setGeneric {methods}R Documentation

Define a New Generic Function

Description

Create a new generic function of the given name, that is, a function that dispatches methods according to the classes of the arguments, from among the formal methods defined for this function.

Usage

setGeneric(name, def= , group=list(), valueClass=character(),
           where= , package= , signature= , useAsDefault= ,
           genericFunction= , simpleInheritanceOnly = )

setGroupGeneric(name, def= , group=list(), valueClass=character(),
                knownMembers=list(), package= , where= )

Arguments

name

The character string name of the generic function. The simplest (and recommended) call, setGeneric(name), looks for a function with this name and creates a corresponding generic function, if the function found was not generic. In the latter case, the existing function becomes the default method.

def

An optional function object, defining the generic. Don't supply this argument if you want to turn an existing non-generic function into a generic. In this case, you usually want to use the simple call with one argument.

Do supply def if there is no current function of this name or for some reason you do not want to use that function to define the generic. In that case, the formal arguments and default values for the generic are taken from def. In most cases, the body of def will then define the default method, as the existing function did in the one-argument call.

If you want to create a new generic function with no default method, then def should be only a call to standardGeneric with the same character string as name.

group

Optionally, a character string giving the name of the group generic function to which this function belongs. See Methods for details of group generic functions in method selection.

valueClass

An optional character vector of one or more class names. The value returned by the generic function must have (or extend) this class, or one of the classes; otherwise, an error is generated.

package

The name of the package with which this function is associated. Usually determined automatically (as the package containing the non-generic version if there is one, or else the package where this generic is to be saved).

where

Where to store the resulting initial methods definition, and possibly the generic function; by default, stored into the top-level environment.

signature

Optionally, the vector of names, from among the formal arguments to the function, that can appear in the signature of methods for this function, in calls to setMethod. If ... is one of the formal arguments, it is treated specially. Starting with version 2.8.0 of R, ... may be signature of the generic function. Methods will then be selected if their signature matches all the ... arguments. See the documentation for topic dotsMethods for details. In the present version, it is not possible to mix ... and other arguments in the signature (this restriction may be lifted in later versions).

By default, the signature is inferred from the implicit generic function corresponding to a non-generic function. If no implicit generic function has been defined, the default is all the formal arguments except ..., in the order they appear in the function definition. In the case that ... is the only formal argument, that is also the default signature. To use ... as the signature in a function that has any other arguments, you must supply the signature argument explicitly. See the “Implicit Generic” section below for more details.

useAsDefault

Override the usual choice of default argument. Argument useAsDefault can be supplied, either as a function to use for the default, or as a logical value. This argument is now rarely needed. See the section on details.

simpleInheritanceOnly

Supply this argument as TRUE to require that methods selected be inherited through simple inheritance only; that is, from superclasses specified in the contains= argument to setClass, or by simple inheritance to a class union or other virtual class. Generic functions should require simple inheritance if they need to be assured that they get the complete original object, not one that has been transformed. Examples of functions requiring simple inheritance are initialize, because by definition it must return an object from the same class as its argument, and show, because it claims to give a full description of the object provided as its argument.

genericFunction

Don't use; for (possible) internal use only.

knownMembers

(For setGroupGeneric only.) The names of functions that are known to be members of this group. This information is used to reset cached definitions of the member generics when information about the group generic is changed.

Value

The setGeneric function exists for its side effect: saving the generic function to allow methods to be specified later. It returns name.

Basic Use

The setGeneric function is called to initialize a generic function as preparation for defining some methods for that function.

The simplest and most common situation is that name is already an ordinary non-generic non-primitive function, and you now want to turn this function into a generic. In this case you will most often supply only name, for example:

setGeneric("colSums")

There must be an existing function of this name, on some attached package (in this case package "base"). A generic version of this function will be created in the current package (or in the global environment if the call to setGeneric() is from an ordinary source file or is entered on the command line). The existing function becomes the default method, and the package slot of the new generic function is set to the location of the original function ("base" in the example). It's an important feature that the same generic function definition is created each time, depending in the example only on the definition of print and where it is found. The signature of the generic function, defining which of the formal arguments can be used in specifying methods, is set by default to all the formal arguments except ....

Note that calling setGeneric() in this form is not strictly necessary before calling setMethod() for the same function. If the function specified in the call to setMethod is not generic, setMethod will execute the call to setGeneric itself. Declaring explicitly that you want the function to be generic can be considered better programming style; the only difference in the result, however, is that not doing so produces a message noting the creation of the generic function.

You cannot (and never need to) create an explicit generic version of the primitive functions in the base package. Those which can be treated as generic functions have methods selected and dispatched from the internal C code, to satisfy concerns for efficiency, and the others cannot be made generic. See the section on Primitive Functions below.

The description above is the effect when the package that owns the non-generic function has not created an implicit generic version. Otherwise, it is this implicit generic function that is used. See the section on Implicit Generic Functions below. Either way, the essential result is that the same version of the generic function will be created each time.

The second common use of setGeneric() is to create a new generic function, unrelated to any existing function, and frequently having no default method. In this case, you need to supply a skeleton of the function definition, to define the arguments for the function. The body of a generic function is usually a standard form, standardGeneric(name) where name is the quoted name of the generic function. When calling setGeneric in this form, you would normally supply the def argument as a function of this form. See the second and third examples below.

The useAsDefault argument controls the default method for the new generic. If not told otherwise, setGeneric will try to find a non-generic version of the function to use as a default. So, if you do have a suitable default method, it is often simpler to first set this up as a non-generic function, and then use the one-argument call to setGeneric at the beginning of this section. See the first example in the Examples section below.

If you don't want the existing function to be taken as default, supply the argument useAsDefault. That argument can be the function you want to be the default method, or FALSE to force no default (i.e., to cause an error if there is no direct or inherited method selected for a call to the function).

Details

The great majority of calls to setGeneric() should either have one argument to ensure that an existing function can have methods, or arguments name and def to create a new generic function and optionally a default method. If that's not what you plan to do, read on.

If you want to change the behavior of an existing function (typically, one in another package) when you create a generic version, you must supply arguments to setGeneric correspondingly. Whatever changes are made, the new generic function will be assigned with a package slot set to the current package, not the one in which the non-generic version of the function is found. This step is required because the version you are creating is no longer the same as that implied by the function in the other package. A message will be printed to indicate that this has taken place and noting one of the differences between the two functions. It tends to be a bad idea, because the two versions are now competing for methods, with many chances for mistakes in programming.

The body of a generic function usually does nothing except for dispatching methods by a call to standardGeneric. Under some circumstances you might just want to do some additional computation in the generic function itself. As long as your function eventually calls standardGeneric that is permissible (though perhaps not a good idea, in that it may make the behavior of your function less easy to understand). If your explicit definition of the generic function does not call standardGeneric you are in trouble, because none of the methods for the function will ever be dispatched.

By default, the generic function can return any object. If valueClass is supplied, it should be a vector of class names; the value returned by a method is then required to satisfy is(object, Class) for one of the specified classes. An empty (i.e., zero length) vector of classes means anything is allowed. Note that more complicated requirements on the result can be specified explicitly, by defining a non-standard generic function.

The setGroupGeneric function behaves like setGeneric except that it constructs a group generic function, differing in two ways from an ordinary generic function. First, this function cannot be called directly, and the body of the function created will contain a stop call with this information. Second, the group generic function contains information about the known members of the group, used to keep the members up to date when the group definition changes, through changes in the search list or direct specification of methods, etc.

Implicit Generic Functions

Saying that a non-generic function “is converted to a generic” is more precisely state that the function is converted to the corresponding implicit generic function. If no special action has been taken, any function corresponds implicitly to a generic function with the same arguments, in which all arguments other than ... can be used. The signature of this generic function is the vector of formal arguments, in order, except for ....

The source code for a package can define an implicit generic function version of any function in that package (see implicitGeneric for the mechanism). You can not, generally, define an implicit generic function in someone else's package. The usual reason for defining an implicit generic is to prevent certain arguments from appearing in the signature, which you must do if you want the arguments to be used literally or if you want to enforce lazy evaluation for any reason. An implicit generic can also contain some methods that you want to be predefined; in fact, the implicit generic can be any generic version of the non-generic function. The implicit generic mechanism can also be used to prohibit a generic version (see prohibitGeneric).

Whether defined or inferred automatically, the implicit generic will be compared with the generic function that setGeneric creates, when the implicit generic is in another package. If the two functions are identical, then the package slot of the created generic will have the name of the package containing the implicit generic. Otherwise, the slot will be the name of the package in which the generic is assigned.

The purpose of this rule is to ensure that all methods defined for a particular combination of generic function and package names correspond to a single, consistent version of the generic function. Calling setGeneric with only name and possibly package as arguments guarantees getting the implicit generic version, if one exists.

Including any of the other arguments can force a new, local version of the generic function. If you don't want to create a new version, don't use the extra arguments.

Generic Functions and Primitive Functions

A number of the basic R functions are specially implemented as primitive functions, to be evaluated directly in the underlying C code rather than by evaluating an R language definition. Most have implicit generics (see implicitGeneric), and become generic as soon as methods (including group methods) are defined on them. Others cannot be made generic.

Even when methods are defined for such functions, the generic version is not visible on the search list, in order that the C version continues to be called. Method selection will be initiated in the C code. Note, however, that the result is to restrict methods for primitive functions to signatures in which at least one of the classes in the signature is a formal S4 class.

To see the generic version of a primitive function, use getGeneric(name). The function isGeneric will tell you whether methods are defined for the function in the current session.

Note that S4 methods can only be set on those primitives which are ‘internal generic’, plus %*%.

References

Chambers, John M. (2008) Software for Data Analysis: Programming with R Springer. (For the R version.)

Chambers, John M. (1998) Programming with Data Springer (For the original S4 version.)

See Also

Methods and the links there for a general discussion, dotsMethods for methods that dispatch on “...”, and setMethod for method definitions.

Examples



## create a new generic function, with a default method
setGeneric("props", function(object) attributes(object))

## A new generic function with no default method
setGeneric("increment",
  function(object, step, ...)
    standardGeneric("increment")
)


###   A non-standard generic function.  It insists that the methods
###   return a non-empty character vector (a stronger requirement than
###    valueClass = "character" in the call to setGeneric)

setGeneric("authorNames",
    function(text) {
      value <- standardGeneric("authorNames")
      if(!(is(value, "character") && any(nchar(value)>0)))
        stop("authorNames methods must return non-empty strings")
      value
      })



## An example of group generic methods, using the class
## "track"; see the documentation of \link{setClass} for its definition

## define a method for the Arith group

setMethod("Arith", c("track", "numeric"),
 function(e1, e2) {
  e1@y <- callGeneric(e1@y , e2)
  e1
})

setMethod("Arith", c("numeric", "track"),
 function(e1, e2) {
  e2@y <- callGeneric(e1, e2@y)
  e2
})

## now arithmetic operators  will dispatch methods:

t1 <- new("track", x=1:10, y=sort(stats::rnorm(10)))

t1 - 100
1/t1



[Package methods version 2.15.3 Index]