An Introduction to R

This is an introduction to R (“GNU S”), a language and environment for statistical

computing and graphics. R is similar to the award-winning1 S system, which was
developed at Bell Laboratories by John Chambers et al. It provides a wide variety of
statistical and graphical techniques (linear and nonlinear modelling, statistical tests,
time series analysis, classification, clustering, ...).
This manual provides information on data types, programming elements, statistical
modelling and graphics.
This manual is for R, version 4.4.1 (2024-06-14).
Copyright © 1990 W. N. Venables
Copyright © 1992 W. N. Venables & D. M. Smith
Copyright © 1997 R. Gentleman & R. Ihaka
Copyright © 1997, 1998 M. Maechler
Copyright © 1999–2024 R Core Team
Permission is granted to make and distribute verbatim copies of this manual provided
the copyright notice and this permission notice are preserved on all copies.
Permission is granted to copy and distribute modified versions of this manual under
the conditions 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 Core Team.

Table of Contents
• Preface
• 1 Introduction and preliminaries
o 1.1 The R environment
o 1.2 Related software and documentation
o 1.3 R and statistics
o 1.4 R and the window system
o 1.5 Using R interactively
o 1.6 An introductory session
o 1.7 Getting help with functions and features
o 1.8 R commands, case sensitivity, etc.
o 1.9 Recall and correction of previous commands
 o 1.10 Executing commands from or diverting output to a file
o 1.11 Data permanency and removing objects
• 2 Simple manipulations; numbers and vectors
o 2.1 Vectors and assignment
o 2.2 Vector arithmetic
o 2.3 Generating regular sequences
o 2.4 Logical vectors
o 2.5 Missing values
o 2.6 Character vectors
o 2.7 Index vectors; selecting and modifying subsets of a data set
o 2.8 Other types of objects
• 3 Objects, their modes and attributes
o 3.1 Intrinsic attributes: mode and length
o 3.2 Changing the length of an object
o 3.3 Getting and setting attributes
o 3.4 The class of an object
• 4 Ordered and unordered factors
o 4.1 A specific example
o 4.2 The function tapply() and ragged arrays
o 4.3 Ordered factors
• 5 Arrays and matrices
o 5.1 Arrays
o 5.2 Array indexing. Subsections of an array
o 5.3 Index matrices
o 5.4 The array() function
▪ 5.4.1 Mixed vector and array arithmetic. The recycling rule
o 5.5 The outer product of two arrays
o 5.6 Generalized transpose of an array
o 5.7 Matrix facilities
▪ 5.7.1 Matrix multiplication
▪ 5.7.2 Linear equations and inversion
▪ 5.7.3 Eigenvalues and eigenvectors
▪ 5.7.4 Singular value decomposition and determinants
▪ 5.7.5 Least squares fitting and the QR decomposition
o 5.8 Forming partitioned matrices, cbind() and rbind()
o 5.9 The concatenation function, c(), with arrays
o 5.10 Frequency tables from factors
• 6 Lists and data frames
o 6.1 Lists
o 6.2 Constructing and modifying lists
▪ 6.2.1 Concatenating lists
o 6.3 Data frames
 ▪ 6.3.1 Making data frames
▪ 6.3.2 attach() and detach()
▪ 6.3.3 Working with data frames
▪ 6.3.4 Attaching arbitrary lists
▪ 6.3.5 Managing the search path
• 7 Reading data from files
o 7.1 The read.table() function
o 7.2 The scan() function
o 7.3 Accessing builtin datasets
▪ 7.3.1 Loading data from other R packages
o 7.4 Editing data
• 8 Probability distributions
o 8.1 R as a set of statistical tables
o 8.2 Examining the distribution of a set of data
o 8.3 One- and two-sample tests
• 9 Grouping, loops and conditional execution
o 9.1 Grouped expressions
o 9.2 Control statements
▪ 9.2.1 Conditional execution: if statements
▪ 9.2.2 Repetitive execution: for loops, repeat and while
• 10 Writing your own functions
o 10.1 Simple examples
o 10.2 Defining new binary operators
o 10.3 Named arguments and defaults
o 10.4 The ‘…’ argument
o 10.5 Assignments within functions
o 10.6 More advanced examples
▪ 10.6.1 Efficiency factors in block designs
▪ 10.6.2 Dropping all names in a printed array
▪ 10.6.3 Recursive numerical integration
o 10.7 Scope
o 10.8 Customizing the environment
o 10.9 Classes, generic functions and object orientation
• 11 Statistical models in R
o 11.1 Defining statistical models; formulae
▪ 11.1.1 Contrasts
o 11.2 Linear models
o 11.3 Generic functions for extracting model information
o 11.4 Analysis of variance and model comparison
▪ 11.4.1 ANOVA tables
o 11.5 Updating fitted models
o 11.6 Generalized linear models
 ▪ 11.6.1 Families
▪ 11.6.2 The glm() function
o 11.7 Nonlinear least squares and maximum likelihood models
▪ 11.7.1 Least squares
▪ 11.7.2 Maximum likelihood
o 11.8 Some non-standard models
• 12 Graphical procedures
o 12.1 High-level plotting commands
▪ 12.1.1 The plot() function
▪ 12.1.2 Displaying multivariate data
▪ 12.1.3 Display graphics
▪ 12.1.4 Arguments to high-level plotting functions
o 12.2 Low-level plotting commands
▪ 12.2.1 Mathematical annotation
▪ 12.2.2 Hershey vector fonts
o 12.3 Interacting with graphics
o 12.4 Using graphics parameters
▪ 12.4.1 Permanent changes: The par() function
▪ 12.4.2 Temporary changes: Arguments to graphics functions
o 12.5 Graphics parameters list
▪ 12.5.1 Graphical elements
▪ 12.5.2 Axes and tick marks
▪ 12.5.3 Figure margins
▪ 12.5.4 Multiple figure environment
o 12.6 Device drivers
▪ 12.6.1 PostScript diagrams for typeset documents
▪ 12.6.2 Multiple graphics devices
o 12.7 Dynamic graphics
• 13 Packages
o 13.1 Standard packages
o 13.2 Contributed packages and CRAN
o 13.3 Namespaces
• 14 OS facilities
o 14.1 Files and directories
o 14.2 Filepaths
o 14.3 System commands
o 14.4 Compression and Archives
• Appendix A A sample session
• Appendix B Invoking R
o B.1 Invoking R from the command line
o B.2 Invoking R under Windows
o B.3 Invoking R under macOS
 o B.4 Scripting with R
• Appendix C The command-line editor
o C.1 Preliminaries
o C.2 Editing actions
o C.3 Command-line editor summary
• Appendix D Function and variable index
• Appendix E Concept index
• Appendix F References

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R [Contents][Index]

Preface
This introduction to R is derived from an original set of notes describing the S and S-
PLUS environments written in 1990–2 by Bill Venables and David M. Smith when at
the University of Adelaide. 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. See Graphical procedures,
which can be read at almost any time and need not wait until all the preceding sections
have been digested.

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R [Contents][Index]

1 Introduction and preliminaries

 • The R environment
• Related software and documentation
• R and statistics
• R and the window system
• Using R interactively
• An introductory session
• Getting help with functions and features
• R commands, case sensitivity, etc.
• Recall and correction of previous commands
• Executing commands from or diverting output to a file
• Data permanency and removing objects

Next: Related software and documentation, Previous: Introduction and preliminaries,

Up: Introduction and preliminaries [Contents][Index]

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 hardcopy, 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.

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preliminaries [Contents][Index]
1.2 Related software and documentation
R can be regarded as an implementation of the S language which was developed at
Bell Laboratories 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 References, 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 What documentation exists for
R? in R FAQ.

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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 https://CRAN.R-project.org) and elsewhere. More details on packages are given later
(see Packages).
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.
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.

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preliminaries [Contents][Index]

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
straightforward if somewhat tedious procedure, and will not be considered further
here. Users in difficulty should seek local expert help.

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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.
2. $ mkdir work
3. $ cd work
4. Start the R program with the command
5. $ R
6. At this point R commands may be issued (see later).
 7. To quit the R program the command is
8. > 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:
2. $ cd work
3. $ R
4. 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.

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 A sample session.

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and preliminaries [Contents][Index]

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 (alternatively ??) allows searching for help in various
ways. For example,
> ??solve
Try ?help.search for details and more 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.

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features, Up: Introduction and preliminaries [Contents][Index]

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 allowed2 (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. Names are effectively unlimited in length.
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 be put almost3 anywhere, starting with a hash mark (‘#’),
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 limited4 to about 4095 bytes (not
characters).

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sensitivity, etc., Up: Introduction and preliminaries [Contents][Index]

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 DEL key or
added with the other keys. More details are provided later: see The command-line editor.
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 R and
Emacs in R FAQ.

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commands, Up: Introduction and preliminaries [Contents][Index]

1.10 Executing commands from or diverting

output to a file
If commands5 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 command
> sink()
restores it to the console once again.

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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 section). 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:
> rm(x, y, z, ink, junk, temp, foo, bar)
All objects created during an R session 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 .RData6 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.

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Introduction to R [Contents][Index]

2 Simple manipulations; numbers

and vectors
• Vectors and assignment
• Vector arithmetic
• Generating regular sequences
• Logical vectors
• Missing values
• Character vectors
• Index vectors; selecting and modifying subsets of a data set
• Other types of objects

Next: Vector arithmetic, Previous: Simple manipulations; numbers and vectors, Up: Simple
manipulations; numbers and vectors [Contents][Index]

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.7
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 an 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
assignment 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 lost8. 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.

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manipulations; numbers and vectors [Contents][Index]

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, 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.

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vectors [Contents][Index]

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 expression, 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.
Arguments 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 arguments
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 arguments
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.
The fifth argument may be named along=vector, which is normally used as the only
argument to create the 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.

Next: Missing values, Previous: Generating regular sequences, Up: Simple manipulations;
numbers and vectors [Contents][Index]

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.

Next: Character vectors, Previous: Logical vectors, Up: Simple manipulations; numbers and
vectors [Contents][Index]

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
computation, the so-called Not a Number, NaN, values. Examples are
> 0/0
or
> 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.

Next: Index vectors; selecting and modifying subsets of a data set, Previous: Missing values,
Up: Simple manipulations; numbers and vectors [Contents][Index]

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 matching 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—see ?Quotes for a full list.
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 argument, 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. 9

Next: Other types of objects, Previous: Character vectors, Up: Simple manipulations; numbers
and vectors [Contents][Index]
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 is recycled to 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
2. > 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. 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
4. > 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.
5. A vector of negative integral quantities. Such an index vector specifies the
values to be excluded rather than included. Thus
6. > y <- x[-(1:5)]
gives y all but the first five elements of x.
7. 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.
 8. > fruit <- c(5, 10, 1, 20)
9. > names(fruit) <- c("orange", "banana", "apple", "peach")
10. > 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.
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)

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manipulations; numbers and vectors [Contents][Index]

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 Arrays and matrices.
• factors provide compact ways to handle categorical data. See Ordered and
unordered factors.
• 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 Lists.
• 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 Data frames.
 • 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 Writing
your own functions.

Next: Ordered and unordered factors, Previous: Simple manipulations; numbers and vectors,
Up: An Introduction to R [Contents][Index]

3 Objects, their modes and

attributes
• Intrinsic attributes: mode and length
• Changing the length of an object
• Getting and setting attributes
• The class of an object

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Up: Objects, their modes and attributes [Contents][Index]

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 numeric10, complex, logical, character and raw.
Vectors must have their values all of the same mode. Thus any given vector must be
unambiguously 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 structure 11.
Further properties of an object are usually provided by attributes(object), see Getting
and setting attributes. 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.12 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.

Next: Getting and setting attributes, Previous: Intrinsic attributes: mode and length,
Up: Objects, their modes and attributes [Contents][Index]

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 The scan() function.)
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.

Next: The class of an object, Previous: Changing the length of an object, Up: Objects, their
modes and attributes [Contents][Index]

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.

Previous: Getting and setting attributes, Up: Objects, their modes and
attributes [Contents][Index]

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 style13 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
> 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 Classes, generic functions and
object orientation, but only briefly.

Next: Arrays and matrices, Previous: Objects, their modes and attributes, Up: An Introduction
to R [Contents][Index]

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 Contrasts), we here look at a specific example.
• A specific example
• The function tapply() and ragged arrays
• Ordered factors

4.1 A specific example

Suppose, for example, we have a sample of 30 tax accountants from all the states and
territories of Australia14 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"

Next: Ordered factors, Previous: Ordered and unordered factors, Up: Ordered and unordered
factors [Contents][Index]

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 statef15, 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:
> stdError <- function(x) sqrt(var(x)/length(x))
(Writing functions will be considered later in Writing your own functions. Note that R’s
a builtin function sd() is something different.) After this assignment, the standard
errors are calculated by
> incster <- tapply(incomes, statef, stdError)
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.

Previous: The function tapply() and ragged arrays, Up: Ordered and unordered
factors [Contents][Index]

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.

Next: Lists and data frames, Previous: Ordered and unordered factors, Up: An Introduction to
R [Contents][Index]

5 Arrays and matrices

• Arrays
• Array indexing. Subsections of an array
• Index matrices
• The array() function
• The outer product of two arrays
• Generalized transpose of an array
• Matrix facilities
• Forming partitioned matrices, cbind() and rbind()
• The concatenation function, c(), with arrays
• Frequency tables from factors

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matrices [Contents][Index]

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 The array() function.
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.

Next: Index matrices, Previous: Arrays, Up: Arrays and matrices [Contents][Index]

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.

Next: The array() function, Previous: Array indexing. Subsections of an array, Up: Arrays
and matrices [Contents][Index]

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)
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.

Next: The outer product of two arrays, Previous: Index matrices, Up: Arrays and
matrices [Contents][Index]

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
> Z <- h ; 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 Mixed vector and array arithmetic. The recycling rule) but dim(h)
<- c(3,4,2) would signal an error about mismatching length. 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.
• Mixed vector and array arithmetic. The recycling rule

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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.

Next: Generalized transpose of an array, Previous: The array() function, Up: Arrays and
matrices [Contents][Index]

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 + x^2) 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 Writing
your own functions.

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(fr, xlab="Determinant", ylab="Frequency")
Notice that plot() here uses a histogram like plot method, because it “sees” that fr is
of class "table". The “obvious” way of doing this problem with for loops, to be
discussed in Grouping, loops and conditional execution, is so inefficient as to be
impractical.
It is also perhaps surprising that about 1 in 20 such matrices is singular.

Next: Matrix facilities, Previous: The outer product of two arrays, Up: Arrays and
matrices [Contents][Index]

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).
Next: Forming partitioned matrices, cbind() and rbind(), Previous: Generalized transpose of
an array, Up: Arrays and matrices [Contents][Index]

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.
• Matrix multiplication
• Linear equations and inversion
• Eigenvalues and eigenvectors
• Singular value decomposition and determinants
• Least squares fitting and the QR decomposition

Next: Linear equations and inversion, Previous: Matrix facilities, Up: Matrix
facilities [Contents][Index]

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.16
The function crossprod() forms “cross products”, 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!

Next: Eigenvalues and eigenvectors, Previous: Matrix multiplication, Up: Matrix

facilities [Contents][Index]

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 x %*% A^{-1} %*% x which is used in multivariate computations,
should be computed by something like17 x %*% solve(A,x), rather than computing the
inverse of A.

Next: Singular value decomposition and determinants, Previous: Linear equations and
inversion, Up: Matrix facilities [Contents][Index]

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

Next: Least squares fitting and the QR decomposition, Previous: Eigenvalues and
eigenvectors, Up: Matrix facilities [Contents][Index]

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),

Previous: Singular value decomposition and determinants, Up: Matrix

facilities [Contents][Index]

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 included and need not be included explicitly as a column
of X. Further note that you almost always will prefer using lm(.) (see Linear models)
to lsfit() for regression modelling.
Another closely related function is qr() and its allies. Consider the following
assignments
> 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 Statistical models in R.

Next: The concatenation function, c(), with arrays, Previous: Matrix facilities, Up: Arrays
and matrices [Contents][Index]

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.

Next: Frequency tables from factors, Previous: Forming partitioned

matrices, cbind() and rbind(), Up: Arrays and matrices [Contents][Index]

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).

Previous: The concatenation function, c(), with arrays, Up: Arrays and
matrices [Contents][Index]
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 calculated 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.

Next: Reading data from files, Previous: Arrays and matrices, Up: An Introduction to
R [Contents][Index]

6 Lists and data frames

• Lists
• Constructing and modifying lists
• Data frames

Next: Constructing and modifying lists, Previous: Lists and data frames, Up: Lists and data
frames [Contents][Index]

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.

Next: Data frames, Previous: Lists, Up: Lists and data frames [Contents][Index]

6.2 Constructing and modifying lists

New lists may be formed from existing objects by the function list(). An assignment
of the form
> 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)
• Concatenating lists

Previous: Constructing and modifying lists, Up: Constructing and modifying

lists [Contents][Index]

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.

Previous: Constructing and modifying lists, Up: Lists and data frames [Contents][Index]
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.
• Vector structures appearing as variables of the data frame must all have
the same length, and matrix structures must all have the same number of rows.
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.
• Making data frames
• attach() and detach()
• Working with data frames
• Attaching arbitrary lists
• Managing the search path

Next: attach() and detach(), Previous: Data frames, Up: Data frames [Contents][Index]

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 Reading data from files.

Next: Working with data frames, Previous: Making data frames, Up: Data
frames [Contents][Index]

6.3.2 attach() and detach()

The $ notation, such as accountants$home, for list components is not always very
convenient. A useful facility would be somehow to make the components of a list or
data frame temporarily visible as variables under their component name, without the
need to quote the list name explicitly each time.
The attach() function takes a ‘database’ such as a list or data frame as its argument.
Thus suppose lentils is a data frame with three
variables lentils$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 workspace 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.

Next: Attaching arbitrary lists, Previous: attach() and detach(), Up: Data
frames [Contents][Index]

6.3.3 Working with data frames

A useful convention that allows you to work with many different problems
comfortably together in the same workspace 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 workspace 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 workspace 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.

Next: Managing the search path, Previous: Working with data frames, Up: Data
frames [Contents][Index]

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,
preferably, by name.

Previous: Attaching arbitrary lists, Up: Data frames [Contents][Index]

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.18
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"

Next: Probability distributions, Previous: Lists and data frames, Up: An Introduction to
R [Contents][Index]

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 Perl19 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
Import/Export manual.
• The read.table() function
• The scan() function
• Accessing builtin datasets
• Editing data

Next: The scan() function, Previous: Reading data from files, Up: Reading data from
files [Contents][Index]

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 character variables. 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
...

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.

Next: Accessing builtin datasets, Previous: The read.table() function, Up: Reading data
from files [Contents][Index]

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 Attaching arbitrary lists).
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.

Next: Editing data, Previous: The scan() function, Up: Reading data from
files [Contents][Index]

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()
All the datasets supplied with R are available directly by name. However, many
packages still use the obsolete 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.
• Loading data from other R packages

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.

Previous: Accessing builtin datasets, Up: Reading data from files [Contents][Index]

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.

Next: Grouping, loops and conditional execution, Previous: Reading data from files, Up: An
Introduction to R [Contents][Index]

8 Probability distributions
• R as a set of statistical tables
• Examining the distribution of a set of data
• One- and two-sample tests
Next: Examining the distribution of a set of data, Previous: Probability distributions,
Up: Probability distributions [Contents][Index]

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
signed rank signrank n
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 (random deviates). The first argument
is x for dxxx, q for pxxx, p for qxxx and n for rxxx (except
for rhyper, rsignrank and rwilcox, for which it is nn). In not quite all cases is the non-
centrality parameter ncp 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,
and dmultinom and rmultinom for the multinomial distribution. Further distributions
are available in contributed packages, notably SuppDists.
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)
See the on-line help on RNG for how random-number generation is done in R.

Next: One- and two-sample tests, Previous: R as a set of statistical tables, Up: Probability
distributions [Contents][Index]

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).
> 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 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.)

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)

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)
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

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.)

Previous: Examining the distribution of a set of data, Up: Probability

distributions [Contents][Index]

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)
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.
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. 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

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 ecdfs, 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
alternative hypothesis: two-sided

Warning message:
cannot compute correct p-values with ties in: ks.test(A, B)

Next: Writing your own functions, Previous: Probability distributions, Up: An Introduction to
R [Contents][Index]

9 Grouping, loops and

conditional execution
• Grouped expressions
• Control statements

Next: Control statements, Previous: Grouping, loops and conditional execution,

Up: Grouping, loops and conditional execution [Contents][Index]

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 as part of an even larger expression, and so on.

Previous: Grouped expressions, Up: Grouping, loops and conditional

execution [Contents][Index]

9.2 Control statements

• Conditional execution: if statements
• Repetitive execution: for loops, repeat and while

Next: Repetitive execution: for loops, repeat and while, Previous: Control statements,
Up: Control statements [Contents][Index]
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 same length
as condition, with elements a[i] if condition[i] is true,
otherwise b[i] (where a and b are recycled as necessary).

Previous: Conditional execution: if statements, Up: Control statements [Contents][Index]

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(),20 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.)
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 Writing your own functions, and where more examples will emerge.

Next: Statistical models in R, Previous: Grouping, loops and conditional execution, Up: An
Introduction to R [Contents][Index]

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.
• Simple examples
• Defining new binary operators
• Named arguments and defaults
• The ‘…’ argument
• Assignments within functions
• More advanced examples
• Scope
• Customizing the environment
• Classes, generic functions and object orientation

Next: Defining new binary operators, Previous: Writing your own functions, Up: Writing your
own functions [Contents][Index]

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
command, 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’X)^{-
}X’y, where (X’X)^{-} is a generalized inverse of X'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.
The classical R function lsfit() does this job quite well, and more21. 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.

Next: Named arguments and defaults, Previous: Simple examples, Up: Writing your own
functions [Contents][Index]

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.

Next: The ‘…’ argument, Previous: Defining new binary operators, Up: Writing your own
functions [Contents][Index]

10.3 Named arguments and defaults

As first noted in Generating regular sequences, 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.
Next: Assignments within functions, Previous: Named arguments and defaults, Up: Writing
your own functions [Contents][Index]

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 Permanent changes: The par() function, 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]
}
Less frequently, a function will need to refer to components of ‘…’. The
expression list(...) evaluates all such arguments and returns them in a named list,
while ..1, ..2, etc. evaluate them one at a time, with ‘..n’ returning the n-th
unmatched argument.

Next: More advanced examples, Previous: The ‘…’ argument, Up: Writing your own
functions [Contents][Index]

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
‘superassignment’ operator, <<- or the function assign() can be used. See
the help document for details.

Next: Scope, Previous: Assignments within functions, Up: Writing your own
functions [Contents][Index]
10.6 More advanced examples
• Efficiency factors in block designs
• Dropping all names in a printed array
• Recursive numerical integration

Next: Dropping all names in a printed array, Previous: More advanced examples, Up: More
advanced examples [Contents][Index]

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 Index matrices.)
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 = I_v - R^{-1/2}N’K^{-
1}NR^{-1/2} = I_v - A’A, where A = K^{-1/2}NR^{-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)
}
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.

Next: Recursive numerical integration, Previous: Efficiency factors in block designs,

Up: More advanced examples [Contents][Index]
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.

Previous: Dropping all names in a printed array, Up: More advanced

examples [Contents][Index]

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
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)
}

Next: Customizing the environment, Previous: More advanced examples, Up: Writing your
own functions [Contents][Index]

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
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 it22. 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()

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

Next: Classes, generic functions and object orientation, Previous: Scope, Up: Writing your
own functions [Contents][Index]

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 .Rprofile23 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). If the environment variable R_PROFILE_USER is set, the file it
points to is used instead of the .Rprofile files.
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, the user
profile, .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?
}

Previous: Customizing the environment, Up: Writing your own functions [Contents][Index]

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() 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)]
}
A function named gen.cl will be invoked by the generic gen for class cl, so do not
name functions in this style unless they are intended to be methods.
The reader is referred to the R Language Definition for a more complete discussion of
this mechanism.

Next: Graphical procedures, Previous: Writing your own functions, Up: An Introduction to
R [Contents][Index]

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.
• Defining statistical models; formulae
• Linear models
• Generic functions for extracting model information
• Analysis of variance and model comparison
• Updating fitted models
• Generalized linear models
• Nonlinear least squares and maximum likelihood models
• Some non-standard models

Next: Linear models, Previous: Statistical models in R, Up: Statistical models in

R [Contents][Index]

11.1 Defining statistical models; formulae

The template for a statistical model is a linear regression model with independent,
homoscedastic errors
y_i = sum_{j=0}^p beta_j x_{ij} + e_i, i = 1, ..., n,
where the e_i are NID(0, sigma^2). In matrix terms this would be written
y = X beta + e
where the y is the response vector, X is the model matrix or design matrix and has
columns x_0, x_1, ..., x_p, the determining variables. Very often x_0 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
polynomials, 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.
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.
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.
• Contrasts

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formulae [Contents][Index]
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,
…, k-th 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 newcomers 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.

Next: Generic functions for extracting model information, Previous: Defining statistical
models; formulae, Up: Statistical models in R [Contents][Index]

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.

Next: Analysis of variance and model comparison, Previous: Linear models, Up: Statistical
models in R [Contents][Index]

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.
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.

Next: Updating fitted models, Previous: Generic functions for extracting model information,
Up: Statistical models in R [Contents][Index]

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 Generic functions for extracting model information 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”.
• ANOVA tables

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comparison [Contents][Index]

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.

Next: Generalized linear models, Previous: Analysis of variance and model comparison,
Up: Statistical models in R [Contents][Index]

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(.) ~ .)
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.

Next: Nonlinear least squares and maximum likelihood models, Previous: Updating fitted
models, Up: Statistical models in R [Contents][Index]

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 x_1, x_2, …, 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
• eta = beta_1 x_1 + beta_2 x_2 + ... + beta_p x_p,
hence x_i has no influence on the distribution of y if and only if beta_i is zero.
• The distribution of y is of the form
 • f_Y(y; mu, phi)
• = exp((A/phi) * (y lambda(mu) - gamma(lambda(mu))) + tau(y, phi))
where phi 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 mu 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, mu, is a smooth invertible function of the linear predictor:
• mu = m(eta), eta = m^{-1}(mu) = ell(mu)
and this inverse function, ell(), 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).
• Families
• The glm() function

Next: The glm() function, Previous: Generalized linear models, Up: Generalized linear
models [Contents][Index]

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
information that are needed to carry out the modeling exercise is called the family of
the generalized linear model.

Previous: Families, Up: Generalized linear models [Contents][Index]

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 Families. 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).

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(beta_0 + beta_1 x)) where for the probit case, F(z) = Phi(z) is the
standard normal distribution function, and in the logit case (the default), F(z) =
e^z/(1+e^z). In both cases the LD50 is LD50 = - beta_0/beta_1 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:
> 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) = mu.
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 y = theta_1 z_1 / (z_2 -
theta_2) + e which may be written alternatively as y = 1 / (beta_1 x_1 + beta_2 x_2) +
e where x_1 = z_2/z_1, x_2 = -1/z_1, beta_1 = 1/theta_1, and beta_2 =
theta_2/theta_1. 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.
Next: Some non-standard models, Previous: Generalized linear models, Up: Statistical models
in R [Contents][Index]

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 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.
• Least squares
• Maximum likelihood

Next: Maximum likelihood, Previous: Nonlinear least squares and maximum likelihood
models, Up: Nonlinear least squares and maximum likelihood models [Contents][Index]

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 fit criterion to be minimized is:
> 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 which is subtracted 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

Previous: Least squares, Up: Nonlinear least squares and maximum likelihood
models [Contents][Index]

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 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
maximum 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.

Previous: Nonlinear least squares and maximum likelihood models, Up: Statistical models in
R [Contents][Index]

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 recommended 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.
Tree models are available in R via the user-contributed
packages rpart and tree.

Next: Packages, Previous: Statistical models in R, Up: An Introduction to

R [Contents][Index]

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
may useful to know that the command used is X11() under UNIX, windows() under
Windows and quartz() under macOS. A new device can always be opened
by dev.new().
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 information 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.
• High-level plotting commands
• Low-level plotting commands
• Interacting with graphics
• Using graphics parameters
• Graphics parameters list
• Device drivers
• Dynamic graphics

Next: Low-level plotting commands, Previous: Graphical procedures, Up: Graphical

procedures [Contents][Index]

12.1 High-level plotting commands

High-level plotting functions are designed to generate a complete plot of the data
passed as arguments 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.
• The plot() function
• Displaying multivariate data
• Display graphics
• Arguments to high-level plotting functions
Next: Displaying multivariate data, Previous: High-level plotting commands, Up: High-level
plotting commands [Contents][Index]

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.
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.

Next: Display graphics, Previous: The plot() function, Up: High-level plotting
commands [Contents][Index]

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().

Next: Arguments to high-level plotting functions, Previous: Displaying multivariate data,

Up: High-level plotting commands [Contents][Index]
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. If the probability=TRUE argument is given, the bars
represent relative frequencies divided by bin width instead of counts.
dotchart(x, …)
Constructs a dot chart of the data in x. In a dot chart 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.

Previous: Display graphics, Up: High-level plotting commands [Contents][Index]

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.

Next: Interacting with graphics, Previous: High-level plotting commands, Up: Graphical
procedures [Contents][Index]

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 corresponding 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)
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 coordinates) 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.
• Mathematical annotation
• Hershey vector fonts

Next: Hershey vector fonts, Previous: Low-level plotting commands, Up: Low-level plotting
commands [Contents][Index]

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)

Previous: Mathematical annotation, Up: Low-level plotting commands [Contents][Index]

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)

Next: Using graphics parameters, Previous: Low-level plotting commands, Up: Graphical
procedures [Contents][Index]

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:
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.

Next: Graphics parameters list, Previous: Interacting with graphics, Up: Graphical
procedures [Contents][Index]

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 justification 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.
 • Permanent changes: The par() function
• Temporary changes: Arguments to graphics functions

Next: Temporary changes: Arguments to graphics functions, Previous: Using graphics

parameters, Up: Using graphics parameters [Contents][Index]

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.
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 settable24 graphical parameters use
> oldpar <- par(no.readonly=TRUE)
... plotting commands ...
> par(oldpar)
Previous: Permanent changes: The par() function, Up: Using graphics
parameters [Contents][Index]

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().

Next: Device drivers, Previous: Using graphics parameters, Up: Graphical

procedures [Contents][Index]

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.
• Graphical elements
• Axes and tick marks
• Figure margins
• Multiple figure environment

Next: Axes and tick marks, Previous: Graphics parameters list, Up: Graphics parameters
list [Contents][Index]

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 a circle. 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 invisible, 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,
respectively.
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,
respectively.
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.
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.

Next: Figure margins, Previous: Graphical elements, Up: Graphics parameters

list [Contents][Index]

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
horizontal, 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.

Next: Multiple figure environment, Previous: Axes and tick marks, Up: Graphics parameters
list [Contents][Index]

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.
A typical figure is

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.

Previous: Figure margins, Up: Graphics parameters list [Contents][Index]

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.

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).
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.

Next: Dynamic graphics, Previous: Graphics parameters list, Up: Graphical

procedures [Contents][Index]

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
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.)
• PostScript diagrams for typeset documents
• Multiple graphics devices

Next: Multiple graphics devices, Previous: Device drivers, Up: Device

drivers [Contents][Index]

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
> 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)

Previous: PostScript diagrams for typeset documents, Up: Device drivers [Contents][Index]
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]
postscript()
pdf()
png()
jpeg()
tiff()
bitmap()
…
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.
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.
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.

Previous: Device drivers, Up: Graphical procedures [Contents][Index]

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://ggobi.org/
and these can be accessed from R via the package rggobi, described
at http://ggobi.org/rggobi.html.
Also, package rgl provides ways to interact with 3D plots, for example of surfaces.

Next: OS facilities, Previous: Graphical procedures, Up: An Introduction to

R [Contents][Index]

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 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 macOS GUIs, see Installing packages in R
Installation and Administration) 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 Namespaces): 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.
• Standard packages
• Contributed packages and CRAN
• Namespaces

Next: Contributed packages and CRAN, Previous: Packages,

Up: Packages [Contents][Index]

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. For a complete list, see R packages in R
FAQ.

Next: Namespaces, Previous: Standard packages, Up: Packages [Contents][Index]

13.2 Contributed packages and CRAN

There are thousands of contributed packages for R, written by many different authors.
Some of these packages implement specialized statistical methods, others give access
to data or hardware, 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 (https://CRAN.R-project.org/ and its mirrors)
and other repositories such as Bioconductor (https://www.bioconductor.org/). The R
FAQ contains a list of CRAN packages current at the time of release, but the
collection of available packages changes very frequently.

Previous: Contributed packages and CRAN, Up: Packages [Contents][Index]

13.3 Namespaces
Packages have namespaces, which 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.
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.

Next: A sample session, Previous: Packages, Up: An Introduction to R [Contents][Index]

14 OS facilities
R has quite extensive facilities to access the OS under which it is running: this allows
it to be used as a scripting language and that ability is much used by R itself, for
example to install packages.
Because R’s own scripts need to work across all platforms, considerable effort has
gone into make the scripting facilities as platform-independent as is feasible.
• Files and directories
• Filepaths
• System commands
• Compression and Archives

Next: Filepaths, Previous: OS facilities, Up: OS facilities [Contents][Index]

14.1 Files and directories

There are many functions to manipulate files and directories. Here are pointers to
some of the more commonly used ones.
To create an (empty) file or directory, use file.create or dir.create. (These are the
analogues of the POSIX utilities touch and mkdir.) For temporary files and directories
in the R session directory see tempfile.
Files can be removed by either file.remove or unlink: the latter can remove directory
trees.
For directory listings use list.files (also available as dir) or list.dirs. These can
select files using a regular expression: to select by wildcards use Sys.glob.
Many types of information on a filepath (including for example if it is a file or
directory) can be found by file.info.
There are several ways to find out if a file ‘exists’ (a file can exist on the filesystem
and not be visible to the current user). There are
functions file.exists, file.access and file_test with various versions of this
test: file_test is a version of the POSIX test command for those familiar with shell
scripting.
Function file.copy is the R analogue of the POSIX command cp.
Choosing files can be done interactively by file.choose: the Windows port has the
more versatile functions choose.files and choose.dir and there are similar functions
in the tcltk package: tk_choose.files and tk_choose.dir.
Functions file.show and file.edit will display and edit one or more files in a way
appropriate to the R port, using the facilities of a console (such as RGui on Windows
or R.app on macOS) if one is in use.
There is some support for links in the filesystem: see
functions file.link and Sys.readlink.

Next: System commands, Previous: Files and directories, Up: OS

facilities [Contents][Index]

14.2 Filepaths
With a few exceptions, R relies on the underlying OS functions to manipulate
filepaths. Some aspects of this are allowed to depend on the OS, and do, even down to
the version of the OS. There are POSIX standards for how OSes should interpret
filepaths and many R users assume POSIX compliance: but Windows does not claim
to be compliant and other OSes may be less than completely compliant.
The following are some issues which have been encountered with filepaths.
• POSIX filesystems are case-sensitive, so foo.png and Foo.PNG are
different files. However, the defaults on Windows and macOS are to be case-
insensitive, and FAT filesystems (commonly used on removable storage) are
not normally case-sensitive (and all filepaths may be mapped to lower case).
• Almost all the Windows’ OS services support the use of slash or backslash as
the filepath separator, and R converts the known exceptions to the form
required by Windows.
• The behaviour of filepaths with a trailing slash is OS-dependent. Such paths are
not valid on Windows and should not be expected to work. POSIX-2008
requires such paths to match only directories, but earlier versions allowed them
to also match files. So they are best avoided.
• Multiple slashes in filepaths such as /abc//def are valid on POSIX
filesystems and treated as if there was only one slash. They
 are usually accepted by Windows’ OS functions. However, leading double
slashes may have a different meaning.
• Windows’ UNC filepaths (such
as \\server\dir1\dir2\file and \\?\UNC\server\dir1\dir2\
file) are not supported, but they may work in some R functions. POSIX
filesystems are allowed to treat a leading double slash specially.
• Windows allows filepaths containing drives and relative to the current directory
on a drive, e.g. d:foo/bar refers to d:/a/b/c/foo/bar if the current
directory on drive d: is /a/b/c. It is intended that these work, but the use of
absolute paths is safer.
Functions basename and dirname select parts of a file path: the recommended way to
assemble a file path from components is file.path. Function pathexpand does ‘tilde
expansion’, substituting values for home directories (the current user’s, and perhaps
those of other users).
On filesystems with links, a single file can be referred to by many filepaths.
Function normalizePath will find a canonical filepath.
Windows has the concepts of short (‘8.3’) and long file names: normalizePath will
return an absolute path using long file names and shortPathName will return a version
using short names. The latter does not contain spaces and uses backslash as the
separator, so is sometimes useful for exporting names from R.
File permissions are a related topic. R has support for the POSIX concepts of
read/write/execute permission for owner/group/all but this may be only partially
supported on the filesystem, so for example on Windows only read-only files (for the
account running the R session) are recognized. Access Control Lists (ACLs) are
employed on several filesystems, but do not have an agreed standard and R has no
facilities to control them. Use Sys.chmod to change permissions.

Next: Compression and Archives, Previous: Filepaths, Up: OS facilities [Contents][Index]

14.3 System commands

Functions system and system2 are used to invoke a system command and optionally
collect its output. system2 is a little more general but its main advantage is that it is
easier to write cross-platform code using it.
system behaves differently on Windows from other OSes (because the API C call of
that name does). Elsewhere it invokes a shell to run the command: the Windows port
of R has a function shell to do that.
To find out if the OS includes a command, use Sys.which, which attempts to do this in
a cross-platform way (unfortunately it is not a standard OS service).
Function shQuote will quote filepaths as needed for commands in the current OS.

Previous: System commands, Up: OS facilities [Contents][Index]

14.4 Compression and Archives

Recent versions of R have extensive facilities to read and write compressed files,
often transparently. Reading of files in R is to a very large extent done
by connections, and the file function which is used to open a connection to a file (or
a URL) and is able to identify the compression used from the ‘magic’ header of the
file.
The type of compression which has been supported for longest is gzip compression,
and that remains a good general compromise. Files compressed by the earlier
Unix compress utility can also be read, but these are becoming rare. Two other forms
of compression, those of the bzip2 and xz utilities are also available. These generally
achieve higher rates of compression (depending on the file, much higher) at the
expense of slower decompression and much slower compression.
There is some confusion between xz and lzma compression
(see https://en.wikipedia.org/wiki/Xz and https://en.wikipedia.org/wiki/LZMA): R can read
files compressed by most versions of either.
File archives are single files which contain a collection of files, the most common
ones being ‘tarballs’ and zip files as used to distribute R packages. R can list and
unpack both (see functions untar and unzip) and create both (for zip with the help of
an external program).

Next: Invoking R, Previous: OS facilities, Up: An Introduction to R [Contents][Index]

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.
Start R appropriately for your platform (see Invoking R).
The R program begins, with a banner.
(Within R code, 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 and look at the analysis. With y to the left of the
tilde, we are modelling y dependent on x.
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$y)
Add in the local regression.
abline(0, 1, lty=3)
The true regression line: (intercept 0, slope 1).
abline(coef(fm))
Unweighted regression line.
abline(coef(fm1), col = "red")
Weighted regression line.
detach()
Remove data frame from the search path.
plot(fitted(fm), resid(fm),
xlab="Fitted values",
ylab="Residuals",
main="Residuals vs Fitted")
A standard regression diagnostic plot to check for heteroscedasticity. Can you
see it?
qqnorm(resid(fm), main="Residuals Rankit Plot")
A normal scores plot to check for skewness, kurtosis and outliers. (Not very
useful here.)
rm(fm, fm1, lrf, x, dummy)
Clean up again.
The next section will look at data from the classical experiment of Michelson to
measure the speed of light. This dataset is available in the morley object, but we will
read it to illustrate the read.table function.
filepath <- system.file("data", "morley.tab" , package="datasets")
filepath
Get the path to the data file.
file.show(filepath)
Optional. Look at the file.
mm <- read.table(filepath)
mm
Read in the Michelson data as a data frame, and look at it. There are five
experiments (column Expt) and each has 20 runs (column Run) and sl is the
recorded speed of light, suitably coded.
mm$Expt <- factor(mm$Expt)
mm$Run <- factor(mm$Run)
Change Expt and Run into factors.
attach(mm)
 Make the data frame visible at position 2 (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 the interval [-pi\, pi]. y is the same.
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 + x^2).
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.

Next: The command-line editor, Previous: A sample session, Up: An Introduction to

R [Contents][Index]

Appendix B Invoking R
Users of R on Windows or macOS should read the OS-specific section first, but
command-line use is also supported.
• Invoking R from the command line
• Invoking R under Windows
 • Invoking R under macOS
• Scripting with R

Next: Invoking R under Windows, Previous: Invoking R, Up: Invoking R [Contents][Index]

B.1 Invoking R from the command line

When working at a command line on UNIX or 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”.
At the Windows command-line, Rterm.exe is preferred to R.
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 information, 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 is
the one pointed to by the environment variable R_ENVIRON_USER if this is set;
otherwise, files .Renviron in the current or in the user’s home directory (in
that order) are searched for. 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 user profile and
sources it. The name of this file is taken from the environment
variable R_PROFILE_USER; if unset, a file called .Rprofile in the current
directory or in the user’s home directory (in that order) is searched for.
 • It also loads a saved workspace from file .RData in the current directory 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. (--encoding enc is
also accepted.) The input is re-encoded to the locale R is running in and needs
to be representable in the latter’s encoding (so e.g. you cannot re-encode Greek
text in a French locale unless that locale uses the UTF-8 encoding).
RHOME
Print the path to the R “home directory” to standard output and exit
successfully. Apart from the front-end shell script and the man page, R
installation puts everything (executables, packages, etc.) into this directory.
--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
(not Rgui.exe) Take input from file: ‘-’ means stdin. Implies --no-
save unless --save has been set. On a Unix-alike, shell metacharacters
should be avoided in file (but spaces are allowed).
-e expression
(not Rgui.exe) 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. Expressions containing spaces or shell
metacharacters will need to be quoted.)
--no-readline
(UNIX only) Turn off command-line editing via readline. This is useful when
running R from within Emacs using the ESS (“Emacs Speaks Statistics”)
package. See The command-line editor, for more information. Command-line
 editing is enabled for default interactive use (see --interactive). This
option also affects tilde-expansion: see the help for path.expand.
--min-vsize=N
--min-nsize=N
For expert use only: set the initial trigger sizes for garbage collection of vector
heap (in bytes) and cons cells (number) respectively. Suffix ‘M’ specifies
megabytes or millions of cells respectively. The defaults are 6Mb and 350k
respectively and can also be set by environment variables R_NSIZE and R_VSIZE.
--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.
--quiet
--silent
-q
Do not print out the initial copyright and welcome messages.
--no-echo
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.
--interactive
(UNIX only) Assert that R really is being run interactively even if input has
been redirected: use if input is from a FIFO or pipe and fed from an interactive
program. (The default is to deduce that R is being run interactively if and only
if stdin is connected to a terminal or pty.) Using -e, -f or --file asserts
non-interactive use even if --interactive is given.
Note that this does not turn on command-line editing.
--ess
(Windows only) Set Rterm up for use by R-inferior-mode in ESS, including
asserting interactive use (without the command-line editor) and no buffering
of stdout.
--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
interactive graphics). Currently, possible values for type are ‘X11’ (the default)
and, provided that ‘Tcl/Tk’ support is available, ‘Tk’. (For back-
compatibility, ‘x11’ and ‘tk’ are accepted.)
--arch=name
(UNIX only) Run the specified sub-architecture.
--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 4095 bytes still applies. Warning and error messages are sent to
the error channel (stderr).
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. Runs R --restore --save with possibly further options
(see ?BATCH).
COMPILE
(UNIX only) Compile C, C++, Fortran … files for use with R.
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
Rd2txt
Convert Rd format to various other formats, including HTML, LaTeX, plain
text, and extracting the examples. Rd2txt can be used as shorthand for Rd2conv
-t txt.
Rd2pdf
Convert Rd format to PDF.
Stangle
Extract S/R code from Sweave or other vignette documentation
Sweave
Process Sweave or other vignette documentation
Rdiff
Diff R output ignoring headers etc
config
Obtain configuration information
javareconf
(Unix only) Update the Java configuration variables
rtags
(Unix only) Create Emacs-style tag files from C, R, and Rd files
open
(Windows only) Open a file via Windows’ file associations
texify
(Windows only) Process (La)TeX files with R’s style files
Use
R CMD command --help
to obtain usage information for each of the tools accessible via the R CMD interface.
In addition, you can use options --arch=, --no-environ, --no-init-
file, --no-site-file and --vanilla between R and CMD: these affect any R
processes run by the tools. (Here --vanilla is equivalent to --no-environ --
no-site-file --no-init-file.) However, note that R CMD does not of itself
use any R startup files (in particular, neither user nor site Renviron files), and all of
the R processes run by these tools (except BATCH) use --no-restore. Most use --
vanilla and so invoke no R startup files: the current exceptions
are INSTALL, REMOVE, Sweave and SHLIB (which uses --no-site-file --no-
init-file).
R CMD cmd args
for any other executable cmd on the path or given by an absolute filepath: this is useful
to have the same environment as R or the specific commands run under, for example
to run ldd or pdflatex. Under Windows cmd can be an executable or a batch file, or if
it has extension .sh or .pl the appropriate interpreter (if available) is called to run it.

Next: Invoking R under macOS, Previous: Invoking R from the command line, Up: Invoking
R [Contents][Index]

B.2 Invoking R under Windows

There are two ways to run R under Windows. Within a terminal window
(e.g. cmd.exe 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. 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 My
Documents in recent versions of Windows). If that fails, and environment
variables HOMEDRIVE and HOMEPATH are defined (and they normally are) 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 on the command line.
If there is an argument ending .RData (in any case) it is interpreted as the path to the
workspace to be restored: it implies --restore and sets the working directory to
the parent of the named file. (This mechanism is used for drag-and-drop and file
association with RGui.exe, but also works for Rterm.exe. If the named file does not
exist it sets the working directory if the parent directory exists.)
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.
--debug
Enable the “Break to debugger” menu item in Rgui, and trigger a break to the
debugger during command line processing.
Under Windows with R CMD you may also specify your
own .bat, .exe, .sh or .pl file. It will be run under the appropriate interpreter
(Perl for .pl) with several environment variables set appropriately,
including R_HOME, R_OSTYPE, PATH, BSTINPUTS 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
appended to TEXINPUTS. (Unfortunately, this does not help with the MiKTeX build of
LaTeX, but R CMD texify mydoc will work in that case.)

Next: Scripting with R, Previous: Invoking R under Windows, Up: Invoking

R [Contents][Index]

B.3 Invoking R under macOS

There are two ways to run R under macOS. Within a Terminal.app window by
invoking R, the methods described in the first subsection 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 macOS application.
The startup procedure under macOS is very similar to that under UNIX,
but R.app does not make use of command-line arguments. 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.

Previous: Invoking R under macOS, Up: Invoking R [Contents][Index]

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 (where the exact quoting needed will depend on the shell in use)
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"). This writes R output
to stdout and stderr, and this can be redirected in the usual way for the shell
running the command.
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 except on Windows, but e.g. macOS users may
need to add /usr/local/bin to their path), 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.
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 --no-echo [other options] <<EOF

R program goes here...

EOF
but here stdin() refers to the program source and "stdin" will not be usable.
Short scripts can be passed to Rscript on the command-line via the -e flag. (Empty
scripts are not accepted.)
Note that on a Unix-alike the input filename (such as foo.R) should not contain
spaces nor shell metacharacters.

Next: Function and variable index, Previous: Invoking R, Up: An Introduction to

R [Contents][Index]

Appendix C The command-line

editor
• Preliminaries
• Editing actions
• Command-line editor summary

C.1 Preliminaries
When the GNU readline library is available at the time R is configured for
compilation under UNIX, an inbuilt command line editor allowing recall, editing and
re-submission of prior commands is used. Note that other versions of readline exist
and may be used by the inbuilt command line editor: this is most common on macOS.
You can find out which version (if any) is available by running extSoftVersion() in
an R session.
It can be disabled (useful for usage with ESS 25) 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 GNU26 readline capabilities, the functions described below are
available, as well as others (probably) documented in man readline or info
readline on your system.

Many of these use either Control or Meta characters. Control characters, such
as Control-m, are obtained by holding the CTRL down while you press the m key, and
are written as C-m below. Meta characters, such as Meta-b, are typed by holding
down META27 and pressing b, and written as M-b in the following. If your terminal does
not have a META key enabled, you can still type Meta characters using two-character
sequences starting with ESC. Thus, to enter M-b, you could type ESCb. The ESC character
sequences are also allowed on terminals with real Meta keys. Note that case is
significant for Meta characters.
Some but not all versions28 of readline will recognize resizing of the terminal window
so this is best avoided.

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 ESC. (The default is Emacs-style, and
only that is described here: for vi mode see the readline documentation.)
Pressing the RET 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. This can be cancelled by C-
g (and on some versions of R by C-c).

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.
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.
DEL
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.
RET
Re-submit the command to R.
The final RET terminates the command line editing sequence.
The readline key bindings can be customized in the usual
way via a ~/.inputrc file. These customizations can be conditioned on
application R, that is by including a section like
$if R
"\C-xd": "q('no')\n"
$endif

Next: Concept index, Previous: The command-line editor, Up: An Introduction to

R [Contents][Index]

Appendix D Function and variable

index
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to: A B C D E F G H I J K L M N O P Q R S T U V W X
Index Entry Section

-
- Vector arithmetic
:
: Generating regular sequences
:: Namespaces
::: Namespaces

!
! Logical vectors
!= Logical vectors

?
? Getting help
?? Getting help

.
. Updating fitted models
.First Customizing the environment
.Last Customizing the environment

*
* Vector arithmetic

/
/ Vector arithmetic

&
& Logical vectors
&& Conditional execution

%
%*% Multiplication
%o% The outer product of two arrays

^
^ Vector arithmetic

+
+ Vector arithmetic
<
< Logical vectors
<<- Scope
<= Logical vectors

=
== Logical vectors

>
> Logical vectors
>= Logical vectors

|
| Logical vectors
|| Conditional execution

~
~ Formulae for statistical models

A
abline Low-level plotting commands
ace Some non-standard models
add1 Updating fitted models
anova Generic functions for extracting model information
anova ANOVA tables
aov Analysis of variance and model comparison
aperm Generalized transpose of an array
array The array() function
as.data.frame Making data frames
as.vector The concatenation function c() with arrays
attach attach() and detach()
attr Getting and setting attributes
attr Getting and setting attributes
attributes Getting and setting attributes
attributes Getting and setting attributes
avas Some non-standard models
axis Low-level plotting commands
B
boxplot One- and two-sample tests
break Repetitive execution
bruto Some non-standard models

C
c Vectors and assignment
c Character vectors
c The concatenation function c() with arrays
c Concatenating lists
C Contrasts
cbind Forming partitioned matrices
coef Generic functions for extracting model information
coefficients Generic functions for extracting model information
contour Display graphics
contrasts Contrasts
coplot Displaying multivariate data
cos Vector arithmetic
crossprod Index matrices
crossprod Multiplication
cut Frequency tables from factors

D
data Accessing builtin datasets
data.frame Making data frames
density Examining the distribution of a set of data
det Singular value decomposition and determinants
detach attach() and detach()
determinant Singular value decomposition and determinants
dev.list Multiple graphics devices
dev.next Multiple graphics devices
dev.off Multiple graphics devices
dev.prev Multiple graphics devices
dev.set Multiple graphics devices
deviance Generic functions for extracting model information
diag Multiplication
dim Arrays
 dotchart Display graphics
drop1 Updating fitted models

E
ecdf Examining the distribution of a set of data
edit Editing data
eigen Eigenvalues and eigenvectors
else Conditional execution
Error Analysis of variance and model comparison
example Getting help
exp Vector arithmetic

F
F Logical vectors
factor Factors
FALSE Logical vectors
fivenum Examining the distribution of a set of data
for Repetitive execution
formula Generic functions for extracting model information
function Writing your own functions

G
getAnywhere Object orientation
getS3method Object orientation
glm The glm() function

H
help Getting help
help Getting help
help.search Getting help
help.start Getting help
hist Examining the distribution of a set of data
hist Display graphics

I
identify Interacting with graphics
if Conditional execution
if Conditional execution
 ifelse Conditional execution
image Display graphics
is.na Missing values
is.nan Missing values

J
jpeg Device drivers

K
ks.test Examining the distribution of a set of data

L
legend Low-level plotting commands
length Vector arithmetic
length The intrinsic attributes mode and length
levels Factors
lines Low-level plotting commands
list Lists
lm Linear models
lme Some non-standard models
locator Interacting with graphics
loess Some non-standard models
loess Some non-standard models
log Vector arithmetic
lqs Some non-standard models
lsfit Least squares fitting and the QR decomposition

M
mars Some non-standard models
max Vector arithmetic
mean Vector arithmetic
methods Object orientation
min Vector arithmetic
mode The intrinsic attributes mode and length

N
NA Missing values
NaN Missing values
 ncol Matrix facilities
next Repetitive execution
nlm Nonlinear least squares and maximum likelihood models
nlm Least squares
nlm Maximum likelihood
nlme Some non-standard models
nlminb Nonlinear least squares and maximum likelihood models
nrow Matrix facilities

O
optim Nonlinear least squares and maximum likelihood models
order Vector arithmetic
ordered Ordered factors
ordered Ordered factors
outer The outer product of two arrays

P
pairs Displaying multivariate data
par The par() function
paste Character vectors
pdf Device drivers
persp Display graphics
plot Generic functions for extracting model information
plot The plot() function
pmax Vector arithmetic
pmin Vector arithmetic
png Device drivers
points Low-level plotting commands
polygon Low-level plotting commands
postscript Device drivers
predict Generic functions for extracting model information
print Generic functions for extracting model information
prod Vector arithmetic

Q
qqline Examining the distribution of a set of data
qqline Display graphics
qqnorm Examining the distribution of a set of data
 qqnorm Display graphics
qqplot Display graphics
qr Least squares fitting and the QR decomposition
quartz Device drivers

R
range Vector arithmetic
rbind Forming partitioned matrices
read.table The read.table() function
rep Generating regular sequences
repeat Repetitive execution
resid Generic functions for extracting model information
residuals Generic functions for extracting model information
rlm Some non-standard models
rm Data permanency and removing objects

S
scan The scan() function
sd The function tapply() and ragged arrays
search Managing the search path
seq Generating regular sequences
shapiro.test Examining the distribution of a set of data
sin Vector arithmetic
sink Executing commands from or diverting output to a file
solve Linear equations and inversion
sort Vector arithmetic
source Executing commands from or diverting output to a file
split Repetitive execution
sqrt Vector arithmetic
stem Examining the distribution of a set of data
step Generic functions for extracting model information
step Updating fitted models
sum Vector arithmetic
summary Examining the distribution of a set of data
summary Generic functions for extracting model information
svd Singular value decomposition and determinants

T
 T Logical vectors
t Generalized transpose of an array
t.test One- and two-sample tests
table Index matrices
table Frequency tables from factors
tan Vector arithmetic
tapply The function tapply() and ragged arrays
text Low-level plotting commands
title Low-level plotting commands
tree Some non-standard models
TRUE Logical vectors

U
unclass The class of an object
update Updating fitted models

V
var Vector arithmetic
var The function tapply() and ragged arrays
var.test One- and two-sample tests
vcov Generic functions for extracting model information
vector Vectors and assignment

W
while Repetitive execution
wilcox.test One- and two-sample tests
windows Device drivers

X
X11 Device drivers

Jump - : ! ? . * / & % ^ + < = > | ~

to: A B C D E F G H I J K L M N O P Q R S T U V W X

Next: References, Previous: Function and variable index, Up: An Introduction to

R [Contents][Index]

Appendix E Concept index

Jump to: A B C D E F G I K L M N O P Q R S T U V W
Index Entry Section

A
Accessing builtin datasets Accessing builtin datasets
Additive models Some non-standard models
Analysis of variance Analysis of variance and model comparison
Arithmetic functions and Vector arithmetic
operators
Arrays Arrays
Assignment Vectors and assignment
Attributes Objects

B
Binary operators Defining new binary operators
Box plots One- and two-sample tests

C
Character vectors Character vectors
Classes The class of an object
Classes Object orientation
Concatenating lists Concatenating lists
Contrasts Contrasts
Control statements Control statements
CRAN Contributed packages and CRAN
Customizing the environment Customizing the environment

D
Data frames Data frames
Default values Named arguments and defaults
Density estimation Examining the distribution of a set of data
Determinants Singular value decomposition and determinants
Diverting input and output Executing commands from or diverting output to a file
Dynamic graphics Dynamic graphics

E
Eigenvalues and eigenvectors Eigenvalues and eigenvectors
Empirical CDFs Examining the distribution of a set of data
F
Factors Factors
Factors Contrasts
Families Families
Formulae Formulae for statistical models

G
Generalized linear models Generalized linear models
Generalized transpose of an array Generalized transpose of an array
Generic functions Object orientation
Graphics device drivers Device drivers
Graphics parameters The par() function
Grouped expressions Grouped expressions

I
Indexing of and by arrays Array indexing
Indexing vectors Index vectors

K
Kolmogorov-Smirnov test Examining the distribution of a set of data

L
Least squares fitting Least squares fitting and the QR decomposition
Linear equations Linear equations and inversion
Linear models Linear models
Lists Lists
Local approximating regressions Some non-standard models
Loops and conditional execution Loops and conditional execution

M
Matrices Arrays
Matrix multiplication Multiplication
Maximum likelihood Maximum likelihood
Missing values Missing values
Mixed models Some non-standard models

N
 Named arguments Named arguments and defaults
Namespace Namespaces
Nonlinear least squares Nonlinear least squares and maximum likelihood
models

O
Object orientation Object orientation
Objects Objects
One- and two-sample tests One- and two-sample tests
Ordered factors Factors
Ordered factors Contrasts
Outer products of arrays The outer product of two arrays

P
Packages R and statistics
Packages Packages
Probability distributions Probability distributions

Q
QR decomposition Least squares fitting and the QR decomposition
Quantile-quantile plots Examining the distribution of a set of data

R
Reading data from files Reading data from files
Recycling rule Vector arithmetic
Recycling rule The recycling rule
Regular sequences Generating regular sequences
Removing objects Data permanency and removing objects
Robust regression Some non-standard models

S
Scope Scope
Search path Managing the search path
Shapiro-Wilk test Examining the distribution of a set of data
Singular value decomposition Singular value decomposition and determinants
Statistical models Statistical models in R
Student’s t test One- and two-sample tests
T
Tabulation Frequency tables from factors
Tree-based models Some non-standard models

U
Updating fitted models Updating fitted models

V
Vectors Simple manipulations numbers and vectors

W
Wilcoxon test One- and two-sample tests
Workspace Data permanency and removing objects
Writing functions Writing your own functions

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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. Chapman & 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, Chapman 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.

Footnotes

(1)

ACM Software Systems award,

1998: https://awards.acm.org/award_winners/chambers_6640862.cfm.
(2)

For portable R code (including that to be used in R packages) only A–Z, a–z, and 0–9
should be used.
(3)

not inside strings, nor within the argument list of a function definition
(4)

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.
(5)

of unlimited length.
(6)

The leading “dot” in this file name makes it invisible in normal file listings in UNIX,
and in default GUI file listings on macOS and Windows.
(7)

With other than vector types of argument, such as list mode arguments, the action
of c() is rather different. See Concatenating lists.
(8)

Actually, it is still available as .Last.value before any other statements are executed.
(9)
paste(..., collapse=ss) joins the arguments into a single character string
putting ss in between, e.g., ss <- "|". There are more tools for character
manipulation, see the help for sub and substring.
(10)

numeric mode is actually an amalgam of two distinct modes,

namely integer and double precision, as explained in the manual.
(11)

Note however that length(object) does not always contain intrinsic useful information,
e.g., when object is a function.
(12)

In general, coercion from numeric to character and back again will not be exactly
reversible, because of roundoff errors in the character representation.
(13)

A different style using ‘formal’ or ‘S4’ classes is provided in package methods.

(14)

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.
(15)

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()).
(16)

Note that x %*% x is ambiguous, as it could mean either x’x or x x’, where x is the
column form. In such cases the smaller matrix seems implicitly to be the interpretation
adopted, so the scalar x’x is in this case the result. The matrix x x’ 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 x’x or x x’ is crossprod(x) or x
%o% x respectively.

(17)
Even better would be to form a matrix square root B with A = BB’ and find the
squared length of the solution of By = x , perhaps using the Cholesky or
eigendecomposition of A.
(18)

See the on-line help for autoload for the meaning of the second term.
(19)

Under UNIX, the utilities sed or awk can be used.

(20)

to be discussed later, or use xyplot from package lattice.

(21)

See also the methods described in Statistical models in R

(22)

In some sense this mimics the behavior in S-PLUS since in S-PLUS this operator
always creates or assigns to a global variable.
(23)

So it is hidden under UNIX.

(24)

Some graphics parameters such as the size of the current device are for information
only.
(25)

The ‘Emacs Speaks Statistics’ package; see the URL https://ESS.R-project.org/

(26)

It is possible to build R using an emulation of GNU readline, such as one based on

NetBSD’s editline (also known as libedit), in which case only a subset of the
capabilities may be provided.
(27)
On a PC keyboard this is usually the Alt key, occasionally the ‘Windows’ key. On a
Mac keyboard normally no meta key is available.
(28)

In particular, not versions 6.3 or later: this is worked around as from R 3.4.0.