Methods_for_S3 Methods For S3 and S4 Dispatch

Description

The S3 and S4 software in R are two generations implementing functional object-oriented programming. S3 is the original, simpler for initial programming but less general, less formal and less open to validation. The S4 formal methods and classes provide these features but require more programming.

In modern R, the two versions attempt to work together. This documentation outlines how to write methods for both systems by defining an S4 method for a function that dispatches S3 methods.

The systems can also be combined by using an S3 class with S4 method dispatch or in S4 class definitions. See setOldClass.

S3 Method Dispatch

The R evaluator will ‘dispatch’ a method from a function call either when the body of the function calls the special primitive UseMethod or when the call is to one of the builtin primitives such as the math functions or the binary operators.

S3 method dispatch looks at the class of the first argument or the class of either argument in a call to one of the primitive binary operators. In pure S3 situations, ‘class’ in this context means the class attribute or the implied class for a basic data type such as "numeric". The first S3 method that matches a name in the class is called and the value of that call is the value of the original function call. For details, see S3Methods.

In modern R, a function meth in a package is registered as an S3 method for function fun and class Class by including in the package's NAMESPACE file the directive

S3method(fun, Class, meth)

By default (and traditionally), the third argument is taken to be the function fun.Class; that is, the name of the generic function, followed by ".", followed by the name of the class.

As with S4 methods, a method that has been registered will be added to a table of methods for this function when the corresponding package is loaded into the session. Older versions of R, copying the mechanism in S, looked for the method in the current search list, but packages should now always register S3 methods rather than requiring the package to be attached.

Methods for S4 Classes

Two possible mechanisms for implementing a method corresponding to an S4 class, there are two possibilities are to register it as an S3 method with the S4 class name or to define and set an S4 method, which will have the side effect of creating an S4 generic version of this function.

For most situations either works, but the recommended approach is to do both: register the S3 method and supply the identical function as the definition of the S4 method. This ensures that the proposed method will be dispatched for any applicable call to the function.

As an example, suppose an S4 class "uncased" is defined, extending "character" and intending to ignore upper- and lower-case. The base function unique dispatches S3 methods. To define the class and a method for this function:

setClass("uncased", contains = "character")

unique.uncased <- function(x, incomparables = FALSE, ...) nextMethod(tolower(x))

setMethod("unique", "uncased", unique.uncased)

In addition, the NAMESPACE for the package should contain:

S3method(unique, uncased)

exportMethods(unique)

The result is to define identical S3 and S4 methods and ensure that all calls to unique will dispatch that method when appropriate.

Details

The reasons for defining both S3 and S4 methods are as follows:

1. An S4 method alone will not be seen if the S3 generic function is called directly. This will be the case, for example, if some function calls unique() from a package that does not make that function an S4 generic.

   However, primitive functions and operators are exceptions: The internal C code will look for S4 methods if and only if the object is an S4 object. S4 method dispatch would be used to dispatch any binary operator calls where either of the operands was an S4 object, for example.

2. An S3 method alone will not be called if there is any eligible non-default S4 method.

   So if a package defined an S3 method for unique for an S4 class but another package defined an S4 method for a superclass of that class, the superclass method would be chosen, probably not what was intended.

S4 and S3 method selection are designed to follow compatible rules of inheritance, as far as possible. S3 classes can be used for any S4 method selection, provided that the S3 classes have been registered by a call to setOldClass, with that call specifying the correct S3 inheritance pattern. S4 classes can be used for any S3 method selection; when an S4 object is detected, S3 method selection uses the contents of extends(class(x)) as the equivalent of the S3 inheritance (the inheritance is cached after the first call).

For the details of S4 and S3 dispatch see Methods_Details and S3Methods.

References

Chambers, John M. (2016) Extending R, Chapman & Hall. (Chapters 9 and 10.)