setAs Methods for Coercing an Object to a Class

Description

A call to setAs defines a method for coercing an object of class from to class to. The methods will then be used by calls to as for objects with class from, including calls that replace part of the object.

Methods for this purpose work indirectly, by defining methods for function coerce. The coerce function is not to be called directly, and method selection uses class inheritance only on the first argument.

Usage

setAs(from, to, def, replace, where = topenv(parent.frame()))

Arguments

from, to	The classes between which the coerce methods def and replace perform coercion.
def	function of one argument. It will get an object from class from and had better return an object of class to. The convention is that the name of the argument is from; if another argument name is used, setAs will attempt to substitute from.
replace	if supplied, the function to use as a replacement method, when as is used on the left of an assignment. Should be a function of two arguments, from, value, although setAs will attempt to substitute if the arguments differ. The remaining argument will not be used in standard applications.
where	the position or environment in which to store the resulting methods. Do not use this argument when defining a method in a package. Only the default, the namespace of the package, should be used in normal situations.

Inheritance and Coercion

Objects from one class can turn into objects from another class either automatically or by an explicit call to the as function. Automatic conversion is special, and comes from the designer of one class of objects asserting that this class extends another class. The most common case is that one or more class names are supplied in the contains= argument to setClass, in which case the new class extends each of the earlier classes (in the usual terminology, the earlier classes are superclasses of the new class and it is a subclass of each of them).

This form of inheritance is called simple inheritance in R. See setClass for details. Inheritance can also be defined explicitly by a call to setIs. The two versions have slightly different implications for coerce methods. Simple inheritance implies that inherited slots behave identically in the subclass and the superclass. Whenever two classes are related by simple inheritance, corresponding coerce methods are defined for both direct and replacement use of as. In the case of simple inheritance, these methods do the obvious computation: they extract or replace the slots in the object that correspond to those in the superclass definition.

The implicitly defined coerce methods may be overridden by a call to setAs; note, however, that the implicit methods are defined for each subclass-superclass pair, so that you must override each of these explicitly, not rely on inheritance.

When inheritance is defined by a call to setIs, the coerce methods are provided explicitly, not generated automatically. Inheritance will apply (to the from argument, as described in the section below). You could also supply methods via setAs for non-inherited relationships, and now these also can be inherited.

For further on the distinction between simple and explicit inheritance, see setIs.

How Functions 'as' and 'setAs' Work

The function as turns object into an object of class Class. In doing so, it applies a “coerce method”, using S4 classes and methods, but in a somewhat special way. Coerce methods are methods for the function coerce or, in the replacement case the function `coerce<-`. These functions have two arguments in method signatures, from and to, corresponding to the class of the object and the desired coerce class. These functions must not be called directly, but are used to store tables of methods for the use of as, directly and for replacements. In this section we will describe the direct case, but except where noted the replacement case works the same way, using `coerce<-` and the replace argument to setAs, rather than coerce and the def argument.

Assuming the object is not already of the desired class, as first looks for a method in the table of methods for the function coerce for the signature c(from = class(object), to = Class), in the same way method selection would do its initial lookup. To be precise, this means the table of both direct and inherited methods, but inheritance is used specially in this case (see below).

If no method is found, as looks for one. First, if either Class or class(object) is a superclass of the other, the class definition will contain the information needed to construct a coerce method. In the usual case that the subclass contains the superclass (i.e., has all its slots), the method is constructed either by extracting or replacing the inherited slots. Non-simple extensions (the result of a call to setIs) will usually contain explicit methods, though possibly not for replacement.

If no subclass/superclass relationship provides a method, as looks for an inherited method, but applying, inheritance for the argument from only, not for the argument to (if you think about it, you'll probably agree that you wouldn't want the result to be from some class other than the Class specified). Thus, selectMethod("coerce", sig, useInherited= c(from=TRUE, to= FALSE)) replicates the method selection used by as().

In nearly all cases the method found in this way will be cached in the table of coerce methods (the exception being subclass relationships with a test, which are legal but discouraged). So the detailed calculations should be done only on the first occurrence of a coerce from class(object) to Class.

Note that coerce is not a standard generic function. It is not intended to be called directly. To prevent accidentally caching an invalid inherited method, calls are routed to an equivalent call to as, and a warning is issued. Also, calls to selectMethod for this function may not represent the method that as will choose. You can only trust the result if the corresponding call to as has occurred previously in this session.

With this explanation as background, the function setAs does a fairly obvious computation: It constructs and sets a method for the function coerce with signature c(from, to), using the def argument to define the body of the method. The function supplied as def can have one argument (interpreted as an object to be coerced) or two arguments (the from object and the to class). Either way, setAs constructs a function of two arguments, with the second defaulting to the name of the to class. The method will be called from as with the object as the from argument and no to argument, with the default for this argument being the name of the intended to class, so the method can use this information in messages.

The direct version of the as function also has a strict= argument that defaults to TRUE. Calls during the evaluation of methods for other functions will set this argument to FALSE. The distinction is relevant when the object being coerced is from a simple subclass of the to class; if strict=FALSE in this case, nothing need be done. For most user-written coerce methods, when the two classes have no subclass/superclass, the strict= argument is irrelevant.

The replace argument to setAs provides a method for `coerce<-`. As with all replacement methods, the last argument of the method must have the name value for the object on the right of the assignment. As with the coerce method, the first two arguments are from, to; there is no strict= option for the replace case.

The function coerce exists as a repository for such methods, to be selected as described above by the as function. Actually dispatching the methods using standardGeneric could produce incorrect inherited methods, by using inheritance on the to argument; as mentioned, this is not the logic used for as. To prevent selecting and caching invalid methods, calls to coerce are currently mapped into calls to as, with a warning message.

Basic Coercion Methods

Methods are pre-defined for coercing any object to one of the basic datatypes. For example, as(x, "numeric") uses the existing as.numeric function. These built-in methods can be listed by showMethods("coerce").

References

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

See Also

If you think of using try(as(x, cl)), consider canCoerce(x, cl) instead.

Examples

## using the definition of class "track" from \link{setClass}



setAs("track", "numeric", function(from) from@y)

t1 <- new("track", x=1:20, y=(1:20)^2)

as(t1, "numeric")

## The next example shows:
##  1. A virtual class to define setAs for several classes at once.
##  2. as() using inherited information

setClass("ca", slots = c(a = "character", id = "numeric"))

setClass("cb", slots = c(b = "character", id = "numeric"))

setClass("id")
setIs("ca", "id")
setIs("cb", "id")


setAs("id", "numeric", function(from) from@id)

CA <- new("ca", a = "A", id = 1)
CB <- new("cb", b = "B", id = 2)

setAs("cb", "ca", function(from, to )new(to, a=from@b, id = from@id))

as(CB, "numeric")