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R has three object oriented (OO) systems: S3, S4 and R5. This page describes S3.
Central to any object-oriented system are the concepts of class and method. A class defines a type of object, describing what properties it possesses, how it behaves, and how it relates to other types of objects. Every object must be an instance of some class. A method is a function associated with a particular type of object.
S3 implements a style of object oriented programming called generic-function OO. This is different to most programming languages, like Java, C++ and C#, which implement message-passing OO. In message-passing style, messages (methods) are sent to objects and the object determines which function to call. Typically this object has a special appearance in the method call, usually appearing before the name of the method/message: e.g. canvas.drawRect("blue"). S3 is different. While computations are still carried out via methods, a special type of function called a generic function decides which method to call. Methods are defined in the same way as a normal function, but are called in a different way, as we'll see shortly.
The primary use of OO programming in R is for print, summary and plot methods. These methods allow us to have one generic function, e.g. print(), that displays the object differently depending on its type: printing a linear model is very different to printing a data frame.
The class of an object is determined by its class attribute, a character vector of class names. The following example shows how to create an object of class foo:
x <- 1
attr(x, "class") <- "foo"
x
# Or in one line
x <- structure(1, class = "foo")
x
Class is stored as an attribute, but it's better to modify it using the class() function, since this communicates your intent more clearly:
class(x) <- "foo"
class(x)
# [1] "foo"
You can use this approach to to turn any object into an object of class "foo", whether it makes sense or not.
Objects are not limited to a single class, and can have many classes:
class(x) <- c("A", "B")
class(x) <- LETTERS
As discussed in the next section, R looks for methods in the order in which they appear in the class vector. So in this example, it would be like class A inherits from class B - if a method isn't defined for A, it will fall back to B. However, if you switched the order of the classes, the opposite would be true! This is because S3 doesn't define any formal relationship between classes, or even any definition of what an individual class is. If you're coming from a strict environment like Java, this will seem pretty frightening (and it is!) but it does give your users a tremendous amount of freedom. While it's very difficult to stop someone from doing something you don't want them to do, your users will never be held back because there is something you haven't implemented yet.
Method dispatch starts with a generic function that decides which specific method to dispatch to. Generic functions all have the same form: a call to UseMethod that specifies the generic name and the object to dispatch on. This means that generic functions are usually very simple, like mean:
mean <- function (x, ...) {
UseMethod("mean", x)
}
Methods are ordinary functions that use a special naming convention: generic.class:
mean.numeric <- function(x, ...) sum(x) / length(x)
mean.data.frame <- function(x, ...) sapply(x, mean, ...)
mean.matrix <- function(x, ...) apply(x, 2, mean)
(These are somewhat simplified versions of the real code).
As you might guess from this example, UseMethod uses the class of x to figure out which method to call. If x had more than one class, e.g. c("foo","bar"), UseMethod would look for mean.foo and if not found, it would then look for mean.bar. As a final fallback, UseMethod will look for a default method, mean.default, and if that doesn't exist it will raise an error. The same approach applies regardless of how many classes an object has:
x <- structure(1, class = letters)
bar <- function(x) UseMethod("bar", x)
bar.z <- function(x) "z"
bar(x)
# [1] "z"
Once UseMethod has found the correct method, it's invoked in a special way. Rather than creating a new evaluation environment, it uses the environment of the current function call (the call to the generic), so any assignments or evaluations that were made before the call to UseMethod will be accessible to the method. The arguments that were used in the call to the generic are passed on to the method in the same order they were received.
Because methods are normal R functions, you can call them directly. However, you shouldn't do this because you lose the benefits of having a generic function:
bar.x <- function(x) "x"
# You can call methods directly, but you shouldn't!
bar.x(x)
# [1] "x"
bar.z(x)
# [1] "z"
To find out which classes a generic function has methods for, you can use the methods function. Remember, in R, that methods are associated with functions (not objects), so you pass in the name of the function, rather than the class, as you might expect:
methods("bar")
# [1] bar.x bar.z
methods("t")
# [1] t.data.frame t.default t.ts*
# Non-visible functions are asterisked
Non-visible functions are functions that haven't been exported by a package, so you'll need to use the getAnywhere function to access them if you want to see the source.
Some internal C functions are also generic, which means that the method dispatch is not performed by R function, but is instead performed by special C functions. It's important to know which functions are internally generic, so you can write methods for them, and so you're aware of the slight differences in method dispatch. It's not easy to tell if a function is internally generic, because it just looks like a typical call to a C:
length <- function (x) .Primitive("length")
cbind <- function (..., deparse.level = 1)
.Internal(cbind(deparse.level, ...))
As well as length and cbind, internal generic functions include dim, c, as.character, names and rep. A complete list can be found in the global variable .S3PrimitiveGenerics, and more details are given in ?InternalMethods.
Internal generic have a slightly different dispatch mechanism to other generic functions: before trying the default method, they will also try dispatching on the implicit class of an object. The implicit class is the default class, i.e., the result of class(unclass(x)). The following example shows the difference:
x <- structure(as.list(1:10), class = "myclass")
length(x)
# [1] 10
mylength <- function(x) UseMethod("mylength", x)
mylength.list <- function(x) length(x)
mylength(x)
# Error in UseMethod("mylength", x) :
# no applicable method for 'mylength' applied to an object of class
# "myclass"
The NextMethod function provides a simple inheritance mechanism, using the fact that the class of an S3 object is a vector. This is very different behaviour to most other languages because it means that it's possible to have different inheritance hierarchies for different objects:
baz <- function(x) UseMethod("baz", x)
baz.A <- function(x) "A"
baz.B <- function(x) "B"
ab <- structure(1, class = c("A", "B"))
ba <- structure(1, class = c("B", "A"))
baz(ab)
baz(ba)
NextMethod() works like UseMethod but instead of dispatching on the first element of the class vector, it will dispatch based on the second (or subsequent) element:
baz.C <- function(x) c("C", NextMethod())
ca <- structure(1, class = c("C", "A"))
cb <- structure(1, class = c("C", "B"))
baz(ca)
baz(cb)
The exact details are a little tricky: NextMethod doesn't actually work with the class attribute of the object, it uses a global variable (.Class) to keep track of which class to call next. This means that manually changing the class of the object will have no impact on the inheritance:
# Turn object into class A - doesn't work!
baz.D <- function(x) {
class(x) <- "A"
NextMethod()
}
da <- structure(1, class = c("D", "A"))
db <- structure(1, class = c("D", "B"))
baz(da)
baz(db)
Methods invoked as a result of a call to NextMethod behave as if they had been invoked from the previous method. The arguments to the inherited method are in the same order and have the same names as the call to the current method, and are therefore are the same as the call to the generic. However, the expressions for the arguments are the names of the corresponding formal arguments of the current method. Thus the arguments will have values that correspond to their value at the time NextMethod was invoked. Unevaluated arguments remain unevaluated. Missing arguments remain missing.
If NextMethod is called in a situation where there is no second class it will return an error. A selection of these errors are shown below so that you know what to look for.
c <- structure(1, class = "C")
baz(c)
# Error in UseMethod("baz", x) :
# no applicable method for 'baz' applied to an object of class "C"
baz.c(c)
# Error in NextMethod() : generic function not specified
baz.c(1)
# Error in NextMethod() : object not specified
(Contents adapted from the R language definition. This document is licensed with the GPL-2 license.)