setGeneric {methods} | R Documentation |
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.
setGeneric(name, def= , group=list(), valueClass=character(),
where= , package= , signature= , useAsDefault= ,
genericFunction= , simpleInheritanceOnly = )
setGroupGeneric(name, def= , group=list(), valueClass=character(),
knownMembers=list(), package= , where= )
name |
The character string name of the generic function.
The simplest (and recommended) call, |
def |
An optional function object, defining the generic.
Don't supply this argument if you want an existing non-generic
function to supply the arguments. Do supply it if there is
no current function of this name, or if you want the generic
function to have different arguments. In that case, the formal arguments
and default values for the generic are taken from Note that |
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
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 (an existing
non-generic function or no default if there is no such function).
Argument |
simpleInheritanceOnly |
Supply this argument as |
genericFunction |
Don't use; for (possible) internal use only. |
knownMembers |
(For |
The setGeneric
function exists for its side effect: saving the
generic function to allow methods to be specified later. It returns
name
.
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).
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.
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.
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.
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 %*%
.
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.)
Methods
and the links there for a general discussion,
dotsMethods
for methods that dispatch on
“...”, and setMethod
for method definitions.
## create a new generic function, with a default method
props <- function(object) attributes(object)
setGeneric("props")
## 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 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