R: General Information on Methods

Methods {methods}

R Documentation

General Information on Methods

Description

This documentation section covers some general topics on how methods work and how the methods package interacts with the rest of R. The information is usually not needed to get started with methods and classes, but may be helpful for moderately ambitious projects, or when something doesn't work as expected.

The section How Methods Work describes the underlying mechanism; Class Inheritance and Method Selection provides more details on how class definitions determine which methods are used.

The section Changes with the Methods Package outlines possible effects on other computations when running with package methods.

How Methods Work

A generic function is a function that has associated with it a collection of other functions (the methods), all of which agree in formal arguments with the generic. In R, the “collection” is an object of class "MethodsList", which contains a named list of methods (the methods slot), and the name of one of the formal arguments to the function (the argument slot). The names of the methods are the names of classes, and the corresponding element defines the method or methods to be used if the corresponding argument has that class. For example, suppose a function f has formal arguments x and y. The methods list object for that function has the object as.name("x") as its argument slot. An element of the methods named "track" is selected if the actual argument corresponding to x is an object of class "track". If there is such an element, it can generally be either a function or another methods list object.

In the first case, the function defines the method to use for any call in which x is of class "track". In the second case, the new methods list object defines the selection of methods depending on the remaining formal arguments, in this example, y. The same selection process takes place, recursively, using the new methods list. Eventually, the selection returns either a function or NULL, meaning that no method matched the actual arguments.

Each method selected corresponds conceptually to a signature; that is a named list of classes, with names corresponding to some or all of the formal arguments. In the previous example, if selecting class "track" for x, finding that the selection was another methods list and then selecting class "numeric" for y would produce a method associated with the signature x = "track", y = "numeric".

The actual selection is done recursively, but you can see the methods arranged by signature by calling the function showMethods, and objects with the methods arranged this way (in two different forms) are returned by the functions listFromMlist and linearizeMlist.

In an R session, each generic function has a single methods list object defining all the currently available methods. The session methods list object is created the first time the function is called by merging all the relevant method definitions currently visible. Whenever something happens that might change the definitions (such as attaching or detaching a package with methods for this function, or explicitly defining or removing methods), the merged methods list object is removed. The next call to the function will recompute the merged definitions.

When methods list are merged, they can come from two sources:

Methods list objects for the same function anywhere on the current search list. These are merged so that methods in an environment earlier in the search list override methods for the same function later in the search list. A method overrides only another method for the same signature. See the comments on class "ANY" in the section on Inheritance.
Methods list objects corresponding the group generic functions, if any, for this function. Any generic function can be defined to belong to a group generic. The methods for the group generic are available as methods for this function. The group generic can itself be defined as belong to a group; as a result there is a list of group generic functions. A method defined for a function and a particular signature overrides a method for the same signature for that function's group generic.

Merging is done first on all methods for a particular function, and then over the generic and its group generics.

The result is a single methods list object that contains all the methods directly defined for this function. As calls to the function occur, this information may be supplemented by inherited methods, which we consider next.

Class Inheritance and Method Selection

If no method is found directly for the actual arguments in a call to a generic function, an attempt is made to match the available methods to the arguments by using inheritance.

Each class definition potentially includes the names of one or more classes that the new class extends. (These are sometimes called the superclasses of the new class.) These classes themselves may extend other classes. Putting all this information together produces the full list of superclasses for this class. (You can see this list for any class "A" from the expression extends("A").) In addition, any class implicitly extends class "ANY".

A method will be selected by inheritance if we can find a method in the methods list for a signature corresponding to any combination of superclasses for each of the relevant arguments. The search for such a method is performed by the function MethodsListSelect, working as follows.

For the first formal argument of the function, a list of classes is made up from the class itself, all its superclasses, and class "ANY". For each of these, the selection computation looks for an element of the methods with the corresponding name. Each time it finds one, it then calls the selection process recursively if necessary to select a method directly or by inheritance for the remaining arguments.

Each one of these recursive calls can fail or it can return a function (the method). As long as the calls fail, the selection process moves on to the next superclass and tries again. The last step corresponds to class "ANY", the default method defined at this level.

The effect of this definition of the selection process is to order all possible inherited methods, first by the superclasses for the first argument, then within this by the superclasses for the second argument, and so on. Superclasses are ordered by how direct they are: first, the direct superclasses, then the superclasses of these classes.

Changes with the Methods Package

The methods package is designed to leave other computations in R unchanged. There are, however, a few areas where the default functions and behavior are overridden when running with the methods package attached. This section outlines those known to have some possible effect.

class:

The methods package enforces the notion that every object has a class; in particular, class(x) is never NULL, as it would be for basic vectors, for example, when not using methods.

In addition, when assigning a class, the value is required to be a single string. (However, objects can have multiple class names if these were generated by old-style class computations. The methods package does not hide the “extra” class names.)

Computations using the notion of NULL class attributes or of class attributes with multiple class names are not really compatible with the ideas in the methods package. Formal classes and class inheritance are designed to give more flexible and reliable implementations of similar ideas.

If you do have to mix the two approaches, any operations that use class attributes in the old sense should be written in terms of attr(x, "class"), not class(x). In particular, test for no class having been assigned with is.null(attr(x, "class")).

Printing

To provide appropriate printing automatically for objects with formal class definitions, the methods package overrides print.default, to look for methods for the generic function show, and to use a default method for objects with formal class definitions.

The revised version of print.default is intended to produce identical printing to the original version for any object that does not have a formally defined class, including honoring old-style print methods. So far, no exceptions are known.

plot

A version of the plot function is included in the current methods package, differing from the one in the base package in that it has a y argument (necessary if methods for plot are to be defined for the y data; see the examples for setMethod). This version will move into base as soon as it is tested.

Author(s)

John Chambers

References

The web page http://www.omegahat.org/RSMethods/index.html is the primary documentation.

The functions in this package emulate the facility for classes and methods described in Programming with Data (John M. Chambers, Springer, 1998). See this book for further details and examples.