An Introduction to R

Table of Contents

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 3.3.3 (2017-03-06).

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 © 1999–2016 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.

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 R-core@R-project.org.

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 Graphics, which can be read at almost any time and need not wait until all the preceding sections have been digested.

1 Introduction and preliminaries

1.1 The R environment

R is an integrated suite of software facilities for data manipulation, calculation and graphical display. Among other things it has

• an effective data handling and storage facility,
• a suite of operators for calculations on arrays, in particular matrices,
• a large, coherent, integrated collection of intermediate tools for data analysis,
• graphical facilities for data analysis and display either directly at the computer or on 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.

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 The R statistical system FAQ.

1.3 R and statistics

Our introduction to the R environment did not mention statistics, yet many people use R as a statistics system. We prefer to think of it of an environment within which many classical and modern statistical techniques have been implemented. A few of these are built into the base R environment, but many are supplied as packages. There are about 25 packages supplied with R (called “standard” and “recommended” packages) and many more are available through the CRAN family of Internet sites (via 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.

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.

1.5 Using R interactively

When you use the R program it issues a prompt when it expects input commands. The default prompt is ‘>’, which on UNIX might be the same as the shell prompt, and so it may appear that nothing is happening. However, as we shall see, it is easy to change to a different R prompt if you wish. We will assume that the UNIX shell prompt is ‘$’.

In using R under UNIX the suggested procedure for the first occasion is as follows:

1. Create a separate sub-directory, say work, to hold data files on which you will use R for this problem. This will be the working directory whenever you use R for this particular problem.

   $ mkdir work
   $ cd work
   

2. Start the R program with the command

   $ R
   

3. At this point R commands may be issued (see later).
4. To quit the R program the command is

   > q()
   

   At this point you will be asked whether you want to save the data from your R session. On some systems this will bring up a dialog box, and on others you will receive a text prompt to which you can respond yes, no or cancel (a single letter abbreviation will do) to save the data before quitting, quit without saving, or return to the R session. Data which is saved will be available in future R sessions.

Further R sessions are simple.

1. Make work the working directory and start the program as before:

   $ cd work
   $ R
   

2. Use the R program, terminating with the q() command at the end of the session.

To use R under Windows the procedure to follow is basically the same. Create a folder as the working directory, and set that in the Start In field in your R shortcut. Then launch R by double clicking on the icon.

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.

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.

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 hashmark (‘#’), everything to the end of the line is a comment.

If a command is not complete at the end of a line, R will give a different prompt, by default

+

on second and subsequent lines and continue to read input until the command is syntactically complete. This prompt may be changed by the user. We will generally omit the continuation prompt and indicate continuation by simple indenting.

Command lines entered at the console are limited⁴ to about 4095 bytes (not characters).

1.9 Recall and correction of previous commands

Under many versions of UNIX and on Windows, R provides a mechanism for recalling and re-executing previous commands. The vertical arrow keys on the keyboard can be used to scroll forward and backward through a command history. Once a command is located in this way, the cursor can be moved within the command using the horizontal arrow keys, and characters can be removed with the 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 The R statistical system FAQ.

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.

1.11 Data permanency and removing objects

The entities that R creates and manipulates are known as objects. These may be variables, arrays of numbers, character strings, functions, or more general structures built from such components.

During an R session, objects are created and stored by name (we discuss this process in the next session). The R command

> objects()

(alternatively, ls()) can be used to display the names of (most of) the objects which are currently stored within R. The collection of objects currently stored is called the workspace.

To remove objects the function rm is available:

> 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.

2 Simple manipulations; numbers and vectors

2.1 Vectors and assignment

R operates on named data structures. The simplest such structure is the numeric vector, which is a single entity consisting of an ordered collection of numbers. To set up a vector named x, say, consisting of five numbers, namely 10.4, 5.6, 3.1, 6.4 and 21.7, use the R command

> x <- c(10.4, 5.6, 3.1, 6.4, 21.7)

This is an assignment statement using the function c() which in this context can take an arbitrary number of vector arguments and whose value is a vector got by concatenating its arguments end to end.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.

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.

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.

2.4 Logical vectors

As well as numerical vectors, R allows manipulation of logical quantities. The elements of a logical vector can have the values TRUE, FALSE, and NA (for “not available”, see below). The first two are often abbreviated as T and F, respectively. Note however that T and F are just variables which are set to TRUE and FALSE by default, but are not reserved words and hence can be overwritten by the user. Hence, you should always use TRUE and FALSE.

Logical vectors are generated by conditions. For example

> temp <- x > 13

sets temp as a vector of the same length as x with values FALSE corresponding to elements of x where the condition is not met and TRUE where it is.

The logical operators are <, <=, >, >=, == for exact equality and != for inequality. In addition if c1 and c2 are logical expressions, then c1 & c2 is their intersection (“and”), c1 | c2 is their union (“or”), and !c1 is the negation of c1.

Logical vectors may be used in ordinary arithmetic, in which case they are coerced into numeric vectors, FALSE becoming 0 and TRUE becoming 1. However there are situations where logical vectors and their coerced numeric counterparts are not equivalent, for example see the next subsection.

2.5 Missing values

In some cases the components of a vector may not be completely known. When an element or value is “not available” or a “missing value” in the statistical sense, a place within a vector may be reserved for it by assigning it the special value NA. In general any operation on an NA becomes an NA. The motivation for this rule is simply that if the specification of an operation is incomplete, the result cannot be known and hence is not available.

The function is.na(x) gives a logical vector of the same size as x with value TRUE if and only if the corresponding element in x is NA.

> z <- c(1:3,NA);  ind <- is.na(z)

Notice that the logical expression x == NA is quite different from is.na(x) since NA is not really a value but a marker for a quantity that is not available. Thus x == NA is a vector of the same length as x all of whose values are NA as the logical expression itself is incomplete and hence undecidable.

Note that there is a second kind of “missing” values which are produced by numerical 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.

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

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

   > 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.

2. A vector of positive integral quantities. In this case the values in the index vector must lie in the set {1, 2, …, length(x)}. The corresponding elements of the vector are selected and concatenated, in that order, in the result. The index vector can be of any length and the result is of the same length as the index vector. For example x[6] is the sixth component of x and

   > x[1:10]
   

   selects the first 10 elements of x (assuming length(x) is not less than 10). Also

   > c("x","y")[rep(c(1,2,2,1), times=4)]
   

   (an admittedly unlikely thing to do) produces a character vector of length 16 consisting of "x", "y", "y", "x" repeated four times.

3. A vector of negative integral quantities. Such an index vector specifies the values to be excluded rather than included. Thus

   > y <- x[-(1:5)]
   

   gives y all but the first five elements of x.

4. A vector of character strings. This possibility only applies where an object has a names attribute to identify its components. In this case a sub-vector of the names vector may be used in the same way as the positive integral labels in item 2 further above.

   > fruit <- c(5, 10, 1, 20)
   > names(fruit) <- c("orange", "banana", "apple", "peach")
   > lunch <- fruit[c("apple","orange")]
   

   The advantage is that alphanumeric names are often easier to remember than numeric indices. This option is particularly useful in connection with data frames, as we shall see later.

An indexed expression can also appear on the receiving end of an assignment, in which case the assignment operation is performed only on those elements of the vector. The expression must be of the form vector[index_vector] as having an arbitrary expression in place of the vector name does not make much sense here.

For example

> x[is.na(x)] <- 0

replaces any missing values in x by zeros and

> y[y < 0] <- -y[y < 0]

has the same effect as

> y <- abs(y)

2.8 Other types of objects

Vectors are the most important type of object in R, but there are several others which we will meet more formally in later sections.

• matrices or more generally arrays are multi-dimensional generalizations of vectors. In fact, they are vectors that can be indexed by two or more indices and will be printed in special ways. See Arrays and matrices.
• factors provide compact ways to handle categorical data. See 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.

3 Objects, their modes and attributes

3.1 Intrinsic attributes: mode and length

The entities R operates on are technically known as objects. Examples are vectors of numeric (real) or complex values, vectors of logical values and vectors of character strings. These are known as “atomic” structures since their components are all of the same type, or mode, namely 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.

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.

3.3 Getting and setting attributes

The function attributes(object) returns a list of all the non-intrinsic attributes currently defined for that object. The function attr(object, name) can be used to select a specific attribute. These functions are rarely used, except in rather special circumstances when some new attribute is being created for some particular purpose, for example to associate a creation date or an operator with an R object. The concept, however, is very important.

Some care should be exercised when assigning or deleting attributes since they are an integral part of the object system used in R.

When it is used on the left hand side of an assignment it can be used either to associate a new attribute with object or to change an existing one. For example

> attr(z, "dim") <- c(10,10)

allows R to treat z as if it were a 10-by-10 matrix.

3.4 The class of an object

All objects in R have a class, reported by the function class. For simple vectors this is just the mode, for example "numeric", "logical", "character" or "list", but "matrix", "array", "factor" and "data.frame" are other possible values.

A special attribute known as the class of the object is used to allow for an object-oriented 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 Object orientation, but only briefly.

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.

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"

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, stderr)

and the values calculated are then

> incster
act    nsw  nt    qld     sa tas   vic     wa
1.5 4.3102 4.5 4.1061 2.7386 0.5 5.244 2.6575

As an exercise you may care to find the usual 95% confidence limits for the state mean incomes. To do this you could use tapply() once more with the length() function to find the sample sizes, and the qt() function to find the percentage points of the appropriate t-distributions. (You could also investigate R’s facilities for t-tests.)

The function tapply() can also be used to handle more complicated indexing of a vector by multiple categories. For example, we might wish to split the tax accountants by both state and sex. However in this simple instance (just one factor) what happens can be thought of as follows. The values in the vector are collected into groups corresponding to the distinct entries in the factor. The function is then applied to each of these groups individually. The value is a vector of function results, labelled by the levels attribute of the factor.

The combination of a vector and a labelling factor is an example of what is sometimes called a ragged array, since the subclass sizes are possibly irregular. When the subclass sizes are all the same the indexing may be done implicitly and much more efficiently, as we see in the next section.

4.3 Ordered factors

The levels of factors are stored in alphabetical order, or in the order they were specified to factor if they were specified explicitly.

Sometimes the levels will have a natural ordering that we want to record and want our statistical analysis to make use of. The ordered() function creates such ordered factors but is otherwise identical to factor. For most purposes the only difference between ordered and unordered factors is that the former are printed showing the ordering of the levels, but the contrasts generated for them in fitting linear models are different.

5 Arrays and matrices

5.1 Arrays

An array can be considered as a multiply subscripted collection of data entries, for example numeric. R allows simple facilities for creating and handling arrays, and in particular the special case of matrices.

A dimension vector is a vector of non-negative integers. If its length is k then the array is k-dimensional, e.g. a matrix is a 2-dimensional array. The dimensions are indexed from one up to the values given in the dimension vector.

A vector can be used by R as an array only if it has a dimension vector as its dim attribute. Suppose, for example, z is a vector of 1500 elements. The assignment

> dim(z) <- c(3,5,100)

gives it the dim attribute that allows it to be treated as a 3 by 5 by 100 array.

Other functions such as matrix() and array() are available for simpler and more natural looking assignments, as we shall see in 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.

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.

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.

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 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.

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.

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 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.

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).

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.