| Methods {methods} | R Documentation |
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; Dispatch and Method Selection provides more
details on how class definitions determine which methods are used.
For additional information specifically about class definitions, see ?Classes.
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.
Each R package will include methods metadata objects corresponding to each generic function for which methods have been defined in that package. When the package is loaded into an R session, the methods for each generic function are cached, that is, stored in the environment of the generic function along with the methods from previously loaded packages. This merged table of methods is used to dispatch or select methods from the generic, using class inheritance and possibly group generic functions to find an applicable method. See the Dispatch section below. The caching computations ensure that only one version of each generic function is visible globally; although different attached packages may contain a copy of the generic function, these are in fact identical.
The methods for a generic are stored according to the
corresponding signature for which the method was defined, in
a call to setMethod. The signature associates one
class name with each of a subset of the formal arguments to the
generic function. Which formal arguments are available, and the
order in which they appear, are determined by the "signature"
slot of the generic function. By default, the signature of the
generic consists of all the formal arguments except ..., in the
order they appear in the function definition.
Trailing arguments in the signature will be inactive if no method has yet been specified that included those arguments. Inactive arguments are not needed or used in labeling the cached methods. (The distinction does not change which methods are dispatched, but ignoring inactive arguments does improve the efficiency of dispatch. Thus, defining the generic signature to contain the most useful arguments first can help efficiency somewhat.)
All arguments in the signature of the generic function will be evaluated when the
function is called, rather than using the traditional lazy
evaluation rules of S. Therefore, it's important to exclude
from the signature any arguments that need to be dealt with
symbolically (such as the first argument to function
substitute). Note that only actual arguments are
evaluated, not default expressions.
A missing argument enters into the method selection as class
"missing" and non-missing arguments according to their actual
class.
As of version 2.4.0 of R, the cached methods are stored in an environment object. The names used for assignment are a concatenation of the class names for the arguments in the active signature.
When a call to a generic function is evaluated, a method is selected corresponding
to the classes of the actual arguments in the signature.
First, the cached methods table is searched for a direct match;
that is, a method stored under the direct class names.
The direct class is the value of class(x) for each non-missing
argument, and class "missing" for each missing argument.
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 contains. (These are sometimes called the
superclasses of the new class.)
The S language has an additional, explicit mechanism for defining superclasses, the
setIs mechanism.
Also, a call to setClassUnion makes the union class a
superclass of each of the members of the union.
All three mechanisms are treated equivalently for purposes of
inheritance: they define the direct superclasses of a
particular class.
The direct superclasses themselves may
contain other classes. Putting all this information together produces
the full list of superclasses for this class.
The superclass list is included in the definition of the class that is
cached during the R session.
Each element of the list describes the nature of the relationship (see
SClassExtension-class for details).
Included in the element is a distance slot giving a numeric
distance between the two classes.
The distance currently is the path length for the relationship:
1 for direct superclasses (regardless of which mechanism
defined them), then 2 for the direct superclasses of those
classes, and so on.
In addition, any class implicitly has class "ANY" as a superclass. The
distance to "ANY" is treated as larger than the distance to any
actual class.
The special class "missing" corresponding to missing arguments
has only "ANY" as a superclass, while "ANY" has no
superclasses.
The information about superclasses is summarized when a class definition is printed.
When a method is to be selected by inheritance, a search is made in
the table for all methods directly corresponding to a combination of
either the direct class or one of its superclasses, for each argument
in the active signature.
For an example, suppose there is only one argument in the signature and that the class of
the corresponding object was "dgeMatrix" (from the
Matrix package on CRAN).
This class has two direct superclasses and through these 4 additional superclasses.
Method selection finds all the methods in the table of directly
specified methods labeled by one of these classes, or by
"ANY".
When there are multiple arguments in the signature, each argument will
generate a similar list of inherited classes.
The possible matches are now all the combinations of classes from each
argument (think of the function outer generating an array of
all possible combinations).
The search now finds all the methods matching any of this combination
of classes.
The computation of distances also has to combine distances for the
individual arguments.
There are many ways to combine the distances; the current
implementation simply adds them.
The result of the search is then a list of zero, one or more methods,
and a parallel vector of distances between the target signature and
the available methods.
If the list has more than one matching method, only those corresponding to
the minimum distance are considered.
There may still be multiple best methods.
The dispatch software considers this an ambiguous case and warns the
user (only on the first call for this selection).
The method occurring first in the list of superclasses is selected. By the mechanism of producing
the extension information, this orders the direct superclasses by the
order they appeared in the original call to setClass,
followed by classes specified in setIs calls, in the
order those calls were evaluated, followed by classes specified in
unions.
Then the superclasses of those classes are appended (note that only
the ordering of classes within a particular generation of superclasses
counts, because only these will have the same distance).
For further discussion of method selection, see the document http://developer.r-project.org/howMethodsWork.pdf.
All this detail about selection is less important than the realization that having ambiguous method selection usually means that you need to be more specific about intentions. It is likely that some consideration other than the ordering of superclasses in the class definition is more important in determining which method should be selected, and the preference may well be different for different generic functions. Where ambiguities arise, the best approach is usually to provide a specific method for the subclass.
When the inherited method has been selected, the selection is cached in the generic function so that future calls with the same class will not require repeating the search. Cached non-direct selections are not themselves used in inheritance searches, since that could result in invalid selections.
Besides being initiated through calls to the generic function, method
selection can be done explicitly by calling the function selectMethod.
The R package methods implements, with a few exceptions, the programming interface for classes and methods in the book Programming with Data (John M. Chambers, Springer, 1998), in particular sections 1.6, 2.7, 2.8, and chapters 7 and 8.
While the programming interface for the methods package follows the reference, the R software is an original implementation, so details in the reference that reflect the S4 implementation may appear differently in R. Also, there are extensions to the programming interface developed more recently than the reference.
setGeneric,
setClass
and the document http://developer.r-project.org/howMethodsWork.pdf.