could be defined by default in the function; these default values may
be modified by the user by specifying options. An R function may require no
argument: either all arguments are defined by default (and their values can be
modified with the options), or no argument has been defined in the function.
We will see later in more details how to use and build functions (p. 67). The
present description is sufficient for the moment to understand how R works.
All the actions of R are done on objects stored in the active memory of
the computer: no temporary files are used (Fig. 1). The readings and writings
of files are used for input and output of data and results (graphics, . . . ). The
user executes the functions via some commands. The results are displayed
directly on the screen, stored in an object, or written on the disk (particularly
for graphics). Since the results are themselves objects, they can be considered
as data and analysed as such. Data files can be read from the local disk or
from a remote server through internet.

.../library/base/

- functions and operators 

keyboard commands /stast/
library of
/graphics/
mouse ... functions

?

- data
“data” objects files
 internet
 XXX
)
 6 XXX
screen ? z
X
“results” objects PS JPEG ...

Active memory Hard disk

Figure 1: A schematic view of how R works.

The functions available to the user are stored in a library localised on

the disk in a directory called R HOME/library (R HOME is the directory
where R is installed). This directory contains packages of functions, which are
themselves structured in directories. The package named base is in a way the
core of R and contains the basic functions of the language, particularly, for
reading and manipulating data. Each package has a directory called R with
a file named like the package (for instance, for the package base, this is the
file R HOME/library/base/R/base). This file contains all the functions of the
package.
One of the simplest commands is to type the name of an object to display
its content. For instance, if an object n contents the value 10:

> n
[1] 10

4
 The digit 1 within brackets indicates that the display starts at the first
element of n. This command is an implicit use of the function print and the
above example is similar to print(n) (in some situations, the function print
must be used explicitly, such as within a function or a loop).
The name of an object must start with a letter (A–Z and a–z) and can
include letters, digits (0–9), dots (.), and underscores ( ). R discriminates
between uppercase letters and lowercase ones in the names of the objects, so
that x and X can name two distinct objects (even under Windows).

2.2 Creating, listing and deleting the objects in memory

An object can be created with the “assign” operator which is written as an

arrow with a minus sign and a bracket; this symbol can be oriented left-to-right
or the reverse:

> n <- 15
> n
[1] 15
> 5 -> n
> n
[1] 5
> x <- 1
> X <- 10
> x
[1] 1
> X
[1] 10

If the object already exists, its previous value is erased (the modification
affects only the objects in the active memory, not the data on the disk). The
value assigned this way may be the result of an operation and/or a function:

> n <- 10 + 2
> n
[1] 12
> n <- 3 + rnorm(1)
> n
[1] 2.208807

The function rnorm(1) generates a normal random variate with mean zero
and variance unity (p. 17). Note that you can simply type an expression
without assigning its value to an object, the result is thus displayed on the
screen but is not stored in memory:

> (10 + 2) * 5
[1] 60

5
 The assignment will be omitted in the examples if not necessary for un-
derstanding.
The function ls lists simply the objects in memory: only the names of the
objects are displayed.

> name <- "Carmen"; n1 <- 10; n2 <- 100; m <- 0.5
> ls()
[1] "m" "n1" "n2" "name"

Note the use of the semi-colon to separate distinct commands on the same
line. If we want to list only the objects which contain a given character in
their name, the option pattern (which can be abbreviated with pat) can be
used:

> ls(pat = "m")

[1] "m" "name"

To restrict the list of objects whose names start with this character:

> ls(pat = "^m")

[1] "m"

The function ls.str displays some details on the objects in memory:

> ls.str()
m : num 0.5
n1 : num 10
n2 : num 100
name : chr "Carmen"

The option pattern can be used in the same way as with ls. Another
useful option of ls.str is max.level which specifies the level of detail for the
display of composite objects. By default, ls.str displays the details of all
objects in memory, included the columns of data frames, matrices and lists,
which can result in a very long display. We can avoid to display all these
details with the option max.level = -1:

> M <- data.frame(n1, n2, m)

> ls.str(pat = "M")
M : ‘data.frame’: 1 obs. of 3 variables:
$ n1: num 10
$ n2: num 100
$ m : num 0.5
> ls.str(pat="M", max.level=-1)
M : ‘data.frame’: 1 obs. of 3 variables:

To delete objects in memory, we use the function rm: rm(x) deletes the
object x, rm(x,y) deletes both the objects x et y, rm(list=ls()) deletes all
the objects in memory; the same options mentioned for the function ls() can
then be used to delete selectively some objects: rm(list=ls(pat="^m")).

6
2.3 The on-line help

The on-line help of R gives very useful information on how to use the functions.
Help is available directly for a given function, for instance:

> ?lm

will display, within R, the help page for the function lm() (linear model). The
commands help(lm) and help("lm") have the same effect. The last one must
be used to access help with non-conventional characters:

> ?*
Error: syntax error
> help("*")
Arithmetic package:base R Documentation

Arithmetic Operators
...

Calling help opens a page (this depends on the operating system) with
general information on the first line such as the name of the package where
is (are) the documented function(s) or operators. Then comes a title followed
by sections which give detailed information.

Description: brief description.

Usage: for a function, gives the name with all its arguments and the possible
options (with the corresponding default values); for an operator gives
the typical use.

Arguments: for a function, details each of its arguments.

Details: detailed description.

Value: if applicable, the type of object returned by the function or the oper-
ator.

See Also: other help pages close or similar to the present one.

Examples: some examples which can generally be executed without opening

the help with the function example.

For beginners, it is good to look at the section Examples. Generally, it

is useful to read carefully the section Arguments. Other sections may be
encountered, such as Note, References or Author(s).
By default, the function help only searches in the packages which are
loaded in memory. The option try.all.packages, which default is FALSE,
allows to search in all packages if its value is TRUE:

7
> help("bs")
No documentation for ’bs’ in specified packages and libraries:
you could try ’help.search("bs")’
> help("bs", try.all.packages = TRUE)
Help for topic ’bs’ is not in any loaded package but
can be found in the following packages:

Package Library
splines /usr/lib/R/library

Note that in this case the help page of the function bs is not displayed.
The user can display help pages from a package not loaded in memory using
the option package:

> help("bs", package = "splines")

bs package:splines R Documentation

B-Spline Basis for Polynomial Splines

Description:

Generate the B-spline basis matrix for a polynomial spline.

...

The help in html format (read, e.g., with Netscape) is called by typing:

> help.start()

A search with keywords is possible with this html help. The section See
Also has here hypertext links to other function help pages. The search with
keywords is also possible in R with the function help.search. The latter
looks for a specified topic, given as a character string, in the help pages of all
installed packages. For instance, help.search("tree") will display a list of
the functions which help pages mention “tree”. Note that if some packages
have been recently installed, it may be useful to refresh the database used by
help.search using the option rebuild (e.g., help.search("tree", rebuild
= TRUE)).
The fonction apropos finds all functions which name contains the character
string given as argument; only the packages loaded in memory are searched:

> apropos(help)
[1] "help" ".helpForCall" "help.search"
[4] "help.start"

8
 3 Data with R

3.1 Objects

We have seen that R works with objects which are, of course, characterized by
their names and their content, but also by attributes which specify the kind of
data represented by an object. In order to understand the usefulness of these
attributes, consider a variable that takes the value 1, 2, or 3: such a variable
could be an integer variable (for instance, the number of eggs in a nest), or
the coding of a categorical variable (for instance, sex in some populations of
crustaceans: male, female, or hermaphrodite).
It is clear that the statistical analysis of this variable will not be the same in
both cases: with R, the attributes of the object give the necessary information.
More technically, and more generally, the action of a function on an object
depends on the attributes of the latter.
All objects have two intrinsic attributes: mode and length. The mode
is the basic type of the elements of the object; there are four main modes:
numeric, character, complex7 , and logical (FALSE or TRUE). Other modes exist
but they do not represent data, for instance function or expression. The length
is the number of elements of the object. To display the mode and the length
of an object, one can use the functions mode and length, respectively:

> x <- 1
> mode(x)
[1] "numeric"
> length(x)
[1] 1
> A <- "Gomphotherium"; compar <- TRUE; z <- 1i
> mode(A); mode(compar); mode(z)
[1] "character"
[1] "logical"
[1] "complex"

Whatever the mode, missing data are represented by NA (not available).

A very large numeric value can be specified with an exponential notation:

> N <- 2.1e23

> N
[1] 2.1e+23

R correctly represents non-finite numeric values, such as ±∞ with Inf and

-Inf, or values which are not numbers with NaN (not a number ).
7
The mode complex will not be discussed in this document.

9
> x <- 5/0
> x
[1] Inf
> exp(x)
[1] Inf
> exp(-x)
[1] 0
> x - x
[1] NaN

A value of mode character is input with double quotes ". It is possible

to include this latter character in the value if it follows a backslash \. The
two charaters altogether \" will be treated in a specific way by some functions
such as cat for display on screen, or write.table to write on the disk (p. 14,
the option qmethod of this function).

> x <- "Double quotes \" delimitate R’s strings."

> x
[1] "Double quotes \" delimitate R’s strings."
> cat(x)
Double quotes " delimitate R’s strings.

Alternatively, variables of mode character can be delimited with single

quotes (’); in this case it is not necessary to escape double quotes with back-
slashes (but single quotes must be!):

> x <- ’Double quotes " delimitate R\’s strings.’

> x
[1] "Double quotes \" delimitate R’s strings."

The following table gives an overview of the type of objects representing

data.

object modes several modes

possible in the
same object?
vector numeric, character, complex or logical No
factor numeric or character No
array numeric, character, complex or logical No
matrix numeric, character, complex or logical No
data frame numeric, character, complex or logical Yes
ts numeric, character, complex or logical No
list numeric, character, complex, logical, Yes
function, expression, . . .

10
 A vector is a variable in the commonly admitted meaning. A factor is a
categorical variable. An array is a table with k dimensions, a matrix being
a particular case of array with k = 2. Note that the elements of an array
or of a matrix are all of the same mode. A data frame is a table composed
with one or several vectors and/or factors all of the same length but possibly
of different modes. A ‘ts’ is a time series data set and so contains additional
attributes such as frequency and dates. Finally, a list can contain any type of
object, included lists!
For a vector, its mode and length are sufficient to describe the data. For
other objects, other information is necessary and it is given by non-intrinsic
attributes. Among these attributes, we can cite dim which corresponds to the
dimensions of an object. For example, a matrix with 2 lines and 2 columns
has for dim the pair of values [2, 2], but its length is 4.

3.2 Reading data in a file

For reading and writing in files, R uses the working directory. To find this
directory, the command getwd() (get working directory) can be used, and the
working directory can be changed with setwd("C:/data") or setwd("/home/-
paradis/R"). It is necessary to give the path to a file if it is not in the working
directory.8
R can read data stored in text (ASCII) files with the following functions:
read.table (which has several variants, see below), scan and read.fwf. R
can also read files in other formats (Excel, SAS, SPSS, . . . ), and access SQL-
type databases, but the functions needed for this are not in the package base.
These functionalities are very useful for a more advanced use of R, but we will
restrict here to reading files in ASCII format.
The function read.table has for effect to create a data frame, and so is
the main way to read data in tabular form. For instance, if one has a file
named data.dat, the command:

> mydata <- read.table("data.dat")

will create a data frame named mydata, and each variable will be named, by de-
fault, V1, V2, . . . and can be accessed individually by mydata$V1, mydata$V2,
. . . , or by mydata["V1"], mydata["V2"], . . . , or, still another solution, by
mydata[, 1], mydata[,2 ], . . . 9 There are several options whose default
values (i.e. those used by R if they are omitted by the user) are detailed in
the following table:

read.table(file, header = FALSE, sep = "", quote = "\"’", dec = ".",

8
Under Windows, it is useful to create a short-cut of Rgui.exe then edit its properties
and change the directory in the field “Start in:” under the tab “Short-cut”: this directory
will then be the working directory if R is started from this short-cut.
9
There is a difference: mydata$V1 and mydata[, 1] are vectors whereas mydata["V1"] is
a data frame. We will see later (p. 18) some details on manipulating objects.

11
 row.names, col.names, as.is = FALSE, na.strings = "NA",
colClasses = NA, nrows = -1,
skip = 0, check.names = TRUE, fill = !blank.lines.skip,
strip.white = FALSE, blank.lines.skip = TRUE,
comment.char = "#")

file the name of the file (within "" or a variable of mode character),
possibly with its path (the symbol \ is not allowed and must be
replaced by /, even under Windows), or a remote access to a file of
type URL (http://...)
header a logical (FALSE or TRUE) indicating if the file contains the names of
the variables on its first line
sep the field separator used in the file, for instance sep="\t" if it is a
tabulation
quote the characters used to cite the variables of mode character
dec the character used for the decimal point
row.names a vector with the names of the lines which can be either a vector of
mode character, or the number (or the name) of a variable of the
file (by default: 1, 2, 3, . . . )
col.names a vector with the names of the variables (by default: V1, V2, V3,
...)
as.is controls the conversion of character variables as factors (if FALSE)
or keeps them as characters (TRUE); as.is can be a logical, numeric
or character vector specifying the variables to be kept as character
na.strings the value given to missing data (converted as NA)
colClasses a vector of mode character giving the classes to attribute to the
columns
nrows the maximum number of lines to read (negative values are ignored)
skip the number of lines to be skipped before reading the data
check.names if TRUE, checks that the variable names are valid for R
fill if TRUE and all lines do not have the same number of variables,
“blanks” are added
strip.white (conditional to sep) if TRUE, deletes extra spaces before and after
the character variables
blank.lines.skip if TRUE, ignores “blank” lines
comment.char a character defining comments in the data file, the rest of the
line after this character is ignored (to disable this argument, use
comment.char = "")

The variants of read.table are useful since they have different default
values:

read.csv(file, header = TRUE, sep = ",", quote="\"", dec=".",

fill = TRUE, ...)
read.csv2(file, header = TRUE, sep = ";", quote="\"", dec=",",
fill = TRUE, ...)
read.delim(file, header = TRUE, sep = "\t", quote="\"", dec=".",
fill = TRUE, ...)
read.delim2(file, header = TRUE, sep = "\t", quote="\"", dec=",",
fill = TRUE, ...)

12
 The function scan is more flexible than read.table. A difference is that
it is possible to specify the mode of the variables, for example:

> mydata <- scan("data.dat", what = list("", 0, 0))

reads in the file data.dat three variables, the first is of mode character and the
next two are of mode numeric. Another important distinction is that scan()
can be used to create different objects, vectors, matrices, data frames, lists,
. . . In the above example, mydata is a list of three vectors. By default, that is
if what is omitted, scan() creates a numeric vector. If the data read do not
correspond to the mode(s) expected (either by default, or specified by what),
an error message is returned. The options are the followings.

scan(file = "", what = double(0), nmax = -1, n = -1, sep = "",

quote = if (sep=="\n") "" else "’\"", dec = ".",
skip = 0, nlines = 0, na.strings = "NA",
flush = FALSE, fill = FALSE, strip.white = FALSE, quiet = FALSE,
blank.lines.skip = TRUE, multi.line = TRUE, comment.char = "",
allowEscapes = TRUE)

file the name of the file (within ""), possibly with its path (the symbol
\ is not allowed and must be replaced by /, even under Windows),
or a remote access to a file of type URL (http://...); if file="", the
data are entered with the keyboard (the entree is terminated by a
blank line)
what specifies the mode(s) of the data (numeric by default)
nmax the number of data to read, or, if what is a list, the number of lines
to read (by default, scan reads the data up to the end of file)
n the number of data to read (by default, no limit)
sep the field separator used in the file
quote the characters used to cite the variables of mode character
dec the character used for the decimal point
skip the number of lines to be skipped before reading the data
nlines the number of lines to read
na.string the value given to missing data (converted as NA)
flush a logical, if TRUE, scan goes to the next line once the number of
columns has been reached (allows the user to add comments in the
data file)
fill if TRUE and all lines do not have the same number of variables,
“blanks” are added
strip.white (conditional to sep) if TRUE, deletes extra spaces before and after
the character variables
quiet a logical, if FALSE, scan displays a line showing which fields have
been read
blank.lines.skip if TRUE, ignores blank lines
multi.line if what is a list, specifies if the variables of the same individual are
on a single line in the file (FALSE)
comment.char a character defining comments in the data file, the rest of the line
after this character is ignored (the default is to have this disabled)
allowEscapes specifies whether C-style escapes (e.g., ‘\t’) be processed (the de-
fault) or read as verbatim

13
 The function read.fwf can be used to read in a file some data in fixed
width format:
read.fwf(file, widths, header = FALSE, sep = "\t",
as.is = FALSE, skip = 0, row.names, col.names,
n = -1, buffersize = 2000, ...)
The options are the same than for read.table() ex- A1.501.2
cept widths which specifies the width of the fields A1.551.3
(buffersize is the maximum number of lines read si- B1.601.4
multaneously). For example, if a file named data.txt has B1.651.5
the data indicated on the right, one can read the data C1.701.6
with the following command: C1.751.7
> mydata <- read.fwf("data.txt", widths=c(1, 4, 3))
> mydata
V1 V2 V3
1 A 1.50 1.2
2 A 1.55 1.3
3 B 1.60 1.4
4 B 1.65 1.5
5 C 1.70 1.6
6 C 1.75 1.7

3.3 Saving data

The function write.table writes in a file an object, typically a data frame but
this could well be another kind of object (vector, matrix, . . . ). The arguments
and options are:
write.table(x, file = "", append = FALSE, quote = TRUE, sep = " ",
eol = "\n", na = "NA", dec = ".", row.names = TRUE,
col.names = TRUE, qmethod = c("escape", "double"))

x the name of the object to be written

file the name of the file (by default the object is displayed on the screen)
append if TRUE adds the data without erasing those possibly existing in the file
quote a logical or a numeric vector: if TRUE the variables of mode character and
the factors are written within "", otherwise the numeric vector indicates
the numbers of the variables to write within "" (in both cases the names
of the variables are written within "" but not if quote = FALSE)
sep the field separator used in the file
eol the character to be used at the end of each line ("\n" is a carriage-return)
na the character to be used for missing data
dec the character used for the decimal point
row.names a logical indicating whether the names of the lines are written in the file
col.names id. for the names of the columns
qmethod specifies, if quote=TRUE, how double quotes " included in variables of mode
character are treated: if "escape" (or "e", the default) each " is replaced
by \", if "d" each " is replaced by ""

14
 To write in a simpler way an object in a file, the command write(x,
file="data.txt") can be used, where x is the name of the object (which
can be a vector, a matrix, or an array). There are two options: nc (or ncol)
which defines the number of columns in the file (by default nc=1 if x is of mode
character, nc=5 for the other modes), and append (a logical) to add the data
without deleting those possibly already in the file (TRUE) or deleting them if
the file already exists (FALSE, the default).
To record a group of objects of any type, we can use the command save(x,
y, z, file= "xyz.RData"). To ease the transfert of data between differ-
ent machines, the option ascii = TRUE can be used. The data (which are
now called a workspace in R’s jargon) can be loaded later in memory with
load("xyz.RData"). The function save.image() is a short-cut for save(list
=ls(all=TRUE), file=".RData").

3.4 Generating data

3.4.1 Regular sequences

A regular sequence of integers, for example from 1 to 30, can be generated
with:

> x <- 1:30

The resulting vector x has 30 elements. The operator ‘:’ has priority on the
arithmetic operators within an expression:

> 1:10-1
[1] 0 1 2 3 4 5 6 7 8 9
> 1:(10-1)
[1] 1 2 3 4 5 6 7 8 9

The function seq can generate sequences of real numbers as follows:

> seq(1, 5, 0.5)

[1] 1.0 1.5 2.0 2.5 3.0 3.5 4.0 4.5 5.0

where the first number indicates the beginning of the sequence, the second one
the end, and the third one the increment to be used to generate the sequence.
One can use also:

> seq(length=9, from=1, to=5)

[1] 1.0 1.5 2.0 2.5 3.0 3.5 4.0 4.5 5.0

One can also type directly the values using the function c:

> c(1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5)

[1] 1.0 1.5 2.0 2.5 3.0 3.5 4.0 4.5 5.0

15
 It is also possible, if one wants to enter some data on the keyboard, to use
the function scan with simply the default options:

> z <- scan()

1: 1.0 1.5 2.0 2.5 3.0 3.5 4.0 4.5 5.0
10:
Read 9 items
> z
[1] 1.0 1.5 2.0 2.5 3.0 3.5 4.0 4.5 5.0

The function rep creates a vector with all its elements identical:

> rep(1, 30)

[1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1

The function sequence creates a series of sequences of integers each ending

by the numbers given as arguments:

> sequence(4:5)
[1] 1 2 3 4 1 2 3 4 5
> sequence(c(10,5))
[1] 1 2 3 4 5 6 7 8 9 10 1 2 3 4 5

The function gl (generate levels) is very useful because it generates regular

series of factors. The usage of this fonction is gl(k, n) where k is the number
of levels (or classes), and n is the number of replications in each level. Two
options may be used: length to specify the number of data produced, and
labels to specify the names of the levels of the factor. Examples:

> gl(3, 5)
[1] 1 1 1 1 1 2 2 2 2 2 3 3 3 3 3
Levels: 1 2 3
> gl(3, 5, length=30)
[1] 1 1 1 1 1 2 2 2 2 2 3 3 3 3 3 1 1 1 1 1 2 2 2 2 2 3 3 3 3 3
Levels: 1 2 3
> gl(2, 6, label=c("Male", "Female"))
[1] Male Male Male Male Male Male
[7] Female Female Female Female Female Female
Levels: Male Female
> gl(2, 10)
[1] 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2
Levels: 1 2
> gl(2, 1, length=20)
[1] 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2
Levels: 1 2
> gl(2, 2, length=20)
[1] 1 1 2 2 1 1 2 2 1 1 2 2 1 1 2 2 1 1 2 2
Levels: 1 2

16
 Finally, expand.grid() creates a data frame with all combinations of vec-
tors or factors given as arguments:

> expand.grid(h=c(60,80), w=c(100, 300), sex=c("Male", "Female"))

h w sex
1 60 100 Male
2 80 100 Male
3 60 300 Male
4 80 300 Male
5 60 100 Female
6 80 100 Female
7 60 300 Female
8 80 300 Female

3.4.2 Random sequences

law function
Gaussian (normal) rnorm(n, mean=0, sd=1)
exponential rexp(n, rate=1)
gamma rgamma(n, shape, scale=1)
Poisson rpois(n, lambda)
Weibull rweibull(n, shape, scale=1)
Cauchy rcauchy(n, location=0, scale=1)
beta rbeta(n, shape1, shape2)
‘Student’ (t) rt(n, df)
Fisher–Snedecor (F ) rf(n, df1, df2)
Pearson (χ2 ) rchisq(n, df)
binomial rbinom(n, size, prob)
multinomial rmultinom(n, size, prob)
geometric rgeom(n, prob)
hypergeometric rhyper(nn, m, n, k)
logistic rlogis(n, location=0, scale=1)
lognormal rlnorm(n, meanlog=0, sdlog=1)
negative binomial rnbinom(n, size, prob)
uniform runif(n, min=0, max=1)
Wilcoxon’s statistics rwilcox(nn, m, n), rsignrank(nn, n)

It is useful in statistics to be able to generate random data, and R can

do it for a large number of probability density functions. These functions are
of the form rfunc (n, p1, p2, ...), where func indicates the probability
distribution, n the number of data generated, and p1, p2, . . . are the values of
the parameters of the distribution. The above table gives the details for each
distribution, and the possible default values (if none default value is indicated,
this means that the parameter must be specified by the user).
Most of these functions have counterparts obtained by replacing the letter
r with d, p or q to get, respectively, the probability density (dfunc (x, ...)),

17
the cumulative probability density (pfunc (x, ...)), and the value of quantile
(qfunc (p, ...), with 0 < p < 1). The last two series of functions can be
used to find critical values or P -values of statistical tests. For instance, the
critical values for a two-tailed test following a normal distribution at the 5%
threshold are:

> qnorm(0.025)
[1] -1.959964
> qnorm(0.975)
[1] 1.959964

For the one-tailed version of the same test, either qnorm(0.05) or 1 -

qnorm(0.95) will be used depending on the form of the alternative hypothesis.
The P -value of a test, say χ2 = 3.84 with df = 1, is:

> 1 - pchisq(3.84, 1)
[1] 0.05004352

3.5 Manipulating objects

3.5.1 Creating objects

We have seen previously different ways to create objects using the assign op-
erator; the mode and the type of objects so created are generally determined
implicitly. It is possible to create an object and specifying its mode, length,
type, etc. This approach is interesting in the perspective of manipulating ob-
jects. One can, for instance, create an ‘empty’ object and then modify its
elements successively which is more efficient than putting all its elements to-
gether with c(). The indexing system could be used here, as we will see later
(p. 26).
It can also be very convenient to create objects from others. For example,
if one wants to fit a series of models, it is simple to put the formulae in a list,
and then to extract the elements successively to insert them in the function
lm.
At this stage of our learning of R, the interest in learning the following
functionalities is not only practical but also didactic. The explicit construction
of objects gives a better understanding of their structure, and allows us to go
further in some notions previously mentioned.

Vector. The function vector, which has two arguments mode and length,
creates a vector which elements have a value depending on the mode
specified as argument: 0 if numeric, FALSE if logical, or "" if charac-
ter. The following functions have exactly the same effect and have for
single argument the length of the vector: numeric(), logical(), and
character().

18
Factor. A factor includes not only the values of the corresponding categorical
variable, but also the different possible levels of that variable (even if they
are not present in the data). The function factor creates a factor with
the following options:

factor(x, levels = sort(unique(x), na.last = TRUE),

labels = levels, exclude = NA, ordered = is.ordered(x))

levels specifies the possible levels of the factor (by default the unique
values of the vector x), labels defines the names of the levels, exclude
the values of x to exclude from the levels, and ordered is a logical
argument specifying whether the levels of the factor are ordered. Recall
that x is of mode numeric or character. Some examples follow.

> factor(1:3)
[1] 1 2 3
Levels: 1 2 3
> factor(1:3, levels=1:5)
[1] 1 2 3
Levels: 1 2 3 4 5
> factor(1:3, labels=c("A", "B", "C"))
[1] A B C
Levels: A B C
> factor(1:5, exclude=4)
[1] 1 2 3 NA 5
Levels: 1 2 3 5

The function levels extracts the possible levels of a factor:

> ff <- factor(c(2, 4), levels=2:5)

> ff
[1] 2 4
Levels: 2 3 4 5
> levels(ff)
[1] "2" "3" "4" "5"

Matrix. A matrix is actually a vector with an additional attribute (dim)

which is itself a numeric vector with length 2, and defines the numbers
of rows and columns of the matrix. A matrix can be created with the
function matrix:

matrix(data = NA, nrow = 1, ncol = 1, byrow = FALSE,

dimnames = NULL)

19
 The option byrow indicates whether the values given by data must fill
successively the columns (the default) or the rows (if TRUE). The option
dimnames allows to give names to the rows and columns.

> matrix(data=5, nr=2, nc=2)

[,1] [,2]
[1,] 5 5
[2,] 5 5
> matrix(1:6, 2, 3)
[,1] [,2] [,3]
[1,] 1 3 5
[2,] 2 4 6
> matrix(1:6, 2, 3, byrow=TRUE)
[,1] [,2] [,3]
[1,] 1 2 3
[2,] 4 5 6

Another way to create a matrix is to give the appropriate values to the

dim attribute (which is initially NULL):

> x <- 1:15

> x
[1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
> dim(x)
NULL
> dim(x) <- c(5, 3)
> x
[,1] [,2] [,3]
[1,] 1 6 11
[2,] 2 7 12
[3,] 3 8 13
[4,] 4 9 14
[5,] 5 10 15

Data frame. We have seen that a data frame is created implicitly by the
function read.table; it is also possible to create a data frame with the
function data.frame. The vectors so included in the data frame must
be of the same length, or if one of the them is shorter, it is “recycled” a
whole number of times:

> x <- 1:4; n <- 10; M <- c(10, 35); y <- 2:4
> data.frame(x, n)
x n
1 1 10
2 2 10

20
 3 3 10
4 4 10
> data.frame(x, M)
x M
1 1 10
2 2 35
3 3 10
4 4 35
> data.frame(x, y)
Error in data.frame(x, y) :
arguments imply differing number of rows: 4, 3

If a factor is included in a data frame, it must be of the same length than

the vector(s). It is possible to change the names of the columns with,
for instance, data.frame(A1=x, A2=n). One can also give names to the
rows with the option row.names which must be, of course, a vector of
mode character and of length equal to the number of lines of the data
frame. Finally, note that data frames have an attribute dim similarly to
matrices.
List. A list is created in a way similar to data frames with the function list.
There is no constraint on the objects that can be included. In contrast
to data.frame(), the names of the objects are not taken by default;
taking the vectors x and y of the previous example:

> L1 <- list(x, y); L2 <- list(A=x, B=y)

> L1
[[1]]
[1] 1 2 3 4

[[2]]
[1] 2 3 4

> L2
$A
[1] 1 2 3 4

$B
[1] 2 3 4

> names(L1)
NULL
> names(L2)
[1] "A" "B"

Time-series. The function ts creates an object of class "ts" from a vector

(single time-series) or a matrix (multivariate time-series), and some op-

21
tions which characterize the series. The options, with the default values,
are:

ts(data = NA, start = 1, end = numeric(0), frequency = 1,

deltat = 1, ts.eps = getOption("ts.eps"), class, names)

data a vector or a matrix

start the time of the first observation, either a number, or a
vector of two integers (see the examples below)
end the time of the last observation specified in the same way
than start
frequency the number of observations per time unit
deltat the fraction of the sampling period between successive
observations (ex. 1/12 for monthly data); only one of
frequency or deltat must be given
ts.eps tolerance for the comparison of series. The frequencies
are considered equal if their difference is less than ts.eps
class class to give to the object; the default is "ts" for a single
series, and c("mts", "ts") for a multivariate series
names a vector of mode character with the names of the individ-
ual series in the case of a multivariate series; by default
the names of the columns of data, or Series 1, Series
2, . . .

A few examples of time-series created with ts:

> ts(1:10, start = 1959)

Time Series:
Start = 1959
End = 1968
Frequency = 1
[1] 1 2 3 4 5 6 7 8 9 10
> ts(1:47, frequency = 12, start = c(1959, 2))
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
1959 1 2 3 4 5 6 7 8 9 10 11
1960 12 13 14 15 16 17 18 19 20 21 22 23
1961 24 25 26 27 28 29 30 31 32 33 34 35
1962 36 37 38 39 40 41 42 43 44 45 46 47
> ts(1:10, frequency = 4, start = c(1959, 2))
Qtr1 Qtr2 Qtr3 Qtr4
1959 1 2 3
1960 4 5 6 7
1961 8 9 10
> ts(matrix(rpois(36, 5), 12, 3), start=c(1961, 1), frequency=12)
Series 1 Series 2 Series 3

22
 Jan 1961 8 5 4
Feb 1961 6 6 9
Mar 1961 2 3 3
Apr 1961 8 5 4
May 1961 4 9 3
Jun 1961 4 6 13
Jul 1961 4 2 6
Aug 1961 11 6 4
Sep 1961 6 5 7
Oct 1961 6 5 7
Nov 1961 5 5 7
Dec 1961 8 5 2

Expression. The objects of mode expression have a fundamental role in R.

An expression is a series of characters which makes sense for R. All valid
commands are expressions. When a command is typed directly on the
keyboard, it is then evaluated by R and executed if it is valid. In many
circumstances, it is useful to construct an expression without evaluating
it: this is what the function expression is made for. It is, of course,
possible to evaluate the expression subsequently with eval().

> x <- 3; y <- 2.5; z <- 1

> exp1 <- expression(x / (y + exp(z)))
> exp1
expression(x/(y + exp(z)))
> eval(exp1)
[1] 0.5749019

Expressions can be used, among other things, to include equations in

graphs (p. 42). An expression can be created from a variable of mode
character. Some functions take expressions as arguments, for example D
which returns partial derivatives:

> D(exp1, "x")

1/(y + exp(z))
> D(exp1, "y")
-x/(y + exp(z))^2
> D(exp1, "z")
-x * exp(z)/(y + exp(z))^2

3.5.2 Converting objects

The reader has surely realized that the differences between some types of
objects are small; it is thus logical that it is possible to convert an object from
a type to another by changing some of its attributes. Such a conversion will be
done with a function of the type as.something . R (version 2.1.0) has, in the

23
packages base and utils, 98 of such functions, so we will not go in the deepest
details here.
The result of a conversion depends obviously of the attributes of the con-
verted object. Genrally, conversion follows intuitive rules. For the conversion
of modes, the following table summarizes the situation.

Conversion to Function Rules

numeric as.numeric FALSE → 0
TRUE → 1
"1", "2", . . . → 1, 2, . . .
"A", . . . → NA
logical as.logical 0→ FALSE
other numbers → TRUE
"FALSE", "F" → FALSE
"TRUE", "T" → TRUE
other characters → NA
character as.character 1, 2, . . . → "1", "2", . . .
FALSE → "FALSE"
TRUE → "TRUE"

There are functions to convert the types of objects (as.matrix, as.ts,

as.data.frame, as.expression, . . . ). These functions will affect attributes
other than the modes during the conversion. The results are, again, generally
intuitive. A situation frequently encountered is the conversion of factors into
numeric values. In this case, R does the conversion with the numeric coding
of the levels of the factor:

> fac <- factor(c(1, 10))

> fac
[1] 1 10
Levels: 1 10
> as.numeric(fac)
[1] 1 2

This makes sense when considering a factor of mode character:

> fac2 <- factor(c("Male", "Female"))

> fac2
[1] Male Female
Levels: Female Male
> as.numeric(fac2)
[1] 2 1

Note that the result is not NA as may have been expected from the table
above.

24
 To convert a factor of mode numeric into a numeric vector but keeping the
levels as they are originally specified, one must first convert into character,
then into numeric.

> as.numeric(as.character(fac))
[1] 1 10

This procedure is very useful if in a file a numeric variable has also non-
numeric values. We have seen that read.table() in such a situation will, by
default, read this column as a factor.

3.5.3 Operators
We have seen previously that there are three main types of operators in R 10 .
Here is the list.

Operators
Arithmetic Comparison Logical
+ addition < lesser than ! x logical NOT
- subtraction > greater than x & y logical AND
* multiplication <= lesser than or equal to x && y id.
/ division >= greater than or equal to x | y logical OR
^ power == equal x || y id.
%% modulo != different xor(x, y) exclusive OR
%/% integer division

The arithmetic and comparison operators act on two elements (x + y, a

< b). The arithmetic operators act not only on variables of mode numeric or
complex, but also on logical variables; in this latter case, the logical values
are coerced into numeric. The comparison operators may be applied to any
mode: they return one or several logical values.
The logical operators are applied to one (!) or two objects of mode logical,
and return one (or several) logical values. The operators “AND” and “OR”
exist in two forms: the single one operates on each elements of the objects and
returns as many logical values as comparisons done; the double one operates
on the first element of the objects.
It is necessary to use the operator “AND” to specify an inequality of the
type 0 < x < 1 which will be coded with: 0 < x & x < 1. The expression 0
< x < 1 is valid, but will not return the expected result: since both operators
are the same, they are executed successively from left to right. The comparison
0 < x is first done and returns a logical value which is then compared to 1
(TRUE or FALSE < 1): in this situation, the logical value is implicitly coerced
into numeric (1 or 0 < 1).
10
The following characters are also operators for R: $, @, [, [[, :, ?, <-, <<-, =, ::. A
table of operators describing precedence rules can be found with ?Syntax.

25
> x <- 0.5
> 0 < x < 1
[1] FALSE

The comparison operators operate on each element of the two objects

being compared (recycling the values of the shortest one if necessary), and
thus returns an object of the same size. To compare ‘wholly’ two objects, two
functions are available: identical and all.equal.

> x <- 1:3; y <- 1:3

> x == y
[1] TRUE TRUE TRUE
> identical(x, y)
[1] TRUE
> all.equal(x, y)
[1] TRUE

identical compares the internal representation of the data and returns

TRUE if the objects are strictly identical, and FALSE otherwise. all.equal
compares the “near equality” of two objects, and returns TRUE or display a
summary of the differences. The latter function takes the approximation of
the computing process into account when comparing numeric values. The
comparison of numeric values on a computer is sometimes surprising!

> 0.9 == (1 - 0.1)

[1] TRUE
> identical(0.9, 1 - 0.1)
[1] TRUE
> all.equal(0.9, 1 - 0.1)
[1] TRUE
> 0.9 == (1.1 - 0.2)
[1] FALSE
> identical(0.9, 1.1 - 0.2)
[1] FALSE
> all.equal(0.9, 1.1 - 0.2)
[1] TRUE
> all.equal(0.9, 1.1 - 0.2, tolerance = 1e-16)
[1] "Mean relative difference: 1.233581e-16"

3.5.4 Accessing the values of an object: the indexing system

The indexing system is an efficient and flexible way to access selectively the
elements of an object; it can be either numeric or logical. To access, for
example, the third value of a vector x, we just type x[3] which can be used
either to extract or to change this value:

> x <- 1:5

26
> x[3]
[1] 3
> x[3] <- 20
> x
[1] 1 2 20 4 5

The index itself can be a vector of mode numeric:

> i <- c(1, 3)

> x[i]
[1] 1 20

If x is a matrix or a data frame, the value of the ith line and j th column
is accessed with x[i, j]. To access all values of a given row or column, one
has simply to omit the appropriate index (without forgetting the comma!):

> x <- matrix(1:6, 2, 3)

> x
[,1] [,2] [,3]
[1,] 1 3 5
[2,] 2 4 6
> x[, 3] <- 21:22
> x
[,1] [,2] [,3]
[1,] 1 3 21
[2,] 2 4 22
> x[, 3]
[1] 21 22

You have certainly noticed that the last result is a vector and not a matrix.
The default behaviour of R is to return an object of the lowest dimension
possible. This can be altered with the option drop which default is TRUE:

> x[, 3, drop = FALSE]

[,1]
[1,] 21
[2,] 22

This indexing system is easily generalized to arrays, with as many indices

as the number of dimensions of the array (for example, a three dimensional
array: x[i, j, k], x[, , 3], x[, , 3, drop = FALSE], and so on). It may
be useful to keep in mind that indexing is made with square brackets, while
parentheses are used for the arguments of a function:

> x(1)
Error: couldn’t find function "x"

27
 Indexing can also be used to suppress one or several rows or columns
using negative values. For example, x[-1, ] will suppress the first row, while
x[-c(1, 15), ] will do the same for the 1st and 15th rows. Using the matrix
defined above:

> x[, -1]

[,1] [,2]
[1,] 3 21
[2,] 4 22
> x[, -(1:2)]
[1] 21 22
> x[, -(1:2), drop = FALSE]
[,1]
[1,] 21
[2,] 22

For vectors, matrices and arrays, it is possible to access the values of an

element with a comparison expression as the index:

> x <- 1:10

> x[x >= 5] <- 20
> x
[1] 1 2 3 4 20 20 20 20 20 20
> x[x == 1] <- 25
> x
[1] 25 2 3 4 20 20 20 20 20 20

A practical use of the logical indexing is, for instance, the possibility to
select the even elements of an integer variable:

> x <- rpois(40, lambda=5)

> x
[1] 5 9 4 7 7 6 4 5 11 3 5 7 1 5 3 9 2 2 5 2
[21] 4 6 6 5 4 5 3 4 3 3 3 7 7 3 8 1 4 2 1 4
> x[x %% 2 == 0]
[1] 4 6 4 2 2 2 4 6 6 4 4 8 4 2 4

Thus, this indexing system uses the logical values returned, in the above
examples, by comparison operators. These logical values can be computed
beforehand, they then will be recycled if necessary:

> x <- 1:40

> s <- c(FALSE, TRUE)
> x[s]
[1] 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36 38 40

28
 Logical indexing can also be used with data frames, but with caution since
different columns of the data drame may be of different modes.
For lists, accessing the different elements (which can be any kind of object)
is done either with single or with double square brackets: the difference is
that with single brackets a list is returned, whereas double brackets extract the
object from the list. The result can then be itself indexed as previously seen for
vectors, matrices, etc. For instance, if the third object of a list is a vector, its
ith value can be accessed using my.list[[3]][i], if it is a three dimensional
array using my.list[[3]][i, j, k], and so on. Another difference is that
my.list[1:2] will return a list with the first and second elements of the
original list, whereas my.list[[1:2]] will no not give the expected result.

3.5.5 Accessing the values of an object with names

The names are labels of the elements of an object, and thus of mode charac-
ter. They are generally optional attributes. There are several kinds of names
(names, colnames, rownames, dimnames).
The names of a vector are stored in a vector of the same length of the
object, and can be accessed with the function names.

> x <- 1:3

> names(x)
NULL
> names(x) <- c("a", "b", "c")
> x
a b c
1 2 3
> names(x)
[1] "a" "b" "c"
> names(x) <- NULL
> x
[1] 1 2 3

For matrices and data frames, colnames and rownames are labels of the
columns and rows, respectively. They can be accessed either with their re-
spective functions, or with dimnames which returns a list with both vectors.

> X <- matrix(1:4, 2)

> rownames(X) <- c("a", "b")
> colnames(X) <- c("c", "d")
> X
c d
a 1 3
b 2 4
> dimnames(X)
[[1]]
[1] "a" "b"

29
[[2]]
[1] "c" "d"

For arrays, the names of the dimensions can be accessed with dimnames:

> A <- array(1:8, dim = c(2, 2, 2))

> A
, , 1

[,1] [,2]
[1,] 1 3
[2,] 2 4

, , 2

[,1] [,2]
[1,] 5 7
[2,] 6 8

> dimnames(A) <- list(c("a", "b"), c("c", "d"), c("e", "f"))

> A
, , e

c d
a 1 3
b 2 4

, , f

c d
a 5 7
b 6 8

If the elements of an object have names, they can be extracted by using

them as indices. Actually, this should be termed ‘subsetting’ rather than
‘extraction’ since the attributes of the original object are kept. For instance,
if a data frame DF contains the variables x, y, and z, the command DF["x"]
will return a data frame with just x; DF[c("x", "y")] will return a data
frame with both variables. This works with lists as well if the elements in the
list have names.
As the reader surely realizes, the index used here is a vector of mode
character. Like the numeric or logical vectors seen above, this vector can be
defined beforehand and then used for the extraction.
To extract a vector or a factor from a data frame, on can use the operator
$ (e.g., DF$x). This also works with lists.

30
3.5.6 The data editor
It is possible to use a graphical spreadsheet-like editor to edit a “data” object.
For example, if X is a matrix, the command data.entry(X) will open a graphic
editor and one will be able to modify some values by clicking on the appropriate
cells, or to add new columns or rows.
The function data.entry modifies directly the object given as argument
without needing to assign its result. On the other hand, the function de
returns a list with the objects given as arguments and possibly modified. This
result is displayed on the screen by default, but, as for most functions, can be
assigned to an object.
The details of using the data editor depend on the operating system.

3.5.7 Arithmetics and simple functions

There are numerous functions in R to manipulate data. We have already seen
the simplest one, c which concatenates the objects listed in parentheses. For
example:

> c(1:5, seq(10, 11, 0.2))

[1] 1.0 2.0 3.0 4.0 5.0 10.0 10.2 10.4 10.6 10.8 11.0

Vectors can be manipulated with classical arithmetic expressions:

> x <- 1:4

> y <- rep(1, 4)
> z <- x + y
> z
[1] 2 3 4 5

Vectors of different lengths can be added; in this case, the shortest vector
is recycled. Examples:

> x <- 1:4

> y <- 1:2
> z <- x + y
> z
[1] 2 4 4 6
> x <- 1:3
> y <- 1:2
> z <- x + y
Warning message:
longer object length
is not a multiple of shorter object length in: x + y
> z
[1] 2 4 4

31
 Note that R returned a warning message and not an error message, thus
the operation has been performed. If we want to add (or multiply) the same
value to all the elements of a vector:

> x <- 1:4

> a <- 10
> z <- a * x
> z
[1] 10 20 30 40

The functions available in R for manipulating data are too many to be

listed here. One can find all the basic mathematical functions (log, exp,
log10, log2, sin, cos, tan, asin, acos, atan, abs, sqrt, . . . ), special func-
tions (gamma, digamma, beta, besselI, . . . ), as well as diverse functions useful
in statistics. Some of these functions are listed in the following table.

sum(x) sum of the elements of x

prod(x) product of the elements of x
max(x) maximum of the elements of x
min(x) minimum of the elements of x
which.max(x) returns the index of the greatest element of x
which.min(x) returns the index of the smallest element of x
range(x) id. than c(min(x), max(x))
length(x) number of elements in x
mean(x) mean of the elements of x
median(x) median of the elements of x
var(x) or cov(x) variance of the elements of x (calculated on n − 1); if x is
a matrix or a data frame, the variance-covariance matrix is
calculated
cor(x) correlation matrix of x if it is a matrix or a data frame (1 if x
is a vector)
var(x, y) or cov(x, y) covariance between x and y, or between the columns of x and
those of y if they are matrices or data frames
cor(x, y) linear correlation between x and y, or correlation matrix if they
are matrices or data frames

These functions return a single value (thus a vector of length one), except
range which returns a vector of length two, and var, cov, and cor which may
return a matrix. The following functions return more complex results.

round(x, n) rounds the elements of x to n decimals

rev(x) reverses the elements of x
sort(x) sorts the elements of x in increasing order; to sort in decreasing order:
rev(sort(x))
rank(x) ranks of the elements of x

32
 log(x, base) computes the logarithm of x with base base
scale(x) if x is a matrix, centers and reduces the data; to center only use
the option center=FALSE, to reduce only scale=FALSE (by default
center=TRUE, scale=TRUE)
pmin(x,y,...) a vector which ith element is the minimum of x[i], y[i], . . .
pmax(x,y,...) id. for the maximum
cumsum(x) a vector which ith element is the sum from x[1] to x[i]
cumprod(x) id. for the product
cummin(x) id. for the minimum
cummax(x) id. for the maximum
match(x, y) returns a vector of the same length than x with the elements of x
which are in y (NA otherwise)
which(x == a) returns a vector of the indices of x if the comparison operation is
true (TRUE), in this example the values of i for which x[i] == a (the
argument of this function must be a variable of mode logical)
choose(n, k) computes the combinations of k events among n repetitions = n!/[(n−
k)!k!]
na.omit(x) suppresses the observations with missing data (NA) (suppresses the
corresponding line if x is a matrix or a data frame)
na.fail(x) returns an error message if x contains at least one NA
unique(x) if x is a vector or a data frame, returns a similar object but with the
duplicate elements suppressed
table(x) returns a table with the numbers of the differents values of x (typically
for integers or factors)
table(x, y) contingency table of x and y
subset(x, ...) returns a selection of x with respect to criteria (..., typically com-
parisons: x$V1 < 10); if x is a data frame, the option select gives
the variables to be kept (or dropped using a minus sign)
sample(x, size) resample randomly and without replacement size elements in the
vector x, the option replace = TRUE allows to resample with replace-
ment

3.5.8 Matrix computation

R has facilities for matrix computation and manipulation. The functions
rbind and cbind bind matrices with respect to the lines or the columns,
respectively:

> m1 <- matrix(1, nr = 2, nc = 2)

> m2 <- matrix(2, nr = 2, nc = 2)
> rbind(m1, m2)
[,1] [,2]
[1,] 1 1
[2,] 1 1
[3,] 2 2
[4,] 2 2
> cbind(m1, m2)
[,1] [,2] [,3] [,4]

33
[1,] 1 1 2 2
[2,] 1 1 2 2

The operator for the product of two matrices is ‘%*%’. For example, con-
sidering the two matrices m1 and m2 above:

> rbind(m1, m2) %*% cbind(m1, m2)

[,1] [,2] [,3] [,4]
[1,] 2 2 4 4
[2,] 2 2 4 4
[3,] 4 4 8 8
[4,] 4 4 8 8
> cbind(m1, m2) %*% rbind(m1, m2)
[,1] [,2]
[1,] 10 10
[2,] 10 10

The transposition of a matrix is done with the function t; this function

works also with a data frame.
The function diag can be used to extract or modify the diagonal of a
matrix, or to build a diagonal matrix.

> diag(m1)
[1] 1 1
> diag(rbind(m1, m2) %*% cbind(m1, m2))
[1] 2 2 8 8
> diag(m1) <- 10
> m1
[,1] [,2]
[1,] 10 1
[2,] 1 10
> diag(3)
[,1] [,2] [,3]
[1,] 1 0 0
[2,] 0 1 0
[3,] 0 0 1
> v <- c(10, 20, 30)
> diag(v)
[,1] [,2] [,3]
[1,] 10 0 0
[2,] 0 20 0
[3,] 0 0 30
> diag(2.1, nr = 3, nc = 5)
[,1] [,2] [,3] [,4] [,5]
[1,] 2.1 0.0 0.0 0 0
[2,] 0.0 2.1 0.0 0 0
[3,] 0.0 0.0 2.1 0 0

34
 R has also some special functions for matrix computation. We can cite
here solve for inverting a matrix, qr for decomposition, eigen for computing
eigenvalues and eigenvectors, and svd for singular value decomposition.

35
 4 Graphics with R

R offers a remarkable variety of graphics. To get an idea, one can type

demo(graphics) or demo(persp). It is not possible to detail here the pos-
sibilities of R in terms of graphics, particularly since each graphical function
has a large number of options making the production of graphics very flexible.
The way graphical functions work deviates substantially from the scheme
sketched at the beginning of this document. Particularly, the result of a graph-
ical function cannot be assigned to an object 11 but is sent to a graphical device.
A graphical device is a graphical window or a file.
There are two kinds of graphical functions: the high-level plotting func-
tions which create a new graph, and the low-level plotting functions which
add elements to an existing graph. The graphs are produced with respect to
graphical parameters which are defined by default and can be modified with
the function par.
We will see in a first time how to manage graphics and graphical devices;
we will then somehow detail the graphical functions and parameters. We will
see a practical example of the use of these functionalities in producing graphs.
Finally, we will see the packages grid and lattice whose functioning is different
from the one summarized above.

4.1 Managing graphics

4.1.1 Opening several graphical devices

When a graphical function is executed, if no graphical device is open, R opens a
graphical window and displays the graph. A graphical device may be open with
an appropriate function. The list of available graphical devices depends on the
operating system. The graphical windows are called X11 under Unix/Linux
and windows under Windows. In all cases, one can open a graphical window
with the command x11() which also works under Windows because of an alias
towards the command windows(). A graphical device which is a file will be
open with a function depending on the format: postscript(), pdf(), png(),
. . . The list of available graphical devices can be found with ?device.
The last open device becomes the active graphical device on which all
subsequent graphs are displayed. The function dev.list() displays the list
of open devices:

> x11(); x11(); pdf()

> dev.list()
11
There are a few remarkable exceptions: hist() and barplot() produce also numeric
results as lists or matrices.

36
X11 X11 pdf
2 3 4
The figures displayed are the device numbers which must be used to change
the active device. To know what is the active device:
> dev.cur()
pdf
4
and to change the active device:
> dev.set(3)
X11
3
The function dev.off() closes a device: by default the active device is
closed, otherwise this is the one which number is given as argument to the
function. R then displays the number of the new active device:
> dev.off(2)
X11
3
> dev.off()
pdf
4
Two specific features of the Windows version of R are worth mentioning:
a Windows Metafile device can be open with the function win.metafile, and
a menu “History” displayed when the graphical window is selected allowing
recording of all graphs drawn during a session (by default, the recording system
is off, the user switches it on by clicking on “Recording” in this menu).

4.1.2 Partitioning a graphic

The function split.screen partitions the active graphical device. For exam-
ple:
> split.screen(c(1, 2))
divides the device into two parts which can be selected with screen(1) or
screen(2); erase.screen() deletes the last drawn graph. A part of the
device can itself be divided with split.screen() leading to the possibility to
make complex arrangements.
These functions are incompatible with others (such as layout or coplot)
and must not be used with multiple graphical devices. Their use should be
limited, for instance, to graphical exploration of data.
The function layout partitions the active graphic window in several parts
where the graphs will be displayed successively. Its main argument is a ma-
trix with integer numbers indicating the numbers of the “sub-windows”. For
example, to divide the device into four equal parts:

37
 > layout(matrix(1:4, 2, 2))

It is of course possible to create this matrix previously allowing to better

visualize how the device is divided:

> mat <- matrix(1:4, 2, 2)

> mat
[,1] [,2]
[1,] 1 3
[2,] 2 4
> layout(mat)

To actually visualize the partition created, one can use the function layout.show
with the number of sub-windows as argument (here 4). In this example, we
will have:

1 3

> layout.show(4)
2 4

The following examples show some of the possibilities offered by layout().

1 4
> layout(matrix(1:6, 3, 2))
> layout.show(6) 2 5

3 6

> layout(matrix(1:6, 2, 3)) 1 3 5

> layout.show(6)
2 4 6

> m <- matrix(c(1:3, 3), 2, 2) 1

> layout(m) 3

> layout.show(3) 2

In all these examples, we have not used the option byrow of matrix(), the
sub-windows are thus numbered column-wise; one can just specify matrix(...,
byrow=TRUE) so that the sub-windows are numbered row-wise. The numbers

38
 in the matrix may also be given in any order, for example, matrix(c(2, 1,
4, 3), 2, 2).
By default, layout() partitions the device with regular heights and widths:
this can be modified with the options widths and heights. These dimensions
are given relatively12 . Examples:

> m <- matrix(1:4, 2, 2)

1 3
> layout(m, widths=c(1, 3),
heights=c(3, 1))
2 4
> layout.show(4)

2
> m <- matrix(c(1,1,2,1),2,2)
> layout(m, widths=c(2, 1), 1

heights=c(1, 2))
> layout.show(2)

Finally, the numbers in the matrix can include zeros giving the possibility
to make complex (or even esoterical) partitions.

2
> m <- matrix(0:3, 2, 2)
> layout(m, c(1, 3), c(1, 3))
1 3
> layout.show(3)

> m <- matrix(scan(), 5, 5)

1: 0 0 3 3 3 1 1 3 3 3
11: 0 0 3 3 3 0 2 2 0 5
21: 4 2 2 0 5 4
1
26: 2
Read 25 items
3
> layout(m)
5
> layout.show(5)

12
They can be given in centimetres, see ?layout.

39
4.2 Graphical functions

Here is an overview of the high-level graphical functions in R.

plot(x) plot of the values of x (on the y-axis) ordered on the x-axis
plot(x, y) bivariate plot of x (on the x-axis) and y (on the y-axis)
sunflowerplot(x, id. but the points with similar coordinates are drawn as a flower
y) which petal number represents the number of points
pie(x) circular pie-chart
boxplot(x) “box-and-whiskers” plot
stripchart(x) plot of the values of x on a line (an alternative to boxplot() for
small sample sizes)
coplot(x~y | z) bivariate plot of x and y for each value (or interval of values) of
z
interaction.plot if f1 and f2 are factors, plots the means of y (on the y-axis) with
(f1, f2, y) respect to the values of f1 (on the x-axis) and of f2 (different
curves); the option fun allows to choose the summary statistic
of y (by default fun=mean)
matplot(x,y) bivariate plot of the first column of x vs. the first one of y, the
second one of x vs. the second one of y, etc.
dotchart(x) if x is a data frame, plots a Cleveland dot plot (stacked plots
line-by-line and column-by-column)
fourfoldplot(x) visualizes, with quarters of circles, the association between two
dichotomous variables for different populations (x must be an
array with dim=c(2, 2, k), or a matrix with dim=c(2, 2) if
k = 1)
assocplot(x) Cohen–Friendly graph showing the deviations from indepen-
dence of rows and columns in a two dimensional contingency
table
mosaicplot(x) ‘mosaic’ graph of the residuals from a log-linear regression of a
contingency table
pairs(x) if x is a matrix or a data frame, draws all possible bivariate plots
between the columns of x
plot.ts(x) if x is an object of class "ts", plot of x with respect to time, x
may be multivariate but the series must have the same frequency
and dates
ts.plot(x) id. but if x is multivariate the series may have different dates
and must have the same frequency
hist(x) histogram of the frequencies of x
barplot(x) histogram of the values of x
qqnorm(x) quantiles of x with respect to the values expected under a normal
law
qqplot(x, y) quantiles of y with respect to the quantiles of x
contour(x, y, z) contour plot (data are interpolated to draw the curves), x
and y must be vectors and z must be a matrix so that
dim(z)=c(length(x), length(y)) (x and y may be omitted)
filled.contour (x, id. but the areas between the contours are coloured, and a legend
y, z) of the colours is drawn as well
image(x, y, z) id. but the actual data are represented with colours
persp(x, y, z) id. but in perspective
stars(x) if x is a matrix or a data frame, draws a graph with segments
or a star where each row of x is represented by a star and the
columns are the lengths of the segments

40
 symbols(x, y, ...) draws, at the coordinates given by x and y, symbols (circles,
squares, rectangles, stars, thermometres or “boxplots”) which
sizes, colours, etc, are specified by supplementary arguments
termplot(mod.obj) plot of the (partial) effects of a regression model (mod.obj)

For each function, the options may be found with the on-line help in R.
Some of these options are identical for several graphical functions; here are
the main ones (with their possible default values):

add=FALSE if TRUE superposes the plot on the previous one (if it

exists)
axes=TRUE if FALSE does not draw the axes and the box
type="p" specifies the type of plot, "p": points, "l": lines, "b":
points connected by lines, "o": id. but the lines are over
the points, "h": vertical lines, "s": steps, the data are
represented by the top of the vertical lines, "S": id. but
the data are represented by the bottom of the vertical
lines
xlim=, ylim= specifies the lower and upper limits of the axes, for ex-
ample with xlim=c(1, 10) or xlim=range(x)
xlab=, ylab= annotates the axes, must be variables of mode character
main= main title, must be a variable of mode character
sub= sub-title (written in a smaller font)

4.3 Low-level plotting commands

R has a set of graphical functions which affect an already existing graph: they
are called low-level plotting commands. Here are the main ones:

points(x, y) adds points (the option type= can be used)

lines(x, y) id. but with lines
text(x, y, labels, adds text given by labels at coordinates (x,y); a typical use is:
...) plot(x, y, type="n"); text(x, y, names)
mtext(text, adds text given by text in the margin specified by side (see
side=3, line=0, axis() below); line specifies the line from the plotting area
...)
segments(x0, y0, draws lines from points (x0,y0) to points (x1,y1)
x1, y1)
arrows(x0, y0, id. with arrows at points (x0,y0) if code=2, at points (x1,y1) if
x1, y1, angle= 30, code=1, or both if code=3; angle controls the angle from the
code=2) shaft of the arrow to the edge of the arrow head
abline(a,b) draws a line of slope b and intercept a
abline(h=y) draws a horizontal line at ordinate y
abline(v=x) draws a vertical line at abcissa x
abline(lm.obj) draws the regression line given by lm.obj (see section 5)

41
 rect(x1, y1, x2, draws a rectangle which left, right, bottom, and top limits are
y2) x1, x2, y1, and y2, respectively
polygon(x, y) draws a polygon linking the points with coordinates given by x
and y
legend(x, y, adds the legend at the point (x,y) with the symbols given by
legend) legend
title() adds a title and optionally a sub-title
axis(side, vect) adds an axis at the bottom (side=1), on the left (2), at the top
(3), or on the right (4); vect (optional) gives the abcissa (or
ordinates) where tick-marks are drawn
box() adds a box around the current plot
rug(x) draws the data x on the x-axis as small vertical lines
locator(n, returns the coordinates (x, y) after the user has clicked n times
type="n", ...) on the plot with the mouse; also draws symbols (type="p") or
lines (type="l") with respect to optional graphic parameters
(...); by default nothing is drawn (type="n")

Note the possibility to add mathematical expressions on a plot with text(x,

y, expression(...)), where the function expression transforms its argu-
ment in a mathematical equation. For example,
> text(x, y, expression(p == over(1, 1+e^-(beta*x+alpha))))
will display, on the plot, the following equation at the point of coordinates
(x, y):
1
p=
1 + e−(β x+α)
To include in an expression a variable we can use the functions substitute
and as.expression; for example to include a value of R 2 (previously com-
puted and stored in an object named Rsquared):
> text(x, y, as.expression(substitute(R^2==r, list(r=Rsquared))))
will display on the plot at the point of coordinates (x, y):
R2 = 0.9856298
To display only three decimals, we can modify the code as follows:
> text(x, y, as.expression(substitute(R^2==r,
+ list(r=round(Rsquared, 3)))))
will display:
R2 = 0.986
Finally, to write the R in italics:
> text(x, y, as.expression(substitute(italic(R)^2==r,
+ list(r=round(Rsquared, 3)))))
R2 = 0.986

42
4.4 Graphical parameters

In addition to low-level plotting commands, the presentation of graphics can

be improved with graphical parameters. They can be used either as options
of graphic functions (but it does not work for all), or with the function par to
change permanently the graphical parameters, i.e. the subsequent plots will
be drawn with respect to the parameters specified by the user. For instance,
the following command:

> par(bg="yellow")

will result in all subsequent plots drawn with a yellow background. There
are 73 graphical parameters, some of them have very similar functions. The
exhaustive list of these parameters can be read with ?par; I will limit the
following table to the most usual ones.

adj controls text justification with respect to the left border of the text so that
0 is left-justified, 0.5 is centred, 1 is right-justified, values > 1 move the text
further to the left, and negative values further to the right; if two values are
given (e.g., c(0, 0)) the second one controls vertical justification with respect
to the text baseline
bg specifies the colour of the background (e.g., bg="red", bg="blue"; the list of
the 657 available colours is displayed with colors())
bty controls the type of box drawn around the plot, allowed values are: "o",
"l", "7", "c", "u" ou "]" (the box looks like the corresponding character); if
bty="n" the box is not drawn
cex a value controlling the size of texts and symbols with respect to the default; the
following parameters have the same control for numbers on the axes, cex.axis,
the axis labels, cex.lab, the title, cex.main, and the sub-title, cex.sub
col controls the colour of symbols; as for cex there are: col.axis, col.lab,
col.main, col.sub
font an integer which controls the style of text (1: normal, 2: italics, 3: bold, 4:
bold italics); as for cex there are: font.axis, font.lab, font.main, font.sub
las an integer which controls the orientation of the axis labels (0: parallel to the
axes, 1: horizontal, 2: perpendicular to the axes, 3: vertical)
lty controls the type of lines, can be an integer (1: solid, 2: dashed, 3: dotted,
4: dotdash, 5: longdash, 6: twodash), or a string of up to eight characters
(between "0" and "9") which specifies alternatively the length, in points or
pixels, of the drawn elements and the blanks, for example lty="44" will have
the same effet than lty=2
lwd a numeric which controls the width of lines
mar a vector of 4 numeric values which control the space between the axes and the
border of the graph of the form c(bottom, left, top, right), the default
values are c(5.1, 4.1, 4.1, 2.1)
mfcol a vector of the form c(nr,nc) which partitions the graphic window as a ma-
trix of nr lines and nc columns, the plots are then drawn in columns (see
section 4.1.2)
mfrow id. but the plots are then drawn in line (see section 4.1.2)
pch controls the type of symbol, either an integer between 1 and 25, or any single
character within "" (Fig. 2)
ps an integer which controls the size in points of texts and symbols

43
 1 2 3 4 5 6 7 8 9 10

11 12 13 14 15 16 17 18 19 20

21 22 23 24 25 "*" "?" "." "X" "a"

* ? X a

Figure 2: The plotting symbols in R (pch=1:25). The colours were obtained

with the options col="blue", bg="yellow", the second option has an effect
only for the symbols 21–25. Any character can be used (pch="*", "?", ".",
. . . ).

pty a character which specifies the type of the plotting region, "s": square, "m":
maximal
tck a value which specifies the length of tick-marks on the axes as a fraction of
the smallest of the width or height of the plot; if tck=1 a grid is drawn
tcl id. but as a fraction of the height of a line of text (by default tcl=-0.5)
xaxt if xaxt="n" the x-axis is set but not drawn (useful in conjunction with
axis(side=1, ...))
yaxt if yaxt="n" the y-axis is set but not drawn (useful in conjunction with
axis(side=2, ...))

4.5 A practical example

In order to illustrate R’s graphical functionalities, let us consider a simple

example of a bivariate graph of 10 pairs of random variates. These values
were generated with:

> x <- rnorm(10)

> y <- rnorm(10)

The wanted graph will be obtained with plot(); one will type the command:

> plot(x, y)

and the graph will be plotted on the active graphical device. The result
is shown on Fig. 3. By default, R makes graphs in an “intelligent” way:

44
 0.5
0.0
y

−0.5
−1.0 −0.5 0.0 0.5 1.0

Figure 3: The function plot used without options.

the spaces between tick-marks on the axes, the placement of labels, etc, are
calculated so that the resulting graph is as intelligible as possible.
The user may, nevertheless, change the way a graph is presented, for in-
stance, to conform to a pre-defined editorial style, or to give it a personal
touch for a talk. The simplest way to change the presentation of a graph is to
add options which will modify the default arguments. In our example, we can
modify significantly the figure in the following way:

plot(x, y, xlab="Ten random values", ylab="Ten other values",

xlim=c(-2, 2), ylim=c(-2, 2), pch=22, col="red",
bg="yellow", bty="l", tcl=0.4,
main="How to customize a plot with R", las=1, cex=1.5)

The result is on Fig. 4. Let us detail each of the used options. First,
xlab and ylab change the axis labels which, by default, were the names of the
variables. Then, xlim and ylim allow us to define the limits on both axes 13 .
The graphical parameter pch is used here as an option: pch=22 specifies a
square which contour and background colours may be different and are given
by, respectively, col and bg. The table of graphical parameters gives the
meaning of the modifications done by bty, tcl, las and cex. Finally, a title
is added with the option main.
The graphical parameters and the low-level plotting functions allow us to
go further in the presentation of a graph. As we have seen previously, some
graphical parameters cannot be passed as arguments to a function like plot.
13
By default, R adds 4% on each side of the axis limit. This behaviour may be altered by
setting the graphical parameters xaxs="i" and yaxs="i" (they can be passed as options to
plot()).

45
 How to customize a plot with R

Ten other values

0

−1

−2

−2 −1 0 1 2

Ten random values

Figure 4: The function plot used with options.

We will now modify some of these parameters with par(), it is thus necessary
to type several commands. When the graphical parameters are changed, it
is useful to save their initial values beforehand to be able to restore them
afterwards. Here are the commands used to obtain Fig. 5.

opar <- par()

par(bg="lightyellow", col.axis="blue", mar=c(4, 4, 2.5, 0.25))
plot(x, y, xlab="Ten random values", ylab="Ten other values",
xlim=c(-2, 2), ylim=c(-2, 2), pch=22, col="red", bg="yellow",
bty="l", tcl=-.25, las=1, cex=1.5)
title("How to customize a plot with R (bis)", font.main=3, adj=1)
par(opar)

Let us detail the actions resulting from these commands. First, the default
graphical parameters are copied in a list called here opar. Three parameters
will be then modified: bg for the colour of the background, col.axis for the
colour of the numbers on the axes, and mar for the sizes of the margins around
the plotting region. The graph is drawn in a nearly similar way to Fig. 4. The
modifications of the margins allowed to use the space around the plotting area.
The title here is added with the low-level plotting function title which allows
to give some parameters as arguments without altering the rest of the graph.
Finally, the initial graphical parameters are restored with the last command.
Now, total control! On Fig. 5, R still determines a few things such as
the number of tick marks on the axes, or the space between the title and the
plotting area. We will see now how to totally control the presentation of the
graph. The approach used here is to plot a “blank” graph with plot(...,
type="n"), then to add points, axes, labels, etc, with low-level plotting func-

46
 How to customize a plot with R (bis)

Ten other values

0

−1

−2

−2 −1 0 1 2

Ten random values

Figure 5: The functions par, plot and title.

tions. We will fancy a few arrangements such as changing the colour of the
plotting area. The commands follow, and the resulting graph is on Fig. 6.

opar <- par()

par(bg="lightgray", mar=c(2.5, 1.5, 2.5, 0.25))
plot(x, y, type="n", xlab="", ylab="", xlim=c(-2, 2),
ylim=c(-2, 2), xaxt="n", yaxt="n")
rect(-3, -3, 3, 3, col="cornsilk")
points(x, y, pch=10, col="red", cex=2)
axis(side=1, c(-2, 0, 2), tcl=-0.2, labels=FALSE)
axis(side=2, -1:1, tcl=-0.2, labels=FALSE)
title("How to customize a plot with R (ter)",
font.main=4, adj=1, cex.main=1)
mtext("Ten random values", side=1, line=1, at=1, cex=0.9, font=3)
mtext("Ten other values", line=0.5, at=-1.8, cex=0.9, font=3)
mtext(c(-2, 0, 2), side=1, las=1, at=c(-2, 0, 2), line=0.3,
col="blue", cex=0.9)
mtext(-1:1, side=2, las=1, at=-1:1, line=0.2, col="blue", cex=0.9)
par(opar)

Like before, the default graphical parameters are saved, and the colour
of the background and the margins are modified. The graph is then drawn
with type="n" to not plot the points, xlab="", ylab="" to not write the
axis labels, and xaxt="n", yaxt="n" to not draw the axes. This results in
drawing only the box around the plotting area, and defining the axes with
respect to xlim et ylim. Note that we could have used the option axes=FALSE
but in this case neither the axes, nor the box would have been drawn.

47
 Ten other values How to customize a plot with R (ter)

−1

−2 0 2
Ten random values

Figure 6: A “hand-made” graph.

The elements are then added in the plotting region so defined with some
low-level plotting functions. Before adding the points, the colour inside the
plotting area is changed with rect(): the size of the rectangle are chosen so
that it is substantially larger than the plotting area.
The points are plotted with points(); a new symbol was used. The axes
are added with axis(): the vector given as second argument specifies the
coordinates of the tick-marks. The option labels=FALSE specifies that no
annotation must be written with the tick-marks. This option also accepts a
vector of mode character, for example labels=c("A", "B", "C").
The title is added with title(), but the font is slightly changed. The
annotations on the axes are written with mtext() (marginal text). The first
argument of this function is a vector of mode character giving the text to be
written. The option line indicates the distance from the plotting area (by
default line=0), and at the coordinnate. The second call to mtext() uses
the default value of side (3). The two other calls to mtext() pass a numeric
vector as first argument: this will be converted into character.

4.6 The grid and lattice packages

The packages grid and lattice implement the grid and lattice systems. Grid is
a new graphical mode with its own system of graphical parameters which are
distinct from those seen above. The two main distinctions of grid compared
to the base graphics are:

• a more flexible way to split graphical devices using viewports which could
be overpalling (graphical objects may even be shared among distinct
viewports, e.g., arrows);

48
 • graphical objects (grob) may be modified or removed from a graph with-
out requiring the re-draw all the graph (as must be done with base
graphics).
Grid graphics cannot usually be combined or mixed with base graphics
(the gridBase package must be used to do this). However, it is possible to use
both graphical modes in the same session on the same graphical device.
Lattice is essentially the implementation in R of the Trellis graphics of
S-PLUS. Trellis is an approach for visualizing multivariate data which is par-
ticularly appropriate for the exploration of relations or interactions among
variables14 . The main idea behind lattice (and Trellis as well) is that of con-
ditional multiple graphs: a bivariate graph will be split in several graphs with
respect to the values of a third variable. The function coplot uses a similar
approach, but lattice offers much wider functionalities. Lattice uses the grid
graphical mode.
Most functions in lattice take a formula as their main argument 15 , for
example y ~ x. The formula y ~ x | z means that the graph of y with
respect to x will be plotted as several graphs with respect to the values of z.
The following table gives the main functions in lattice. The formula given
as argument is the typical necessary formula, but all these functions accept
a conditional formula (y ~ x | z) as main argument; in the latter case, a
multiple graph, with respect to the values of z, is plotted as will be seen in
the examples below.

barchart(y ~ x) histogram of the values of y with respect to those of x

bwplot(y ~ x) “box-and-whiskers” plot
densityplot(~ x) density functions plot
dotplot(y ~ x) Cleveland dot plot (stacked plots line-by-line and
column-by-column)
histogram(~ x) histogram of the frequencies of x
qqmath(~ x) quantiles of x with respect to the values expected under
a theoretical distribution
stripplot(y ~ x) single dimension plot, x must be numeric, y may be a
factor
qq(y ~ x) quantiles to compare two distributions, x must be nu-
meric, y may be numeric, character, or factor but must
have two ‘levels’
xyplot(y ~ x) bivariate plots (with many functionalities)
levelplot(z ~ x*y) coloured plot of the values of z at the coordinates given
contourplot(z ~ x*y) by x and y (x, y and z are all of the same length)
cloud(z ~ x*y) 3-D perspective plot (points)
wireframe(z ~ x*y) id. (surface)
splom(~ x) matrix of bivariate plots
parallel(~ x) parallel coordinates plot

Let us see now some examples in order to illustrate a few aspects of lattice.
The package must be loaded in memory with the command library(lattice)
14
http://cm.bell-labs.com/cm/ms/departments/sia/project/trellis/index.html
15
plot() also accepts a formula as its main argument: if x and y are two vectors of the
same length, plot(y ~ x) and plot(x, y) will give identical graphs.

49
 −4 −2 0 2 4

n = 35 n = 40 n = 45
0.6
0.5
0.4
0.3
0.2
0.1
0
n = 20 n = 25 n = 30
0.6
0.5

Density
0.4
0.3
0.2
0.1
0
n=5 n = 10 n = 15
0.6
0.5
0.4
0.3
0.2
0.1
0

−4 −2 0 2 4 −4 −2 0 2 4
x

Figure 7: The function densityplot.

so that the functions can be accessed.

Let us start with the graphs of density functions. Such graphs can be
done simply with densityplot(~ x) which will plot a curve of the empirical
density function with the points corresponding to the observations on the x-
axis (similarly to rug()). Our example will be slightly more complicated with
the superposition, on each plot, of the curves of empirical density and those
predicted from a normal law. It is necessary to use the argument panel which
defines what is drawn on each plot. The commands are:

n <- seq(5, 45, 5)

x <- rnorm(sum(n))
y <- factor(rep(n, n), labels=paste("n =", n))
densityplot(~ x | y,
panel = function(x, ...) {
panel.densityplot(x, col="DarkOliveGreen", ...)
panel.mathdensity(dmath=dnorm,
args=list(mean=mean(x), sd=sd(x)),
col="darkblue")
})

The first three lines of command generate a random sample of independent

normal variates which is split in sub-samples of size equal to 5, 10, 15, . . . , and
45. Then comes the call to densityplot producing a plot for each sub-sample.
panel takes as argument a function. In our example, we have defined a func-
tion which calls two functions pre-defined in lattice: panel.densityplot to
draw the empirical density function, and panel.mathdensity to draw the den-
sity function predicted from a normal law. The function panel.densityplot
is called by default if no argument is given to panel: the command densityplot

50
 165 170 175 180 185

472−544 544−616 616−688

−10
−15
−20
−25
−30
−35
−40
256−328 328−400 400−472
−10
−15
−20

lat
−25
−30
−35
−40
40−112 112−184 184−256
−10
−15
−20
−25
−30
−35
−40
165 170 175 180 185 165 170 175 180 185
long

Figure 8: The function xyplot with the data “quakes”.

(~ x | y) would have resulted in the same graph than Fig. 7 but without the
blue curves.
The next examples are taken, more or less modified, from the help pages
of lattice, and use some data sets available in R: the locations of 1000 seismic
events near the Fiji Islands, and some flower measurements made on three
species of iris.
Fig. 8 shows the geographic locations of the seismic events with respect to
depth. The commands necessary for this graph are:

data(quakes)
mini <- min(quakes$depth)
maxi <- max(quakes$depth)
int <- ceiling((maxi - mini)/9)
inf <- seq(mini, maxi, int)
quakes$depth.cat <- factor(floor(((quakes$depth - mini) / int)),
labels=paste(inf, inf + int, sep="-"))
xyplot(lat ~ long | depth.cat, data = quakes)

The first command loads the data quakes in memory. The five next com-
mands create a factor by dividing the depth (variable depth) in nine equally-
ranged intervals: the levels of this factor are labelled with the lower and upper
bounds of these intervals. It then suffices to call the function xyplot with the
appropriate formula and an argument data indicating where xyplot must look
for the variables16 .
With the data iris, the overlap among the different species is sufficiently
small so they can be plotted on the figure (Fig. 9). The commands are:
16
plot() cannot take an argument data, the location of the variables must be given
explicitly, for example plot(quakes$long ~ quakes$lat).

51
 7
o
o o
o
o
setosa o
versicolor o o o
6 o o
o o
virginica o o o
o o o
o o o o o
o o
o o
o o
o o
o o o o o o o
5 o o o o
o o o
o o
o o o o
o o o
o o o o

Petal.Length
o o o
o
o o o
o o
4 o o o
o o o
o
o
o
o
o
3 o

2
o o
o o o o
o o o
o o o o
o o o
o o o
o
o
1 o

0 0.5 1 1.5 2 2.5

Petal.Width

Figure 9: The function xyplot with the data “iris”.

data(iris)
xyplot(
Petal.Length ~ Petal.Width, data = iris, groups=Species,
panel = panel.superpose,
type = c("p", "smooth"), span=.75,
auto.key = list(x = 0.15, y = 0.85)
)

The call to the function xyplot is here a bit more complex than in the
previous example and uses several options that we will detail. The option
groups, as suggested by its name, defines groups that will be used by the
other options. We have already seen the option panel which defines how the
different groups will be represented on the graph: we use here a pre-defined
function panel.superpose in order to superpose the groups on the same plot.
No option is passed to panel.superpose, the default colours will be used to
distinguish the groups. The option type, like in plot(), specifies how the
data are represented, but here we can give several arguments as a vector:
"p" to draw points and "smooth" to draw a smooth curve which degree of
smoothness is specified by span. The option auto.key adds a legend to the
graph: it is only necessary to give, as a list, the coordinates where the legend
is to be plotted. Note that here these coordinates are relative to the size of
the plot (i.e. in [0, 1]).
We will see now the function splom with the same data on iris. The
following commands were used to produce Fig. 10:

splom(
~iris[1:4], groups = Species, data = iris, xlab = "",
panel = panel.superpose,

52
 Setosa Versicolor Virginica
o oo o o ooo o o o o oooooo oo 2.5 1.5 2 2.5
ooo
o o ooo oo
oo o
o o o ooooo oo
ooo oo oooooo oo o o oo
o o
oooo o ooooooo ooo
ooo 2
o ooooooooo ooo oo
o
o oo
ooo
ooo o ooo
ooooooooo
o o oooo
o ooooo o o o oooo
ooooo oooooo o o
oooo 1.5
o ooo o oo
oo oooo
oo ooo oo oooo o
oo
o oo ooooo o o o oo ooo
ooo Petal.Width
ooo oooooo ooo
o ooo
oo o
oo
oo
oooooooo
o
1
oo ooo ooo oo 0.5
ooo o
oooo
oooo
oo o
o o oo o o ooo
oooo
oooooo
oo ooo o oo
ooooo
oo oooo
oo o
o ooo
oo
ooooo
oo
oooo 0 0.5 1
0
o oo 7
oo o o 4 5 6 7 oooo
oo oo ooo oo o
o ooo o o
oooo oo o o o 6 o ooo o
ooooooooo oooo
o oooo o ooo o o
oooo
o o oo ooo o o
oooooooooo o o oo ooo 5 oooo o
ooo oo
oo
o oooo ooo oooooooo oo o
oo oo oo
ooooo oooo
ooo
ooooooooooo ooo o
oo ooooo
oo oo
oooooo 4 Petal.Length 4 o oo
oo o
o oo
oo
o
o o o oo oo
o
oo oo o
o o 3 o
oo ooo o 2
oooooo oo
oo o
ooo
ooo
o
ooooooooooooo oo oooo o oo o 1 oo
oooo
oooo o o o o o o o oo 2 3 4 1 oo
o
o 4.5
3.5 4 4.5 o o
ooo 4
o
oooo oo
oo
ooo
o oo oo oooo
o oo ooo
o oo
o ooooooo ooo o 3.5 ooo oo
oo o oo
o
oo o
ooo oo
oo o ooo oo oooo ooo o o ooo
ooooooo o oo ooooo
ooooo Sepal.Width ooo oo
ooo oooo
oooooooooo o
o o ooo o oo o
oo
o o oo oo oo
o oo
oo
oooooo
ooooooo oo 3 ooo oo o oo oooo
oo oooooooooo
ooooooo o
oo
oo
o oo
o
oo
o
oo
o
o oo
ooo
o
ooo
oo
o ooooo
oo
oo ooo
o oo
oo
oo o o o
o ooooooooo ooooo o o ooooooo o
oo oo
oooo o
oo o ooo o 2.5 o o oo oo o
ooooooo oooooo oooo o
o oo o ooo o o o o oo o o o
oo
o oo
o 2 2.5 3 2 o o
8 o o o
7 8 ooo o o o ooo o
oooo
oo o oo
oo o
o oooo oo o o
7 oo
o oooooo oo oo
o ooo o
oooo
o o oooooo
oooooo
o o
oo oo o
oo ooooo
oooooo
oo oooooooo ooooo ooo o
oo
oo o o o
o ooo
Sepal.Length oo oooo
ooo o
oo o o o o oo o
o o o ooo
6 o oooo
oo oo
o
oooooo ooo o o oooo o
o
oo o
ooo
ooo
oooo o o o ooo ooo oooooo
ooo o ooo oo
o o o oo o o
ooo
oo oo ooooooo o ooo
oo
o oo o oo o o
ooo
oo o o
oo oo oo
o o oo
o o o
oo ooo o oo
oooo o
5 o ooo o oo
o
o
oooooo ooo
oo
oo
ooo o
ooo o oo
oo
oo o o oo
ooo o o o
oo
oo o o
o oo o o oo ooo oo
oo
5 6 oo
o o ooo oo

Figure 10: The function splom with the data “iris” (1).

auto.key = list(columns = 3)
)
The main argument is this time a matrix (the four first columns of iris).
The result is the set of possible bivariate plots among the columns of the
matrix, like the standard function pairs. By default, splom adds the text
“Scatter Plot Matrix” under the x-axis: to avoid this, the option xlab=""
was used. The other options are similar to the previous example, except that
columns = 3 for auto.key was specified so the legend is displayed in three
columns.
Fig. 10 could have been done with pairs(), but this latter function cannot
make conditional graphs like on Fig. 11. The code used is relatively simple:
splom(~iris[1:3] | Species, data = iris, pscales = 0,
varnames = c("Sepal\nLength", "Sepal\nWidth", "Petal\nLength"))
The sub-graphs being relatively small, we added two options to improve
the legibility of the figure: pscales = 0 removes the tick-marks on the axes
(all sub-graphs are drawn on the same scales), and the names of the variables
were re-defined to display them on two lines ("\n" codes for a line break in a
character string).
The last example uses the method of parallel coordinates for the ex-
ploratory analysis of multivariate data. The variables are arranged on an
axis (e.g., the y-axis), and the observed values are plotted on the other axis
(the variables are scaled similarly, e.g., by standardizing them). The different
values of the same individual are joined by a line. With the data iris, Fig. 12
is obtained with the following code:
parallel(~iris[, 1:4] | Species, data = iris, layout = c(3, 1))

53
 virginica

Petal
Length

Sepal
Width

Sepal
Length

setosa versicolor

Petal Petal
Length Length

Sepal Sepal
Width Width

Sepal Sepal
Length Length

Scatter Plot Matrix

Figure 11: The function splom with the data “iris” (2).

Min Max

setosa versicolor virginica

Petal.Width

Petal.Length

Sepal.Width

Sepal.Length

Min Max Min Max

Figure 12: The function parallel with the data “iris”.

54
 5 Statistical analyses with R

Even more than for graphics, it is impossible here to go in the details of the
possibilities offered by R with respect to statistical analyses. My goal here is
to give some landmarks with the aim to have an idea of the features of R to
perform data analyses.
The package stats contains functions for a wide range of basic statisti-
cal analyses: classical tests, linear models (including least-squares regression,
generalized linear models, and analysis of variance), distributions, summary
statistics, hierarchical clustering, time-series analysis, nonlinear least squares,
and multivariate analysis. Other statistical methods are available in a large
number of packages. Some of them are distributed with a base installation
of R and are labelled recommanded, and many other packages are contributed
and must be installed by the user.
We will start with a simple example which requires no other package than
stats in order to introduce the general approach to data analysis in R. Then,
we will detail some notions, formulae and generic functions, which are useful
whatever the type of analysis performed. We will conclude with an overview
on packages.

5.1 A simple example of analysis of variance

The function for the analysis of variance in stats is aov. In order to try it, let
us take a data set distributed with R: InsectSprays. Six insecticides were
tested in field conditions, the observed response was the number of insects.
Each insecticide was tested 12 times, thus there are 72 observations. We will
not consider here the graphical exploration of the data, but will focus on a
simple analysis of variance of the response with respect to the insecticide. After
loading the data in memory with the function data, the analysis is performed
after a square-root transformation of the response:

> data(InsectSprays)
> aov.spray <- aov(sqrt(count) ~ spray, data = InsectSprays)

The main (and mandatory) argument of aov is a formula which specifies

the response on the left-hand side of the tilde symbol ~ and the predictor
on the right-hand side. The option data = InsectSprays specifies that the
variables must be found in the data frame InsectSprays. This syntax is
equivalent to:

> aov.spray <- aov(sqrt(InsectSprays$count) ~ InsectSprays$spray)

or still (if we know the column numbers of the variables):

55
> aov.spray <- aov(sqrt(InsectSprays[, 1]) ~ InsectSprays[, 2])

The first syntax is to be preferred since it is clearer.

The results are not displayed since they are assigned to an object called
aov.spray. We will then used some functions to extract the results, for exam-
ple print to display a brief summary of the analysis (mostly the estimated pa-
rameters) and summary to display more details (included the statistical tests):

> aov.spray
Call:
aov(formula = sqrt(count) ~ spray, data = InsectSprays)

Terms:
spray Residuals
Sum of Squares 88.43787 26.05798
Deg. of Freedom 5 66

Residual standard error: 0.6283453

Estimated effects may be unbalanced
> summary(aov.spray)
Df Sum Sq Mean Sq F value Pr(>F)
spray 5 88.438 17.688 44.799 < 2.2e-16 ***
Residuals 66 26.058 0.395
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

We may remind that typing the name of the object as a command is similar
to the command print(aov.spray). A graphical representation of the results
can be done with plot() or termplot(). Before typing plot(aov.spray) we
will divide the graphics into four parts so that the four diagnostics plots will
be done on the same graph. The commands are:

> opar <- par()

> par(mfcol = c(2, 2))
> plot(aov.spray)
> par(opar)
> termplot(aov.spray, se=TRUE, partial.resid=TRUE, rug=TRUE)

and the resulting graphics are on Figs. 13 and 14.

5.2 Formulae

Formulae are a key element in statistical analyses with R: the notation used
is the same for (almost) all functions. A formula is typically of the form y
~ model where y is the analysed response and model is a set of terms for
which some parameters are to be estimated. These terms are separated with
arithmetic symbols but they have here a particular meaning.

56
 Residuals vs Fitted Scale−Location plot

Standardized residuals

1.5
27 39
27 25
39

1.0
Residuals

1.0
0.0

0.5
−1.5

0.0
25

1.5 2.5 3.5 1.5 2.5 3.5

Fitted values Fitted values

Normal Q−Q plot Cook’s distance plot

Standardized residuals

0.08
27
39 27

Cook’s distance
2
39
25

0.04
0

0.00
−2
25

−2 −1 0 1 2 0 20 40 60

Theoretical Quantiles Obs. number

Figure 13: Graphical representation of the results from the function aov with
plot().

a+b additive effects of a and of b

X if X is a matrix, this specifies an additive effect of each of
its columns, i.e. X[,1]+X[,2]+...+X[,ncol(X)]; some
of the columns may be selected with numeric indices (e.g.,
X[,2:4])
a:b interactive effect between a and b
a*b additive and interactive effects (identical to a+b+a:b)
poly(a, n) polynomials of a up to degree n
^n includes all interactions up to level n, i.e. (a+b+c)^2 is
identical to a+b+c+a:b+a:c+b:c
b %in% a the effects of b are nested in a (identical to a+a:b, or
a/b)
-b removes the effect of b, for example: (a+b+c)^2-a:b is
identical to a+b+c+a:c+b:c
-1 y~x-1 is a regression through the origin (id. for y~x+0 or
0+y~x)
1 y~1 fits a model with no effects (only the intercept)
offset(...) adds an effect to the model without estimating any pa-
rameter (e.g., offset(3*x))
We see that the arithmetic operators of R have in a formula a different
meaning than they have in expressions. For example, the formula y~x1+x2
defines the model y = β1 x1 + β2 x2 + α, and not (if the operator + would have
its usual meaning) y = β(x1 + x2 ) + α. To include arithmetic operations in a
formula, we can use the function I: the formula y~I(x1+x2) defines the model
y = β(x1 + x2 ) + α. Similarly, to define the model y = β 1 x + β2 x2 + α, we
will use the formula y ~ poly(x, 2) (and not y ~ x + x^2). However, it is

57
 2
1
Partial for spray

0
−1
−2
−3
0 1 2 3 4 5 6

spray

Figure 14: Graphical representation of the results from the function aov with
termplot().

possible to include a function in a formula in order to transform a variable as

seen above with the insect sprays analysis of variance.
For analyses of variance, aov() accepts a particular syntax to define ran-
dom effects. For instance, y ~ a + Error(b) means the additive effects of
the fixed term a and the random one b.

5.3 Generic functions

We remember that R’s functions act with respect to the attributes of the
objects possibly passed as arguments. The class is an attribute deserving some
attention here. It is very common that the R statistical functions return an
object of class with the same name (e.g., aov returns an object of class "aov",
lm returns one of class "lm"). The functions that we can use subsequently to
extract the results will act specifically with respect to the class of the object.
These functions are called generic.
For instance, the function which is most often used to extract results from
analyses is summary which displays detailed results. Whether the object given
as argument is of class "lm" (linear model) or "aov" (analysis of variance),
it sounds obvious that the information to display will not be the same. The
advantage of generic functions is that the syntax is the same in all cases.
An object containing the results of an analysis is generally a list, and the
way it is displayed is determined by its class. We have already seen this notion
that the action of a function depends on the kind of object given as argument.
It is a general feature of R17 . The following table gives the main generic func-
17
There are more than 100 generic functions in R.

58
tions which can be used to extract information from objects resulting from an
analysis. The typical usage of these functions is:

> mod <- lm(y ~ x)

> df.residual(mod)
[1] 8

print returns a brief summary

summary returns a detailed summary
df.residual returns the number of residual degrees of freedom
coef returns the estimated coefficients (sometimes with their standard-errors)
residuals returns the residuals
deviance returns the deviance
fitted returns the fitted values
logLik computes the logarithm of the likelihood and the number of parameters
AIC computes the Akaike information criterion or AIC (depends on logLik())

A function like aov or lm returns a list with its different elements corre-
sponding to the results of the analysis. If we take our example of an analysis
of variance with the data InsectSprays, we can look at the structure of the
object returned by aov:

> str(aov.spray, max.level = -1)

List of 13
- attr(*, "class")= chr [1:2] "aov" "lm"

Another way to look at this structure is to display the names of the object:

> names(aov.spray)
[1] "coefficients" "residuals" "effects"
[4] "rank" "fitted.values" "assign"
[7] "qr" "df.residual" "contrasts"
[10] "xlevels" "call" "terms"
[13] "model"

The elements can then be extracted as we have already seen:

> aov.spray$coefficients
(Intercept) sprayB sprayC sprayD
3.7606784 0.1159530 -2.5158217 -1.5963245
sprayE sprayF
-1.9512174 0.2579388

summary() also creates a list which, in the case of aov(), is simply a table
of tests:

59
> str(summary(aov.spray))
List of 1
$ :Classes anova and ‘data.frame’: 2 obs. of 5 variables:
..$ Df : num [1:2] 5 66
..$ Sum Sq : num [1:2] 88.4 26.1
..$ Mean Sq: num [1:2] 17.688 0.395
..$ F value: num [1:2] 44.8 NA
..$ Pr(>F) : num [1:2] 0 NA
- attr(*, "class")= chr [1:2] "summary.aov" "listof"
> names(summary(aov.spray))
NULL

Generic functions do not generally perform any action on objects: they

call the appropriate function with respect to the class of the argument. A
function called by a generic is a method in R’s jargon. Schematically, a method
is constructed as generic.cls , where cls is the class of the object. For
instance, in the case of summary, we can display the corresponding methods:

> apropos("^summary")
[1] "summary" "summary.aov"
[3] "summary.aovlist" "summary.connection"
[5] "summary.data.frame" "summary.default"
[7] "summary.factor" "summary.glm"
[9] "summary.glm.null" "summary.infl"
[11] "summary.lm" "summary.lm.null"
[13] "summary.manova" "summary.matrix"
[15] "summary.mlm" "summary.packageStatus"
[17] "summary.POSIXct" "summary.POSIXlt"
[19] "summary.table"

We can see the difference for this generic in the case of a linear regression,
compared to an analysis of variance, with a small simulated example:

> x <- y <- rnorm(5)

> lm.spray <- lm(y ~ x)
> names(lm.spray)
[1] "coefficients" "residuals" "effects"
[4] "rank" "fitted.values" "assign"
[7] "qr" "df.residual" "xlevels"
[10] "call" "terms" "model"
> names(summary(lm.spray))
[1] "call" "terms" "residuals"
[4] "coefficients" "sigma" "df"
[7] "r.squared" "adj.r.squared" "fstatistic"
[10] "cov.unscaled"

The following table shows some generic functions that do supplementary

analyses from an object resulting from an analysis, the main argument being

60
this latter object, but in some cases a further argument is necessary like for
predict or update.

add1 tests successively all the terms that can be added to a model
drop1 tests successively all the terms that can be removed from a model
step selects a model with AIC (calls add1 and drop1)
anova computes a table of analysis of variance or deviance for one or several
models
predict computes the predicted values for new data from a fitted model
update re-fits a model with a new formula or new data

There are also various utilities functions that extract information from a
model object or a formula, such as alias which finds the linearly dependent
terms in a linear model specified by a formula.
Finally, there are, of course, graphical functions such as plot which dis-
plays various diagnostics, or termplot (see the above example), though this
latter function is not generic but calls predict.

5.4 Packages

The following table lists the standard packages which are distributed with a
base installation of R. Some of them are loaded in memory when R starts; this
can be displayed with the function search:

> search()
[1] ".GlobalEnv" "package:methods"
[3] "package:stats" "package:graphics"
[5] "package:grDevices" "package:utils"
[7] "package:datasets" "Autoloads"
[9] "package:base"

The other packages may be used after being loaded:

> library(grid)

The list of the functions in a package can be displayed with:

> library(help = grid)

or by browsing the help in html format. The information relative to each

function can be accessed as previously seen (p. 7).

61
 Package Description
base base R functions
datasets base R datasets
grDevices graphics devices for base and grid graphics
graphics base graphics
grid grid graphics
methods definition of methods and classes for R objects and program-
ming tools
splines regression spline functions and classes
stats statistical functions
stats4 statistical functions using S4 classes
tcltk functions to interface R with Tcl/Tk graphical user interface
elements
tools tools for package development and administration
utils R utility functions

Many contributed packages add to the list of statistical methods available

in R. They are distributed separately, and must be installed and loaded in
R. A complete list of the contributed packages, with descriptions, is on the
CRAN Web site18 . Several of these packages are recommanded since they cover
statistical methods often used in data analysis. The recommended packages
are often distributed with a base installation of R. They are briefly described
in the following table.

Package Description
boot resampling and bootstraping methods
class classification methods
cluster clustering methods
foreign functions for reading data stored in various formats (S3,
Stata, SAS, Minitab, SPSS, Epi Info)
KernSmooth methods for kernel smoothing and density estimation (in-
cluding bivariate kernels)
lattice Lattice (Trellis) graphics
MASS contains many functions, tools and data sets from the li-
braries of “Modern Applied Statistics with S” by Venables
& Ripley
mgcv generalized additive models
nlme linear and non-linear mixed-effects models
nnet neural networks and multinomial log-linear models
rpart recursive partitioning
spatial spatial analyses (“kriging”, spatial covariance, . . . )
survival survival analyses
18
http://cran.r-project.org/src/contrib/PACKAGES.html

62
 There are two other main repositories of R packages: the Omegahat Project
for Statistical Computing19 which focuses on web-based applications and in-
terfaces between softwares and languages, and the Bioconductor Project 20
specialized in bioinformatic applications (particularly for the analysis of micro-
array data).
The procedure to install a package depends on the operating system and
whether R was installed from the sources or pre-compiled binaries. In the
latter situation, it is recommended to use the pre-compiled packages available
on CRAN’s site. Under Windows, the binary Rgui.exe has a menu “Packages”
allowing to install packages via internet from the CRAN Web site, or from
zipped files on the local disk.
If R was compiled, a package can be installed from its sources which are
distributed as a ‘.tar.gz’ file. For instance, if we want to install the package gee,
we will first download the file gee 4.13-6.tar.gz (the number 4.13-6 indicates
the version of the package; generally only one version is available on CRAN).
We will then type from the system (and not in R) the command:

R CMD INSTALL gee_4.13-6.tar.gz

There are several useful functions to manage packages such as installed.

packages, CRAN.packages, or download.packages. It is also useful to type
regularly the command:

> update.packages()

which checks the versions of the packages installed against those available
on CRAN (this command can be called from the menu “Packages” under
Windows). The user can then update the packages with more recent versions
than those installed on the computer.

19
http://www.omegahat.org/R/
20
http://www.bioconductor.org/

63
 6 Programming with R in pratice

Now that we have done an overview of R’s functionalities, let us return to the
language and programming. We will see a few simple ideas likely to be used
in practice.

6.1 Loops and vectorization

An advantage of R compared to softwares with pull-down menus is the possibil-

ity to program simply a series of analyses which will be executed successively.
This is common to any computer language, but R has some particular features
which make programming easier for non-specialists.
Like other languages, R has some control structures which are not dissim-
ilar to those of the C language. Suppose we have a vector x, and for each
element of x with the value b, we want to give the value 0 to another variable
y, otherwise 1. We first create a vector y of the same length than x:

y <- numeric(length(x))
for (i in 1:length(x)) if (x[i] == b) y[i] <- 0 else y[i] <- 1

Several instructions can be executed if they are placed within braces:

for (i in 1:length(x)) {
y[i] <- 0
...
}

if (x[i] == b) {
y[i] <- 0
...
}

Another possible situation is to execute an instruction as long as a condi-

tion is true:

while (myfun > minimum) {

...
}

However, loops and control structures can be avoided in most situations

thanks to a feature of R: vectorization. Vectorization makes loops implicit in
expression, and we have seen many cases. Let us consider the addition of two
vectors:

64
> z <- x + y

This addition could be written with a loop, as this is done in most lan-
guages:

> z <- numeric(length(x))

> for (i in 1:length(z)) z[i] <- x[i] + y[i]

In this case, it is necessary to create the vector z beforehand because of

the use of the indexing system. We realize that this explicit loop will work
only if x and y are of the same length: it must be changed if this is not true,
whereas the first expression will work in all situations.
The conditional executions (if ... else) can be avoided with the use
of the logical indexing; coming back to the above example:

> y[x == b] <- 0

> y[x != b] <- 1

In addition to being simpler, vectorized expressions are computationally

more efficient, particularly with large quantities of data.
There are also several functions of the type ‘apply’ which avoids writing
loops. apply acts on the rows and/or columns of a matrix, its syntax is
apply(X, MARGIN, FUN, ...), where X is a matrix, MARGIN indicates whether
to consider the rows (1), the columns (2), or both (c(1, 2)), FUN is a function
(or an operator, but in this case it must be specified within brackets) to apply,
and ... are possible optional arguments for FUN. A simple example follows.

> x <- rnorm(10, -5, 0.1)

> y <- rnorm(10, 5, 2)
> X <- cbind(x, y) # the columns of X keep the names "x" and "y"
> apply(X, 2, mean)
x y
-4.975132 4.932979
> apply(X, 2, sd)
x y
0.0755153 2.1388071

lapply() acts on a list: its syntax is similar to apply and it returns a list.

> forms <- list(y ~ x, y ~ poly(x, 2))

> lapply(forms, lm)
[[1]]

Call:
FUN(formula = X[[1]])

Coefficients:

65
(Intercept) x
31.683 5.377

[[2]]

Call:
FUN(formula = X[[2]])

Coefficients:
(Intercept) poly(x, 2)1 poly(x, 2)2
4.9330 1.2181 -0.6037

sapply() is a flexible variant of lapply() which can take a vector or a

matrix as main argument, and returns its results in a more user-friendly form,
generally as a table.

6.2 Writing a program in R

Typically, an R program is written in a file saved in ASCII format and named

with the extension ‘.R’. A typical situation where a program is useful is when
one wants to do the same tasks several times. In our first example, we want
to do the same plot for three different species of birds, the data being in three
distinct files. We will proceed step by step, and see different ways to program
this very simple problem.
First, let us make our program in the most intuitive way by executing suc-
cessively the needed commands, taking care to partition the graphical device
beforehand.

layout(matrix(1:3, 3, 1)) # partition the graphics

data <- read.table("Swal.dat") # read the data
plot(data$V1, data$V2, type="l")
title("swallow") # add a title
data <- read.table("Wren.dat")
plot(data$V1, data$V2, type="l")
title("wren")
data <- read.table("Dunn.dat")
plot(data$V1, data$V2, type="l")
title("dunnock")

The character ‘#’ is used to add comments in a program: R then goes to

the next line.
The problem of this first program is that it may become quite long if we
want to add other species. Moreover, some commands are executed several
times, thus they can be grouped together and executed after changing some
arguments. The strategy used here is to put these arguments in vectors of
mode character, and then use the indexing to access these different values.

66
layout(matrix(1:3, 3, 1)) # partition the graphics
species <- c("swallow", "wren", "dunnock")
file <- c("Swal.dat" , "Wren.dat", "Dunn.dat")
for(i in 1:length(species)) {
data <- read.table(file[i]) # read the data
plot(data$V1, data$V2, type="l")
title(species[i]) # add a title
}

Note that there are no double quotes around file[i] in read.table()

since this argument is of mode character.
Our program is now more compact. It is easier to add other species since
the vectors containing the species and file names are at the beginning of the
program.
The above programs will work correctly if the data files ‘.dat’ are located
in the working directory of R, otherwise the user must either change the work-
ing directory, or specifiy the path in the program (for example: file <-
"/home/paradis/data/Swal.dat"). If the program is written in the file My-
birds.R, it will be called by typing:

> source("Mybirds.R")

Like for any input from a file, it is necessary to give the path to access the
file if it is not in the working directory.

6.3 Writing your own functions

We have seen that most of R’s work is done with functions which arguments
are given within parentheses. Users can write their own functions, and these
will have exactly the same properties than other functions in R.
Writing your own functions allows an efficient, flexible, and rational use of
R. Let us come back to our example of reading some data followed by plotting
a graph. If we want to do this operation in different situations, it may be a
good idea to write a function:

myfun <- function(S, F)

{
data <- read.table(F)
plot(data$V1, data$V2, type="l")
title(S)
}

To be executed, this function must be loaded in memory, and this can be

done in several ways. The lines of the function can be typed directly on the
keyboard, like any other command, or copied and pasted from an editor. If
the function has been saved in a text file, it can be loaded with source()

67
like another program. If the user wants some functions to be loaded each
time when R starts, they can be saved in a workspace .RData which will be
loaded in memory if it is in the working directory. Another possibility is to
configure the file ‘.Rprofile’ or ‘Rprofile’ (see ?Startup for details). Finally,
it is possible to create a package, but this will not be discussed here (see the
manual “Writing R Extensions”).
Once the function is loaded, we will be able with a single command to read
the data and plot the graph, for instance with myfun("swallow", "Swal.dat").
Thus, we have now a third version of our program:

layout(matrix(1:3, 3, 1))
myfun("swallow", "Swal.dat")
myfun("wren", "Wrenn.dat")
myfun("dunnock", "Dunn.dat")

We may also use sapply() leading to a fourth version of our program:

layout(matrix(1:3, 3, 1))
species <- c("swallow", "wren", "dunnock")
file <- c("Swal.dat" , "Wren.dat", "Dunn.dat")
sapply(species, myfun, file)

In R, it is not necessary to declare the variables used within a function.

When a function is executed, R uses a rule called lexical scoping to decide
whether an object is local to the function, or global. To understand this
mechanism, let us consider the very simple function below:

> foo <- function() print(x)

> x <- 1
> foo()
[1] 1

The name x is not used to create an object within foo(), so R will seek
in the enclosing environment if there is an object called x, and will print its
value (otherwise, a message error is displayed, and the execution is halted).
If x is used as the name of an object within our function, the value of x in
the global environment is not used.

> x <- 1
> foo2 <- function() { x <- 2; print(x) }
> foo2()
[1] 2
> x
[1] 1

This time print() uses the object x that is defined within its environment,
that is the environment of foo2.

68
 The word “enclosing” above is important. In our two example functions,
there are two environments: the global one, and the one of the function foo
or foo2. If there are three or more nested environments, the search for the
objects is made progressively from a given environment to the enclosing one,
and so on, up to the global one.
There are two ways to specify arguments to a function: by their positions
or by their names (also called tagged arguments). For example, let us consider
a function with three arguments:

foo <- function(arg1, arg2, arg3) {...}

foo() can be executed without using the names arg1, . . . , if the corre-
sponding objects are placed in the correct position, for instance: foo(x, y,
z). However, the position has no importance if the names of the arguments
are used, e.g. foo(arg3 = z, arg2 = y, arg1 = x). Another feature of
R’s functions is the possibility to use default values in their definition. For
instance:

foo <- function(arg1, arg2 = 5, arg3 = FALSE) {...}

The commands foo(x), foo(x, 5, FALSE), and foo(x, arg3 = FALSE) will
have exactly the same result. The use of default values in a function definition
is very useful, particularly when used with tagged arguments (i.e. to change
only one default value such as foo(x, arg3 = TRUE).
To conclude this section, let us see another example which is not purely
statistical, but it illustrates the flexibility of R. Consider we wish to study the
behaviour of a non-linear model: Ricker’s model defined by:
Nt
  
Nt+1 = Nt exp r 1 −
K
This model is widely used in population dynamics, particularly of fish. We
want, using a function, to simulate this model with respect to the growth rate
r and the initial number in the population N 0 (the carrying capacity K is
often taken equal to 1 and this value will be taken as default); the results will
be displayed as a plot of numbers with respect to time. We will add an option
to allow the user to display only the numbers in the last few time steps (by
default all results will be plotted). The function below can do this numerical
analysis of Ricker’s model.

ricker <- function(nzero, r, K=1, time=100, from=0, to=time)

{
N <- numeric(time+1)
N[1] <- nzero
for (i in 1:time) N[i+1] <- N[i]*exp(r*(1 - N[i]/K))
Time <- 0:time
plot(Time, N, type="l", xlim=c(from, to))
}

69
 Try it yourself with:

> layout(matrix(1:3, 3, 1))

> ricker(0.1, 1); title("r = 1")
> ricker(0.1, 2); title("r = 2")
> ricker(0.1, 3); title("r = 3")

70
 7 Literature on R

Manuals. Several manuals are distributed with R in R HOME/doc/manual/:

• An Introduction to R [R-intro.pdf],
• R Installation and Administration [R-admin.pdf],
• R Data Import/Export [R-data.pdf],
• Writing R Extensions [R-exts.pdf],
• R Language Definition [R-lang.pdf].

The files may be in different formats (pdf, html, texi, . . . ) depending on

the type of installation.

FAQ. R is also distributed with an FAQ (Frequently Asked Questions) local-

ized in the directory R HOME/doc/html/. A version of the R-FAQ is
regularly updated on CRAN’s Web site:
http://cran.r-project.org/doc/FAQ/R-FAQ.html

On-line resources. The CRAN Web site hosts several documents, biblio-
graphic resources, and links to other sites. There are also a list of publi-
cations (books and articles) about R or statistical methods 21 and some
documents and tutorials written by R’s users 22 .

Mailing lists. There are four discussion lists on R; to subscribe, send a mes-
sage, or read the archives see: http://www.R-project.org/mail.html.
The general discussion list ‘r-help’ is an interesting source of information
for the users of R (the three other lists are dedicated to annoucements
of new versions, and for developers). Many users have sent to ‘r-help’
functions or programs which can be found in the archives. If a problem
is encountered with R, it is thus important to proceed in the following
order before sending a message to ‘r-help’:

1. read carefully the on-line help (possibly using the search engine);
2. read the R-FAQ;
3. search the archives of ‘r-help’ at the above address, or by using one
of the search engines developed on some Web sites 23 ;
4. read the “posting guide”24 before sending your question(s).
21
http://www.R-project.org/doc/bib/R-publications.html
22
http://cran.r-project.org/other-docs.html
23
The addresses of these sites are listed at http://cran.r-project.org/search.html
24
http://www.r-project.org/posting-guide.html

71
R News. The electronic journal R News aims to fill the gap between the
electronic discussion lists and traditional scientific publications. The
first issue was published on January 2001 25 .

Citing R in a publication. Finally, if you mention R in a publication, you

must cite the following reference:

R Development Core Team (2005). R: A language and envi-

ronment for statistical computing. R Foundation for Statisti-
cal Computing, Vienna, Austria. ISBN 3-900051-07-0, URL:
http://www.R-project.org.

25
http://cran.r-project.org/doc/Rnews/

72