Methods package:methods R Documentation _G_e_n_e_r_a_l _I_n_f_o_r_m_a_t_i_o_n _o_n _M_e_t_h_o_d_s _D_e_s_c_r_i_p_t_i_o_n: 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; "S3 Methods" gives the rules applied when S4 classes and methods interact with older S3 methods; "Method Selection and Dispatch" provides more details on how class definitions determine which methods are used; "Generic Functions" discusses generic functions as objects. For additional information specifically about class definitions, see 'Classes'. _H_o_w _M_e_t_h_o_d_s _W_o_r_k: A generic function has associated with it a collection of other functions (the methods), all of which have the same formal arguments as the generic. See the "Generic Functions" section below for more on generic functions themselves. 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 (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 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"'. 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. _S_3 _M_e_t_h_o_d_s: The functions for which S4 methods will be written often include some for which S3 methods exist, corresponding to S3 classes for the first formal argument of an S3 generic function or of a primitive function, or for either of the arguments in a call to one of the primitive binary operators. In the case of true functions, S3 methods will be dispatched by the original version of the function. The usual way this happens is by the function becoming the default method for the S4 generic, implicitly by a call to 'setMethod' or explicitly by the call 'setGeneric("f")' where the original 'f()' contained the call 'UseMethod("f")'. The S4 method selection code matches the classes of the arguments as described in the previous section. Matching will be applied for the class of S3 objects as well as S4 objects, but only the first string in an S3 class attribute is used. If no non-default S4 method matches the call, the default S4 method can then operate as an S3 generic to select S3 methods for 'f()'. Primitive functions and operators dispatch both S4 and S3 methods from the internal C code. The method selection mechanism works essentially the same way, with two exceptions. There is no explicit generic function, either S3 or S4, meaning that the selection of an S3 method if no S4 method is found is built in and not a result of an explicit default method. Also, the internal code does not look for S4 methods unless the first argument or one of the arguments to an operator is an S4 object. S4 methods can be defined for an S3 generic function and an S3 class. But if the function is a primitive, such methods will not be selected if the object in question is not an S4 object. In the examples below, for instance, an S4 method for signature '"data.frame"' for function 'f3()' would be called for the S3 object 'df1'. A similar S4 method for primitive function '`[`' would be ignored for that object, but would be called for the S4 object 'mydf1' that inherits from '"data.frame"'. It's an unfortunate inconsistency, but enforced by the passion for efficiency in dispatching methods for primitives. The common case is that objects from S4 classes will use S4 methods, except when the function's default definition is wanted. For example, if an S4 class extends one of the basic object types the base code for that type may do what we want. Objects not from an S4 class will continue to follow S3 method selection. The rest of this section describes S3 method selection in two special cases. In one case, the S4 class contains an S3 class (and has ensured that objects have all the structure needed for the S3 class). In the second case, S3 methods have been written for an S4 class; that is, a function _f.class_, where _f_ is an S3 generic function and _class_ is the name of an S4 class, other than a registered S3 class. The first case is now supported and recommended, the second case is discouraged, but occasionally needed (see section 4 of the paper in the references). The following rules define selection of an S3 method for an S4 object. S4 objects are defined internally by a bit in the C structure. In practice, any object generated from an S4 class will be an S4 object, as well as the result of most computations on such objects. Older computations defined for non-S4 classes or object types may or may not return S4 objects when the arguments are such objects. An S3 method will be selected applying the following criteria in order: 1. the _class_ for the method matches the name of the S4 class exactly; 2. the object has a slot '".S3Class"' and _class_ is selected by S3 inheritance, treating that slot as the S3 class of the object; The second criterion will apply if either the S4 class contains an S3 class or the argument 'S3methods=TRUE' was given to 'setClass' for the class of the object or for one of its superclasses. If an S4 class extends an S3 class, and if no S4 methods take precedence, we expect that the correct S3 method for the inherited S3 class will be chosen. This will happen, so long as the S3 class has been registered by a call to 'setOldClass'. If so, the object from the S4 class will inherit a special slot that will be used as the class for S3 dispatch. Effectively, this slot is a proxy for the class attribute expected by S3 dispatch. It can even vary in its inheritance between objects, as happens with some S3 classes, such as 'POSIXt', if the replacement version of 'S3Class' is used to set it. If the class so selected is one of the basic S3 classes, the object is converted to an S3 object with this vector as its class attribute. A second nonstandard situation arises when an S3 method has been explicitly written for an S4 class. Versions of R through 2.9.0 did not recognize S4 inheritance in dispatching S3 methods, so that subclasses of the S4 class would not then inherit the S3 method. The version of R{} accompanying this documentation fixes this problem, to the extent practical, as follows. S3 method selection will resemble S4 selection for the same class _if_ the call to 'setClass' has included the argument 'S3methods = TRUE'. If not, the current behavior (R 2.9.1) is to select S3 methods defined for this class, but not for its subclasses (largely for back compatibility; in future versions of R, S3 methods may be ignored for S4 classes unless 'S3methods' is set.) The implementation uses the same special slot as above for inheriting from an S3 class. Subclasses of a class set this way will inherit the same special slot and the same S3 method selection. It's even possible to set the slot in individual objects, as above, but the possibilities for confusion are serious. Looking in the other direction, it remains true that S4 selection has no knowledge of S3 methods. This can cause problems when a class that expects to inherit the S3 method, '"classA"' in the example below, also inherits from another S4 class. If that class inherits an S4 method for a function, no matter how indirectly, that S4 method will be selected for an object from '"classA"', even though there is a directly defined S3 method. The S3 method can only be accessed through the default S4 method. These problems are relatively unlikely to occur, but anyone defining a class that extends both S3 and S4 classes needs to be careful. _M_e_t_h_o_d _S_e_l_e_c_t_i_o_n _a_n_d _D_i_s_p_a_t_c_h: _D_e_t_a_i_l_s: 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. Each class definition may include a list of one or more _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. The S language has two additional mechanisms for defining superclasses. A call to 'setIs' can create an inheritance relationship that is not the simple one of containing the superclass representation in the new class. In this case, explicit methods are defined to relate the subclass and the superclass. Also, a call to 'setClassUnion' creates a union class that is a superclass of each of the members of the union. All three mechanisms are treated equivalently for purposes of method selection: they define the _direct_ superclasses of a particular class. For more details on the mechanisms, see 'Classes'. The direct superclasses themselves may have superclasses, defined by any of the same mechanisms, and similarly for 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. Each element of the list describes the nature of the relationship (see 'SClassExtension' for details). Included in the element is a 'distance' slot giving a numeric distance between the two classes. The distance 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. When a class definition is created or modified, the superclasses are ordered, first by a stable sort of the all superclasses by distance. If the set of superclasses has duplicates (that is, if some class is inherited through more than one relationship), these are removed, if possible, so that the list of superclasses is consistent with the superclasses of all direct superclasses. See the reference on inheritance for details. 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 recommended package 'Matrix'). 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. For each argument, the position in the list of superclasses of that argument's class defines which method or methods (if the same class appears more than once) match best. When there is only one argument, the best match is unambiguous. With more than one argument, there may be zero or one match that is among the best matches for _all_ arguments. If there is no best match, the selection is ambiguous and a message is printed noting which method was selected (the first method lexicographicaly 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'. 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 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'. 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 first reference. _G_e_n_e_r_i_c _F_u_n_c_t_i_o_n_s: 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 first reference and also section 2 of _R Internals_. _M_e_t_h_o_d _D_e_f_i_n_i_t_i_o_n_s: 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. _R_e_f_e_r_e_n_c_e_s: Chambers, John M. (2008) _Software for Data Analysis: Programming with R_ Springer. (For the R version: see section 10.6 for method selection and section 10.5 for generic functions). Chambers, John M.(2009) _Developments in Class Inheritance and Method Selection_ . Chambers, John M. (1998) _Programming with Data_ Springer (For the original S4 version.) _S_e_e _A_l_s_o: For more specific information, see 'setGeneric', 'setMethod', and 'setClass'. For the use of ... in methods, see dotsMethods. _E_x_a_m_p_l_e_s: ## The rules for inheriting S3 methods. f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate inheritance ## A class that extends a registered S3 class inherits that class' S3 ## methods. The S3 methods will be passed an object with the S3 class setClass("myFrame", contains = "data.frame", representation(date = "POSIXt", type = "character")) df1 <- data.frame(x = 1:10, y = rnorm(10), z = sample(letters,10)) mydf1 <- new("myFrame", df1, date = Sys.time()) ## "myFrame" objects inherit "data.frame" S3 methods; e.g., for `[` mydf1[1:2, ] # a data frame object (with extra attributes "date" and "type") ## Extending an S3 class with inconsistent (instance-based) inheritance setClass("myDateTime", contains = "POSIXt") now <- Sys.time() # class(now) is c("POSIXt", "POSIXct") nowLt <- as.POSIXlt(now)# class(nowLt) is c("POSIXt", "POSIXlt") mCt <- new("myDateTime", now) mLt <- new("myDateTime", nowLt) ## S3 methods will be selected using instance-based information f3.POSIXct <- function(x) "The POSIXct result" f3.POSIXlt <- function(x) "The POSIXlt result" stopifnot(identical(f3(mCt), f3.POSIXct(mCt))) stopifnot(identical(f3(mLt), f3.POSIXlt(mLt))) ## An S4 class that does not contain a registered S3 class or object type ## selects S3 methods according to its S4 "inheritance" ## but only if the class definition requests this via S3methods=TRUE ## ( from version 2.9.1 on) setClass("classA", contains = "numeric", representation(realData = "numeric"), S3methods = TRUE) Math.classA <- function(x) {(getFunction(.Generic))(x@realData)} x <- new("classA", log(1:10), realData = 1:10) stopifnot(identical(abs(x), 1:10)) setClass("classB", contains = "classA") y <- new("classB", x) stopifnot(identical(abs(y), 1:10)) # (version 2.9.0 or earlier fails here) ## Note: with a class that tries to combine both S3 and S4 superclasses. ## The S3 inheritance is used and the S3 method for ## the S4 superclass will not be selected. setClass("classC", representation(x = "numeric")) # an S3 method for "[" (not a good idea, but it would work) `[.classc` <- function(x, ..., drop = TRUE) {x@x[...]} setClass("classD", contains = c("classC", "data.frame")) ## by the rule mentioned in the S3 method section, the ## S3 methods are selected from the S3 class defined; that is, "data.frame" ## If the user expected to inherit `[.classC`, no luck. xd <- new("classD", df1, x = 1:50) ## Note the error from `[.data.frame` try(xd[1:25])