setClass {methods}R Documentation

Create a Class Definition

Description

Create a class definition, specifying the representation (the slots) and/or the classes contained in this one (the superclasses), plus other optional details. As a side effect, the class definition is stored in the specified environment. A generator function is returned as the value of setClass(), suitable for creating objects from the class if the class is not virtual. Of the many arguments to the function only Class, slots= and contains= are usually needed.

Usage

setClass(Class, representation, prototype, contains=character(),
         validity, access, where, version, sealed, package,
         S3methods = FALSE, slots)

Arguments

Class

character string name for the class.

slots

a named list or named character vector. The names are the names of the slots in the new class and the elements are the character string names of the corresponding classes.

In rare cases where there is ambiguity about the class of a slot, because two classes of the same name are imported from different packages, the corresponding element of the argument must have a "package" attribute to disambiguate the choice.

It is allowed to provide an unnamed character vector as a limiting case, with the elements taken as slot names and all slots having the unrestricted class "ANY".

contains

the names (and optionally package slots) for the superclasses of this class. The special superclass "VIRTUAL" causes the new class to be created as a virtual class; see the section on virtual classes in Classes.

prototype

an object providing the default data for the slots in this class. By default, each will be the prototype object for the superclass. If provided, using a call to prototype will carry out some checks.

where

the environment in which to store the definition. Should not be supplied in standard use. For calls to setClass() appearing in the source code for a package, will default to the namespace of the package. For calls typed or sourced at the top level in a session, will default to the global environment.

validity

if supplied, should be a validity-checking method for objects from this class (a function that returns TRUE if its argument is a valid object of this class and one or more strings describing the failures otherwise). See validObject for details.

S3methods, representation, access, version

All these arguments are deprecated from version 3.0.0 of R and should be avoided.

S3methods is a flag indicating that old-style methods will be written involving this class. Modern versions of R attempt to match formal and old-style methods consistently, so this argument is largely irrelevant.

representation is an argument inherited from S that included both slots and contains, but the use of the latter two arguments is clearer and recommended.

access and version are included for historical compatibility with S-Plus, but ignored.

sealed

if TRUE, the class definition will be sealed, so that another call to setClass will fail on this class name.

package

an optional package name for the class. Should very rarely be used. By default the name of the package in which the class definition is assigned.

Value

A generator function suitable for creating objects from the class is returned, invisibly. A call to this function generates a call to new for the class. The call takes any number of arguments, which will be passed on to the initialize method. If no initialize method is defined for the class or one of its superclasses, the default method expects named arguments with the name of one of the slots.

Typically the generator function is assigned the name of the class, for programming clarity. This is not a requirement and objects from the class can also be generated directly from new. The advantages of the generator function are a slightly simpler and clearer call, and that the call will contain the package name of the class (eliminating any ambiguity if two classes from different packages have the same name).

If the class is virtual, an attempt to generate an object from either the generator or new() will result in an error.

Basic Use: Slots and Inheritance

The two essential arguments other than the class name are slots and contains, defining the explicit slots and the inheritance (superclasses). Together, these arguments define all the information in an object from this class; that is, the names of all the slots and the classes required for each of them.

The name of the class determines which methods apply directly to objects from this class. The inheritance information specifies which methods apply indirectly, through inheritance. See Methods.

The slots in a class definition will be the union of all the slots specified directly by slots and all the slots in all the contained classes. There can only be one slot with a given name; specifically, the direct and inherited slot names must be unique. That does not, however, prevent the same class from being inherited via more than one path.

One kind of element in the contains= argument is special, specifying one of the R object types or one of a few other special R types (matrix and array). See the section on inheriting from object types, below.

Slot names "class" and "Class" are not allowed. There are other slot names with a special meaning; these names start with the "." character. To be safe, you should define all of your own slots with names starting with an alphabetic character.

Inheriting from Object Types

In addition to containing other S4 classes, a class definition can contain either an S3 class (see the next section) or a built-in R pseudo-class—one of the R object types or one of the special R pseudo-classes "matrix" and "array". A class can contain at most one of the object types, directly or indirectly. When it does, that contained class determines the “data part” of the class.

Objects from the new class try to inherit the built in behavior of the contained type. In the case of normal R data types, including vectors, functions and expressions, the implementation is relatively straightforward. For any object x from the class, typeof(x) will be the contained basic type; and a special pseudo-slot, .Data, will be shown with the corresponding class. See the "numWithId" example below.

Classes may also inherit from "vector", "matrix" or "array". The data part of these objects can be any vector data type.

For an object from any class that does not contain one of these types or classes, typeof(x) will be "S4".

Some R data types do not behave normally, in the sense that they are non-local references or other objects that are not duplicated. Examples include those corresponding to classes "environment", "externalptr", and "name". These can not be the types for objects with user-defined classes (either S4 or S3) because setting an attribute overwrites the object in all contexts. It is possible to define a class that inherits from such types, through an indirect mechanism that stores the inherited object in a reserved slot. See the example for class "stampedEnv" below. S3 method dispatch and the relevant as.type() functions should behave correctly, but code that uses the type of the object directly will not.

Also, keep in mind that the object passed to low-level computations will be the underlying object type, without any of the slots defined in the class. To return the full information, you will usually have to define a method that sets the data part.

Inheriting from S3 Classes

Old-style S3 classes have no formal definition. Objects are “from” the class when their class attribute contains the character string considered to be the class name.

Using such classes with formal classes and methods is necessarily a risky business, since there are no guarantees about the content of the objects or about consistency of inherited methods. Given that, it is still possible to define a class that inherits from an S3 class, providing that class has been registered as an old class (see setOldClass).

Broadly speaking, both S3 and S4 method dispatch try to behave sensibly with respect to inheritance in either system. Given an S4 object, S3 method dispatch and the inherits function should use the S4 inheritance information. Given an S3 object, an S4 generic function will dispatch S4 methods using the S3 inheritance, provided that inheritance has been declared via setOldClass.

Classes and Packages

Class definitions normally belong to packages (but can be defined in the global environment as well, by evaluating the expression on the command line or in a file sourced from the command line). The corresponding package name is part of the class definition; that is, part of the classRepresentation object holding that definition. Thus, two classes with the same name can exist in different packages, for most purposes.

When a class name is supplied for a slot or a superclass in a call to setClass, a corresponding class definition will be found, looking from the namespace of the current package, assuming the call in question appears directly in the source for the package, as it should to avoid ambiguity. The class definition must be found in the namespace of the current package, in the imports for that namespace or in the basic classes defined by the methods package. (The methods package must be included in the Depends directive of the package's "DESCRIPTION" file in order for the "CMD check" utility to find these classes.)

When this rule does not identify a class uniquely (because it appears in more than one imported package) then the packageSlot of the character string name needs to be supplied with the name. This should be a rare occurrence.

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

Classes for a general discussion of classes, Methods for an analogous discussion of methods, makeClassRepresentation

Examples


## A simple class with two slots
track <- setClass("track",
         slots = c(x="numeric", y="numeric"))
## an object from the class
t1 <- track(x = 1:10, y = 1:10 + rnorm(10))

## A class extending the previous, adding one more slot
trackCurve <- setClass("trackCurve",
    slots = c(smooth = "numeric"),
    contains = "track")

## an object containing a superclass object
t1s <- trackCurve(t1, smooth = 1:10)

## A class similar to "trackCurve", but with different structure
## allowing matrices for the "y" and "smooth" slots
setClass("trackMultiCurve",
         slots = c(x="numeric", y="matrix", smooth="matrix"),
         prototype = list(x=numeric(), y=matrix(0,0,0),
                          smooth= matrix(0,0,0)))
## See ?setIs for further examples using these classes

## A class that extends the built-in data type "numeric"

numWithId <- setClass("numWithId", slots = c(id = "character"),
         contains = "numeric")

numWithId(1:3, id = "An Example")

## inherit from reference object of type "environment"
stampedEnv <-setClass("stampedEnv", contains = "environment",
      slots = c(update = "POSIXct"))
setMethod("[[<-", c("stampedEnv", "character", "missing"),
   function(x, i, j, ..., value) {
       ev <- as(x, "environment")
       ev[[i]] <- value  #update the object in the environment
       x@update <- Sys.time() # and the update time
       x})


e1 <- stampedEnv(update = Sys.time())

e1[["noise"]] <- rnorm(10)



[Package methods version 3.1.0 Index]