R: Specify a Superclass Explicitly

setIs {methods} | R Documentation

## Specify a Superclass Explicitly

### Description

`setIs` is an explicit alternative to the `contains=` argument to `setClass`. It is only needed to create relations with explicit test or coercion. These have not proved to be of much practical value, so this function should not likely be needed in applications.

Where the programming goal is to define methods for transforming one class of objects to another, it is usually better practice to call `setAs()`, which requires the transformations to be done explicitly.

### Usage

    setIs(class1, class2, test=NULL, coerce=NULL, replace=NULL,
          by = character(), where = topenv(parent.frame()), classDef =,
          extensionObject = NULL, doComplete = TRUE)

### Arguments

`class1, class2` | the names of the classes between which `is` relations are to be examined defined, or (more efficiently) the class definition objects for the classes.
`coerce, replace` | functions optionally supplied to coerce the object to `class2`, and to alter the object so that `is(object, class2)` is identical to `value`. See the details section below.
`test` | a conditional relationship is defined by supplying this function. Conditional relations are discouraged and are not included in selecting methods. See the details section below. The remaining arguments are for internal use and/or usually omitted.
`extensionObject` | alternative to the `test, coerce, replace, by` arguments; an object from class `SClassExtension` describing the relation. (Used in internal calls.)
`doComplete` | when `TRUE`, the class definitions will be augmented with indirect relations as well. (Used in internal calls.)
`by` | In a call to `setIs`, the name of an intermediary class. Coercion will proceed by first coercing to this class and from there to the target class. (The intermediate coercions have to be valid.)
`where` | In a call to `setIs`, where to store the metadata defining the relationship. Default is the global environment for calls from the top level of the session or a source file evaluated there. When the call occurs in the top level of a file in the source of a package, the default will be the namespace or environment of the package. Other uses are tricky and not usually a good idea, unless you really know what you are doing.
`classDef` | Optional class definition for `class` , required internally when `setIs` is called during the initial definition of the class by a call to `setClass`. Don't use this argument, unless you really know why you're doing so.

### Details

Arranging for a class to inherit from another class is a key tool in programming. In R, there are three basic techniques, the first two providing what is called “simple” inheritance, the preferred form:

1. By the `contains=` argument in a call to `setClass`. This is and should be the most common mechanism. It arranges that the new class contains all the structure of the existing class, and in particular all the slots with the same class specified. The resulting class extension is defined to be `simple`, with important implications for method definition (see the section on this topic below).

2. Making `class1` a subclass of a virtual class either by a call to `setClassUnion` to make the subclass a member of a new class union, or by a call to `setIs` to add a class to an existing class union or as a new subclass of an existing virtual class. In either case, the implication should be that methods defined for the class union or other superclass all work correctly for the subclass. This may depend on some similarity in the structure of the subclasses or simply indicate that the superclass methods are defined in terms of generic functions that apply to all the subclasses. These relationships are also generally simple.

3. Supplying `coerce` and `replace` arguments to `setAs`. R allows arbitrary inheritance relationships, using the same mechanism for defining coerce methods by a call to `setAs`. The difference between the two is simply that `setAs` will require a call to `as` for a conversion to take place, whereas after the call to `setIs`, objects will be automatically converted to the superclass.

   The automatic feature is the dangerous part, mainly because it results in the subclass potentially inheriting methods that do not work. See the section on inheritance below. If the two classes involved do not actually inherit a large collection of methods, as in the first example below, the danger may be relatively slight.

   If the superclass inherits methods where the subclass has only a default or remotely inherited method, problems are more likely. In this case, a general recommendation is to use the `setAs` mechanism instead, unless there is a strong counter reason. Otherwise, be prepared to override some of the methods inherited.

With this caution given, the rest of this section describes what happens when `coerce=` and `replace=` arguments are supplied to `setIs`.

The `coerce` and `replace` arguments are functions that define how to coerce a `class1` object to `class2`, and how to replace the part of the subclass object that corresponds to `class2`. The first of these is a function of one argument which should be `from`, and the second of two arguments (`from`, `value`). For details, see the section on coerce functions below .

When `by` is specified, the coerce process first coerces to this class and then to `class2`. It's unlikely you would use the `by` argument directly, but it is used in defining cached information about classes.

The value returned (invisibly) by `setIs` is the revised class definition of `class1`.

### Coerce, replace, and test functions

The `coerce` argument is a function that turns a `class1` object into a `class2` object. The `replace` argument is a function of two arguments that modifies a `class1` object (the first argument) to replace the part of it that corresponds to `class2` (supplied as `value`, the second argument). It then returns the modified object as the value of the call. In other words, it acts as a replacement method to implement the expression `as(object, class2) <- value`.

The easiest way to think of the `coerce` and `replace` functions is by thinking of the case that `class1` contains `class2` in the usual sense, by including the slots of the second class. (To repeat, in this situation you would not call `setIs`, but the analogy shows what happens when you do.)

The `coerce` function in this case would just make a `class2` object by extracting the corresponding slots from the `class1` object. The `replace` function would replace in the `class1` object the slots corresponding to `class2`, and return the modified object as its value.

For additional discussion of these functions, see the documentation of the `setAs` function. (Unfortunately, argument `def` to that function corresponds to argument `coerce` here.)

The inheritance relationship can also be conditional, if a function is supplied as the `test` argument. This should be a function of one argument that returns `TRUE` or `FALSE` according to whether the object supplied satisfies the relation `is(object, class2)`. Conditional relations between classes are discouraged in general because they require a per-object calculation to determine their validity. They cannot be applied as efficiently as ordinary relations and tend to make the code that uses them harder to interpret. NOTE: conditional inheritance is not used to dispatch methods. Methods for conditional superclasses will not be inherited. Instead, a method for the subclass should be defined that tests the conditional relationship.

### Inherited methods

A method written for a particular signature (classes matched to one or more formal arguments to the function) naturally assumes that the objects corresponding to the arguments can be treated as coming from the corresponding classes. The objects will have all the slots and available methods for the classes.

The code that selects and dispatches the methods ensures that this assumption is correct. If the inheritance was “simple”, that is, defined by one or more uses of the `contains=` argument in a call to `setClass`, no extra work is generally needed. Classes are inherited from the superclass, with the same definition.

When inheritance is defined by a general call to `setIs`, extra computations are required. This form of inheritance implies that the subclass does not just contain the slots of the superclass, but instead requires the explicit call to the coerce and/or replace method. To ensure correct computation, the inherited method is supplemented by calls to `as` before the body of the method is evaluated.

The calls to `as` generated in this case have the argument `strict = FALSE`, meaning that extra information can be left in the converted object, so long as it has all the appropriate slots. (It's this option that allows simple subclass objects to be used without any change.) When you are writing your coerce method, you may want to take advantage of that option.

Methods inherited through non-simple extensions can result in ambiguities or unexpected selections. If `class2` is a specialized class with just a few applicable methods, creating the inheritance relation may have little effect on the behavior of `class1`. But if `class2` is a class with many methods, you may find that you now inherit some undesirable methods for `class1`, in some cases, fail to inherit expected methods. In the second example below, the non-simple inheritance from class `"factor"` might be assumed to inherit S3 methods via that class. But the S3 class is ambiguous, and in fact is `"character"` rather than `"factor"`.

For some generic functions, methods inherited by non-simple extensions are either known to be invalid or sufficiently likely to be so that the generic function has been defined to exclude such inheritance. For example `initialize` methods must return an object of the target class; this is straightforward if the extension is simple, because no change is made to the argument object, but is essentially impossible. For this reason, the generic function insists on only simple extensions for inheritance. See the `simpleInheritanceOnly` argument to `setGeneric` for the mechanism. You can use this mechanism when defining new generic functions.

If you get into problems with functions that do allow non-simple inheritance, there are two basic choices. Either back off from the `setIs` call and settle for explicit coercing defined by a call to `setAs`; or, define explicit methods involving `class1` to override the bad inherited methods. The first choice is the safer, when there are serious problems.

### References

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

### Examples

    ## Two examples of setIs() with coerce= and replace= arguments
    ## The first one works fairly well, because neither class has many
    ## inherited methods do be disturbed by the new inheritance

    ## The second example does NOT work well, because the new superclass,
    ## "factor", causes methods to be inherited that should not be.

    ## First example:
    ## a class definition (see \link{setClass} for class "track")
    setClass("trackCurve", contains = "track",
             slots = c( smooth = "numeric"))
    ## 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 = structure(list(), x=numeric(), y=matrix(0,0,0),

                                   smooth= matrix(0,0,0)))
    ## Automatically convert an object from class "trackCurve" into
    ## "trackMultiCurve", by making the y, smooth slots into 1-column matrices
    setIs("trackCurve",
          "trackMultiCurve",
          coerce = function(obj) {
            new("trackMultiCurve",
                x = obj@x,
                y = as.matrix(obj@y),
                smooth = as.matrix(obj@smooth))
          },
          replace = function(obj, value) {
            obj@y <- as.matrix(value@y)
            obj@x <- value@x
            obj@smooth <- as.matrix(value@smooth)
            obj})

    ## Second Example:
    ## A class that adds a slot to "character"
    setClass("stringsDated", contains = "character",
             slots = c(stamp="POSIXt"))

    ## Convert automatically to a factor by explicit coerce
    setIs("stringsDated", "factor",
          coerce = function(from) factor(from@.Data),
          replace= function(from, value) {
                      from@.Data <- as.character(value); from })

    ll <- sample(letters, 10, replace = TRUE)
    ld <- new("stringsDated", ll, stamp = Sys.time())

    levels(as(ld, "factor"))
    levels(ld) # will be NULL--see comment in section on inheritance above.

    ## In contrast, a class that simply extends "factor"
    ## has no such ambiguities
    setClass("factorDated", contains = "factor",
             slots = c(stamp="POSIXt"))
    fd <- new("factorDated", factor(ll), stamp = Sys.time())
    identical(levels(fd), levels(as(fd, "factor")))

[Package methods version 4.0.5 Index]