Methods_Details - R Documentation

`Methods_Details` General Information on Methods

Description

This documentation 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.

For additional information see documentation for the important steps: (setMethod(), setClass() and setGeneric()). Also Methods_for_Nongenerics on defining formal methods for functions that are not currently generic functions; Methods_for_S3 for the relation to S3 classes and methods; Classes_Details for class definitions and Chapters 9 and 10 of the reference.

How Methods Work

A call to a generic function selects a method matching the actual arguments in the call. The body of the method is evaluated in the frame of the call to the generic function. A generic function is identified by its name and by the package to which it correspond. Unlike ordinary functions, the generic has a slot that specifies its package.

In an R session, there is one version of each such generic, regardless of where the call to that generic originated, and the generic function has a table of all the methods currently available for it; that is, all the methods in packages currently loaded into the session.

Methods are frequently defined for functions that are non-generic in their original package,. for example, for function plot() in package graphics. An identical version of the corresponding generic function may exist in several packages. All methods will be dispatched consistently from the R session.

Each R package with a call to setMethod in its source code will include a methods metadata object for that generic. When the package is loaded into an R session, the methods for each generic function are cached, that is, added to the environment of the generic function. This merged table of methods is used to dispatch or select methods from the generic, using class inheritance and possibly group generic functions (see GroupGenericFunctions) to find an applicable method. See the “Method Selection and 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 behave identically with respect to method selection.

In contrast, it is possible for the same function name to refer to more than one generic function, when these have different package slots. In the latter case, R considers the functions unrelated: A generic function is defined by the combination of name and package. See the “Generic Functions” section below.

The methods for a generic are stored according to the corresponding signature in the call to setMethod that defined the method. 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 itself. 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 of the generic will be inactive if no method has yet been specified that included those arguments in its signature. 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 improves the efficiency of dispatch.)

All arguments in the signature of the generic function will be evaluated when the function is called, rather than using lazy evaluation. Therefore, it's important to exclude from the signature any arguments that need to be dealt with symbolically (such as the expr argument to function with). Note that only actual arguments are evaluated, not default expressions. A missing argument enters into the method selection as class "missing".

The cached methods are stored in an environment object. The names used for assignment are a concatenation of the class names for the active arguments in the method signature.

Method Selection: Details

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 an exact match; that is, a method stored under the signature defined by the string value of class(x) for each non-missing argument, and "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 the superclass information about the actual classes. A method found by this search is cached in the generic function so that future calls with the same argument classes will not require repeating the search. In any likely application, the search for inherited methods will be a negligible overhead.

Each class definition may include a list of one or more direct superclasses of the new class. The simplest and most common specification is by the contains= argument in the call to setClass. Each class named in this argument is a superclass of the new class. A class will also have as a direct superclass any class union to which it is a member. Class unions are created by a call to setClassUnion. Additional members can be added to the union by a simple call to setIs. Superclasses specified by either mechanism are the direct superclasses.

Inheritance specified in either of these forms is simple in the sense that all the information needed for the superclass is asserted to be directly available from the object. R inherited from S a more general form of inheritance in which inheritance may require some transformation or be conditional on a test. This more general form has not proved to be useful in general practical situations. Since it also adds some computational costs non-simple inheritance is not recommended. See setIs for the general version.

The direct superclasses themselves may have direct superclasses and similarly through further generations. 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. The distance between the two classes is defined to be the number of generations: 1 for direct superclasses (regardless of which mechanism defined them), then 2 for the direct superclasses of those classes, and so on. To see all the superclasses, with their distance, print the class definition by calling getClass. 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.

When a method is to be selected by inheritance, a search is made in the table for all methods 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 recommended package Matrix). This class has (currently) three direct superclasses and through these additional superclasses at distances 2 through 4. A method that had been defined for any of these classes or for class "ANY" (the default method) would be eligible. Methods for the shortest difference are preferred. If there is only one best method in this sense, method selection is unambiguous.

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. For each argument, the distance to the superclass defines which method(s) are preferred for that argument. A method is considered best for selection if it is among the best (i.e., has the least distance) for each argument.

The end result is that zero, one or more methods may be “best”. If one, this method is selected and cached in the table of methods. If there is more than one best match, the selection is ambiguous and a message is printed noting which method was selected (the first method lexicographically in the ordering) and what other methods could have been selected. Since the ambiguity is usually nothing the end user could control, this is not a warning. Package authors should examine their package for possible ambiguous inheritance by calling testInheritedMethods.

Cached inherited selections are not themselves used in future inheritance searches, since that could result in invalid selections. If you want inheritance computations to be done again (for example, because a newly loaded package has a more direct method than one that has already been used in this session), call resetGeneric. Because classes and methods involving them tend to come from the same package, the current implementation does not reset all generics every time a new package is loaded.

Besides being initiated through calls to the generic function, method selection can be done explicitly by calling the function selectMethod. Note that some computations may use this function directly, with optional arguments. The prime example is the use of coerce() methods by function as(). There has been some confusion from comparing coerce methods to a call to selectMethod with other options.

Method Evaluation: Details

Once a method has been selected, the evaluator creates a new context in which a call to the method is evaluated. The context is initialized with the arguments from the call to the generic function. These arguments are not rematched. All the arguments in the signature of the generic will have been evaluated (including any that are currently inactive); arguments that are not in the signature will obey the usual lazy evaluation rules of the language. If an argument was missing in the call, its default expression if any will not have been evaluated, since method dispatch always uses class missing for such arguments.

A call to a generic function therefore has two contexts: one for the function and a second for the method. The argument objects will be copied to the second context, but not any local objects created in a nonstandard generic function. The other important distinction is that the parent (“enclosing”) environment of the second context is the environment of the method as a function, so that all R programming techniques using such environments apply to method definitions as ordinary functions.

For further discussion of method selection and dispatch, see the references in the sections indicated.

Generic Functions

In principle, a generic function could be any function that evaluates a call to standardGeneric(), the internal function that selects a method and evaluates a call to the selected method. In practice, generic functions are special objects that in addition to being from a subclass of class "function" also extend the class genericFunction. Such objects have slots to define information needed to deal with their methods. They also have specialized environments, containing the tables used in method selection.

The slots "generic" and "package" in the object are the character string names of the generic function itself and of the package from which the function is defined. As with classes, generic functions are uniquely defined in R by the combination of the two names. There can be generic functions of the same name associated with different packages (although inevitably keeping such functions cleanly distinguished is not always easy). On the other hand, R will enforce that only one definition of a generic function can be associated with a particular combination of function and package name, in the current session or other active version of R.

Tables of methods for a particular generic function, in this sense, will often be spread over several other packages. The total set of methods for a given generic function may change during a session, as additional packages are loaded. Each table must be consistent in the signature assumed for the generic function.

R distinguishes standard and nonstandard generic functions, with the former having a function body that does nothing but dispatch a method. For the most part, the distinction is just one of simplicity: knowing that a generic function only dispatches a method call allows some efficiencies and also removes some uncertainties.

In most cases, the generic function is the visible function corresponding to that name, in the corresponding package. There are two exceptions, implicit generic functions and the special computations required to deal with R's primitive functions. Packages can contain a table of implicit generic versions of functions in the package, if the package wishes to leave a function non-generic but to constrain what the function would be like if it were generic. Such implicit generic functions are created during the installation of the package, essentially by defining the generic function and possibly methods for it, and then reverting the function to its non-generic form. (See implicitGeneric for how this is done.) The mechanism is mainly used for functions in the older packages in R, which may prefer to ignore S4 methods. Even in this case, the actual mechanism is only needed if something special has to be specified. All functions have a corresponding implicit generic version defined automatically (an implicit, implicit generic function one might say). This function is a standard generic with the same arguments as the non-generic function, with the non-generic version as the default (and only) method, and with the generic signature being all the formal arguments except ....

The implicit generic mechanism is needed only to override some aspect of the default definition. One reason to do so would be to remove some arguments from the signature. Arguments that may need to be interpreted literally, or for which the lazy evaluation mechanism of the language is needed, must not be included in the signature of the generic function, since all arguments in the signature will be evaluated in order to select a method. For example, the argument expr to the function with is treated literally and must therefore be excluded from the signature.

One would also need to define an implicit generic if the existing non-generic function were not suitable as the default method. Perhaps the function only applies to some classes of objects, and the package designer prefers to have no general default method. In the other direction, the package designer might have some ideas about suitable methods for some classes, if the function were generic. With reasonably modern packages, the simple approach in all these cases is just to define the function as a generic. The implicit generic mechanism is mainly attractive for older packages that do not want to require the methods package to be available.

Generic functions will also be defined but not obviously visible for functions implemented as primitive functions in the base package. Primitive functions look like ordinary functions when printed but are in fact not function objects but objects of two types interpreted by the R evaluator to call underlying C code directly. Since their entire justification is efficiency, R refuses to hide primitives behind a generic function object. Methods may be defined for most primitives, and corresponding metadata objects will be created to store them. Calls to the primitive still go directly to the C code, which will sometimes check for applicable methods. The definition of “sometimes” is that methods must have been detected for the function in some package loaded in the session and isS4(x) is TRUE for the first argument (or for the second argument, in the case of binary operators). You can test whether methods have been detected by calling isGeneric for the relevant function and you can examine the generic function by calling getGeneric, whether or not methods have been detected. For more on generic functions, see the references and also section 2 of the R Internals document supplied with R.

Method Definitions

All method definitions are stored as objects from the MethodDefinition class. Like the class of generic functions, this class extends ordinary R functions with some additional slots: "generic", containing the name and package of the generic function, and two signature slots, "defined" and "target", the first being the signature supplied when the method was defined by a call to setMethod. The "target" slot starts off equal to the "defined" slot. When an inherited method is cached after being selected, as described above, a copy is made with the appropriate "target" signature. Output from showMethods, for example, includes both signatures.

Method definitions are required to have the same formal arguments as the generic function, since the method dispatch mechanism does not rematch arguments, for reasons of both efficiency and consistency.

References

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

Chambers, John M. (2008) Software for Data Analysis: Programming with R Springer. (Section 10.5 for some details.)

Methods_Details General Information on Methods