Objects With Fields Treated by Reference (\abbrOOP-style)

Description

The software described here allows packages to define reference classes that behave in the style of “\abbrOOP” languages such as Java and C++. This model for \abbrOOP differs from the functional model implemented by S4 (and S3) classes and methods, in which methods are defined for generic functions. Methods for reference classes are “encapsulated” in the class definition.

Computations with objects from reference classes invoke methods on them and extract or set their fields, using the `$` operator in R. The field and method computations potentially modify the object. All computations referring to the objects see the modifications, in contrast to the usual functional programming model in R.

A call to setRefClass in the source code for a package defines the class and returns a generator object. Subsequent calls to the $methods() method of the generator will define methods for the class. As with functional classes, if the class is exported from the package, it will be available when the package is loaded.

Methods are R functions. In their usual implementation, they refer to fields and other methods of the class directly by name. See the section on “Writing Reference Methods”.

As with functional classes, reference classes can inherit from other reference classes via a contains= argument to setRefClass. Fields and methods will be inherited, except where the new class overrides method definitions. See the section on “Inheritance”.

Usage

setRefClass(Class, fields = , contains = , methods =,
     where =, inheritPackage =, ...)

getRefClass(Class, where =)

Arguments

Value

setRefClass() returns a generator function suitable for creating objects from the class, invisibly. A call to this function 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 fields and unnamed arguments, if any, that are objects from one of the superclasses of this class (but only superclasses that are themselves reference classes have any effect).

The generator function is similar to the S4 generator function returned by setClass. In addition to being a generator function, however, it is also a reference class generator object, with reference class methods for various utilities. See the section on reference class generator objects below.

getRefClass() also returns the generator function for the class. Note that the package slot in the value is the correct package from the class definition, regardless of the where argument, which is used only to find the class if necessary.

Reference Objects

Normal objects in R are passed as arguments in function calls consistently with functional programming semantics; that is, changes made to an object passed as an argument are local to the function call. The object that supplied the argument is unchanged.

The functional model (sometimes called pass-by-value, although this is inaccurate for R) is suitable for many statistical computations and is implicit, for example, in the basic R software for fitting statistical models. In some other situations, one would like all the code dealing with an object to see the exact same content, so that changes made in any computation would be reflected everywhere. This is often suitable if the object has some “objective” reality, such as a window in a user interface.

In addition, commonly used languages, including Java, C++ and many others, support a version of classes and methods assuming reference semantics. The corresponding programming mechanism is to invoke a method on an object. In the R syntax we use "$" for this operation; one invokes a method, m1 say, on an object x by the expression x$m1(...).

Methods in this paradigm are associated with the object, or more precisely with the class of the object, as opposed to methods in a function-based class/method system, which are fundamentally associated with the function (in R, for example, a generic function in an R session has a table of all its currently known methods). In this document “methods for a class” as opposed to “methods for a function” will make the distinction.

Objects in this paradigm usually have named fields on which the methods operate. In the R implementation, the fields are defined when the class is created. The field itself can optionally have a specified class, meaning that only objects from this class or one of its subclasses can be assigned to the field. By default, fields have class "ANY".

Fields are accessed by reference. In particular, invoking a method may modify the content of the fields.

Programming for such classes involves writing new methods for a particular class. In the R implementation, these methods are R functions, with zero or more formal arguments. For standard reference methods, the object itself is not an explicit argument to the method. Instead, fields and methods for the class can be referred to by name in the method definition. The implementation uses R environments to make fields and other methods available by name within the method. Specifically, the parent environment of the method is the object itself. See the section on “Writing Reference Methods”. This special use of environments is optional. If a method is defined with an initial formal argument .self, that will be passed in as the whole object, and the method follows the standard rules for any function in a package. See the section on “External Methods”

The goal of the software described here is to provide a uniform programming style in R for software dealing with reference classes, whether implemented directly in R or through an interface to one of the \abbrOOP languages.

Writing Reference Methods

Reference methods are functions supplied as elements of a named list, either when invoking $methods() on a generator object g or as the argument methods in a call to setRefClass. The two mechanisms have the same effect, but the first makes the code more readable.

Methods are written as ordinary R functions but have some special features and restrictions in their usual form. In contrast to some other languages (e.g., Python), the object itself does not need to be an argument in the method definition. The body of the function can contain calls to any other reference method, including those inherited from other reference classes and may refer to methods and to fields in the object by name.

Alternatively, a method may be an external method. This is signalled by .self being the first formal argument to the method. The body of the method then works like any ordinary function. The methods are called like other methods (without the .self argument, which is supplied internally and always refers to the object itself). Inside the method, fields and other methods are accessed in the form .self$x. External methods exist so that reference classes can inherit the package environment of superclasses in other packages; see the section on “External Methods”.

Fields may be modified in a method by using the non-local assignment operator, <<-, as in the $edit and $undo methods in the example below. Note that non-local assignment is required: a local assignment with the <- operator just creates a local object in the function call, as it would in any R function. When methods are installed, a heuristic check is made for local assignments to field names and a warning issued if any are detected.

Reference methods should be kept simple; if they need to do some specialized R computation, that computation should use a separate R function that is called from the reference method. Specifically, methods can not use special features of the enclosing environment mechanism, since the method's environment is used to access fields and other methods. In particular, methods should not use non-exported entries in the package's namespace, because the methods may be inherited by a reference class in another package.

Two method names are interpreted specially, initialize and finalize. If an initialize method is defined, it will be invoked when an object is generated from the class. See the discussion of method $new(...) in the section “Initialization Methods”.

If a finalize method is defined, a function will be registered to invoke it before the environment in the object is discarded by the garbage collector; finalizers are registered with atexit=TRUE, and so are also run at the end of R sessions. See the matrix viewer example for both initialize and finalize methods.

Reference methods can not themselves be generic functions; if you want additional function-based method dispatch, write a separate generic function and call that from the method.

Two special object names are available. The entire object can be referred to in a method by the reserved name .self. The object .refClassDef contains the definition of the class of the object. These are accessed as fields but are read-only, with one exception. In principal, the .self field can be modified in the $initialize method, because the object is still being created at this stage. This is not recommended, as it can invalidate the object with respect to its class.

The methods available include methods inherited from superclasses, as discussed in the section “Inheritance”.

Only methods actually used will be included in the environment corresponding to an individual object. To declare that a method requires a particular other method, the first method should include a call to $usingMethods() with the name of the other method as an argument. Declaring the methods this way is essential if the other method is used indirectly (e.g., via sapply() or do.call()). If it is called directly, code analysis will find it. Declaring the method is harmless in any case, however, and may aid readability of the source code.

Documentation for the methods can be obtained by the $help method for the generator object. Methods for classes are not documented in the Rd format used for R functions. Instead, the $help method prints the calling sequence of the method, followed by self-documentation from the method definition, in the style of Python. If the first element of the body of the method is a literal character string (possibly multi-line), that string is interpreted as documentation. See the method definitions in the example.

Initialization Methods

If the class has a method defined for $initialize(), this method will be called once the reference object has been created. You should write such a method for a class that needs to do some special initialization. In particular, a reference method is recommended rather than a method for the S4 generic function initialize(), because some special initialization is required for reference objects before the initialization of fields. As with S4 classes, methods are written for $initialize() and not for $new(), both for the previous reason and also because $new() is invoked on the generator object and would be a method for that class.

The default method for $initialize() is equivalent to invoking the method $initFields(...). Named arguments assign initial values to the corresponding fields. Unnamed arguments must be objects from this class or a reference superclass of this class. Fields will be initialized to the contents of the fields in such objects, but named arguments override the corresponding inherited fields. Note that fields are simply assigned. If the field is itself a reference object, that object is not copied. The new and previous object will share the reference. Also, a field assigned from an unnamed argument counts as an assignment for locked fields. To override an inherited value for a locked field, the new value must be one of the named arguments in the initializing call. A later assignment of the field will result in an error.

Initialization methods need some care in design. The generator for a reference class will be called with no arguments, for example when copying the object. To ensure that these calls do not fail, the method must have defaults for all arguments or check for missing(). The method should include ... as an argument and pass this on via $callSuper() (or $initFields() if you know that your superclasses have no initialization methods). This allows future class definitions that subclass this class, with additional fields.

Inheritance

Reference classes inherit from other reference classes by using the standard R inheritance; that is, by including the superclasses in the contains= argument when creating the new class. The names of the reference superclasses are in slot refSuperClasses of the class definition. Reference classes can inherit from ordinary S4 classes also, but this is usually a bad idea if it mixes reference fields and non-reference slots. See the comments in the section on “Implementation”.

Class fields are inherited. A class definition can override a field of the same name in a superclass only if the overriding class is a subclass of the class of the inherited field. This ensures that a valid object in the field remains valid for the superclass as well.

Inherited methods are installed in the same way as directly specified methods. The code in a method can refer to inherited methods in the same way as directly specified methods.

A method may override a method of the same name in a superclass. The overriding method can call the superclass method by callSuper(...) as described below.

Methods Provided for all Objects

All reference classes inherit from the class "envRefClass". All reference objects can use the following methods.

$callSuper(...)

Calls the method inherited from a reference superclass. The call is meaningful only from within another method, and will be resolved to call the inherited method of the same name. The arguments to $callSuper are passed to the superclass version. See the matrix viewer class in the example.

Note that the intended arguments for the superclass method must be supplied explicitly; there is no convention for supplying the arguments automatically, in contrast to the similar mechanism for functional methods.

$copy(shallow = FALSE)

Creates a copy of the object. With reference classes, unlike ordinary R objects, merely assigning the object with a different name does not create an independent copy. If shallow is FALSE, any field that is itself a reference object will also be copied, and similarly recursively for its fields. Otherwise, while reassigning a field to a new reference object will have no side effect, modifying such a field will still be reflected in both copies of the object. The argument has no effect on non-reference objects in fields. When there are reference objects in some fields but it is asserted that they will not be modified, using shallow = TRUE will save some memory and time.

$field(name, value)

With one argument, returns the field of the object with character string name. With two arguments, the corresponding field is assigned value. Assignment checks that name specifies a valid field, but the single-argument version will attempt to get anything of that name from the object's environment.

The $field() method replaces the direct use of a field name, when the name of the field must be calculated, or for looping over several fields.

$export(Class)

Returns the result of coercing the object to Class (typically one of the superclasses of the object's class). Calling the method has no side effect on the object itself.

$getRefClass(); $getClass()

These return respectively the generator object and the formal class definition for the reference class of this object, efficiently.

$import(value, Class = class(value))

Import the object value into the current object, replacing the corresponding fields in the current object. Object value must come from one of the superclasses of the current object's class. If argument Class is supplied, value is first coerced to that class.

$initFields(...)

Initialize the fields of the object from the supplied arguments. This method is usually only called from a class with a $initialize() method. It corresponds to the default initialization for reference classes. If there are slots and non-reference superclasses, these may be supplied in the ... argument as well.

Typically, a specialized $initialize() method carries out its own computations, then invokes $initFields() to perform standard initialization, as shown in the matrixViewer class in the example below.

$show()

This method is called when the object is printed automatically, analogously to the show function. A general method is defined for class "envRefClass". User-defined reference classes will often define their own method: see the Example below.

Note two points in the example. As with any show() method, it is a good idea to print the class explicitly to allow for subclasses using the method. Second, to call the function show() from the method, as opposed to the $show() method itself, refer to methods::show() explicitly.

$trace(what, ...), $untrace(what)

Apply the tracing and debugging facilities of the trace function to the reference method what.

All the arguments of the trace function can be supplied, except for signature, which is not meaningful.

The reference method can be invoked on either an object or the generator for the class. See the section on Debugging below for details.

$usingMethods(...)

Reference methods used by this method are named as the arguments either quoted or unquoted. In the code analysis phase of installing the present method, the declared methods will be included. It is essential to declare any methods used in a nonstandard way (e.g., via an apply function). Methods called directly do not need to be declared, but it is harmless to do so. $usingMethods() does nothing at run time.

Objects also inherit two reserved fields:

.self

a reference to the entire object;

.refClassDef

the class definition.

The defined fields should not override these, and in general it is unwise to define a field whose name begins with ".", since the implementation may use such names for special purposes.

External Methods; Inter-Package Superclasses

The environment of a method in a reference class is the object itself, as an environment. This allows the method to refer directly to fields and other methods, without using the whole object and the "$" operator. The parent of that environment is the namespace of the package in which the reference class is defined. Computations in the method have access to all the objects in the package's namespace, exported or not.

When defining a class that contains a reference superclass in another package, there is an ambiguity about which package namespace should have that role. The argument inheritPackage to setRefClass() controls whether the environment of new objects should inherit from an inherited class in another package or continue to inherit from the current package's namespace.

If the superclass is “lean”, with few methods, or exists primarily to support a family of subclasses, then it may be better to continue to use the new package's environment. On the other hand, if the superclass was originally written as a standalone, this choice may invalidate existing superclass methods. For the superclass methods to continue to work, they must use only exported functions in their package and the new package must import these.

Either way, some methods may need to be written that do not assume the standard model for reference class methods, but behave essentially as ordinary functions would in dealing with reference class objects.

The mechanism is to recognize external methods. An external method is written as a function in which the first argument, named .self, stands for the reference class object. This function is supplied as the definition for a reference class method. The method will be called, automatically, with the first argument being the current object and the other arguments, if any, passed along from the actual call.

Since an external method is an ordinary function in the source code for its package, it has access to all the objects in the namespace. Fields and methods in the reference class must be referred to in the form .self$name.

If for some reason you do not want to use .self as the first argument, a function f() can be converted explicitly as externalRefMethod(f), which returns an object of class "externalRefMethod" that can be supplied as a method for the class. The first argument will still correspond to the whole object.

External methods can be supplied for any reference class, but there is no obvious advantage unless they are needed. They are more work to write, harder to read and (slightly) slower to execute.

NOTE: If you are the author of a package whose reference classes are likely to be subclassed in other packages, you can avoid these questions entirely by writing methods that only use exported functions from your package, so that all the methods will work from another package that imports yours.

Reference Class Generators

The call to setRefClass defines the specified class and returns a “generator function” object for that class. This object has class "refObjectGenerator"; it inherits from "function" via "classGeneratorFunction" and can be called to generate new objects from the reference class.

The returned object is also a reference class object, although not of the standard construction. It can be used to invoke reference methods and access fields in the usual way, but instead of being implemented directly as an environment it has a subsidiary generator object as a slot, a standard reference object (of class "refGeneratorSlot"). Note that if one wanted to extend the reference class generator capability with a subclass, this should be done by subclassing "refGeneratorSlot", not "refObjectGenerator".

The fields are def, the class definition, and className, the character string name of the class. Methods generate objects from the class, to access help on reference methods, and to define new reference methods for the class. The currently available methods are:

$new(...)

This method is equivalent to calling the generator function returned by setRefClass.

$help(topic)

Prints brief help on the topic. The topics recognized are reference method names, quoted or not.

The information printed is the calling sequence for the method, plus self-documentation if any. Reference methods can have an initial character string or vector as the first element in the body of the function defining the method. If so, this string is taken as self-documentation for the method (see the section on “Writing Reference Methods” for details).

If no topic is given or if the topic is not a method name, the definition of the class is printed.

$methods(...)

With no arguments, returns the names of the reference methods for this class. With one character string argument, returns the method of that name.

Named arguments are method definitions, which will be installed in the class, as if they had been supplied in the methods argument to setRefClass(). Supplying methods in this way, rather than in the call to setRefClass(), is recommended for the sake of clearer source code. See the section on “Writing Reference Methods” for details.

All methods for a class should be defined in the source code that defines the class, typically as part of a package. In particular, methods can not be redefined in a class in an attached package with a namespace: The class method checks for a locked binding of the class definition.

The new methods can refer to any currently defined method by name (including other methods supplied in this call to $methods()). Note though that previously defined methods are not re-analyzed meaning that they will not call the new method (unless it redefines an existing method of the same name).

To remove a method, supply NULL as its new definition.

$fields()

Returns a list of the fields, each with its corresponding class. Fields for which an accessor function was supplied in the definition have class "activeBindingFunction".

$lock(...)

The fields named in the arguments are locked; specifically, after the lock method is called, the field may be set once. Any further attempt to set it will generate an error.

If called with no arguments, the method returns the names of the locked fields.

Fields that are defined by an explicit accessor function can not be locked (on the other hand, the accessor function can be defined to generate an error if called with an argument).

All code to lock fields should normally be part of the definition of a class; that is, the read-only nature of the fields is meant to be part of the class definition, not a dynamic property added later. In particular, fields can not be locked in a class in an attached package with a namespace: The class method checks for a locked binding of the class definition. Locked fields can not be subsequently unlocked.

$trace(what, ..., classMethod = FALSE)

Establish a traced version of method what for objects generated from this class. The generator object tracing works like the $trace() method for objects from the class, with two differences. Since it changes the method definition in the class object itself, tracing applies to all objects, not just the one on which the trace method is invoked.

Second, the optional argument classMethod = TRUE allows tracing on the methods of the generator object itself. By default, what is interpreted as the name of a method in the class for which this object is the generator.

$accessors(...)

A number of systems using the \abbrOOP programming paradigm recommend or enforce getter and setter methods corresponding to each field, rather than direct access by name. If you like this style and want to extract a field named abc by x$getAbc() and assign it by x$setAbc(value), the $accessors method is a convenience function that creates such getter and setter methods for the specified fields. Otherwise there is no reason to use this mechanism. In particular, it has nothing to do with the general ability to define fields by functions as described in the section on “Reference Objects”.

Implementation; Reference Classes as S4 Classes

Reference classes are implemented as S4 classes with a data part of type "environment". Fields correspond to named objects in the environment. A field associated with a function is implemented as an active binding. In particular, fields with a specified class are implemented as a special form of active binding to enforce valid assignment to the field.

As a related feature, the element in the fields= list supplied to setRefClass can be an accessor function, a function of one argument that returns the field if called with no argument or sets it to the value of the argument otherwise. Accessor functions are used internally and for inter-system interface applications, but not generally recommended as they blur the concept of fields as data within the object.

A field, say data, can be accessed generally by an expression of the form x$data for any object from the relevant class. In an internal method for this class, the field can be accessed by the name data. A field that is not locked can be set by an expression of the form x$data <- value. Inside an internal method, a field can be assigned by an expression of the form x <<- value. Note the non-local assignment operator. The standard R interpretation of this operator works to assign it in the environment of the object. If the field has an accessor function defined, getting and setting will call that function.

When a method is invoked on an object, the function defining the method is installed in the object's environment, with the same environment as the environment of the function.

Reference classes can have validity methods in the same sense as any S4 class (see setValidity). Such methods are often a good idea; they will be called by calling validObject and a validity method, if one is defined, will be called when a reference object is created (from version 3.4 of R on). Just remember that these are S4 methods. The function will be called with the object as its argument. Fields and methods must be accessed using $.

Note: Slots. Because of the implementation, new reference classes can inherit from non-reference S4 classes as well as reference classes, and can include class-specific slots in the definition. This is usually a bad idea, if the slots from the non-reference class are thought of as alternatives to fields. Slots will as always be treated functionally. Therefore, changes to the slots and the fields will behave inconsistently, mixing the functional and reference paradigms for properties of the same object, conceptually unclear and prone to errors. In addition, the initialization method for the class will have to sort out fields from slots, with a good chance of creating anomalous behavior for subclasses of this class.

Inheriting from a class union, however, is a reasonable strategy (with all members of the union likely to be reference classes).

Debugging

The standard R debugging and tracing facilities can be applied to reference methods. Reference methods can be passed to debug and its relatives from an object to debug further method invocations on that object; for example, debug(xx$edit).

Somewhat more flexible use is available for a reference method version of the trace function. A corresponding $trace() reference method is available for either an object or for the reference class generator (xx$trace() or mEdit$trace() in the example below). Using $trace() on an object sets up a tracing version for future invocations of the specified method for that object. Using $trace() on the generator for the class sets up a tracing version for all future objects from that class (and sometimes for existing objects from the class if the method is not declared or previously invoked).

In either case, all the arguments to the standard trace function are available, except for signature= which is meaningless since reference methods can not be S4 generic functions. This includes the typical style trace(what, browser) for interactive debugging and trace(what, edit = TRUE) to edit the reference method interactively.

References

Chambers, John M. (2016) Extending R, Chapman & Hall. (Chapters 9 and 11.)

Examples

## a simple editor for matrix objects.  Method  $edit() changes some
## range of values; method $undo() undoes the last edit.
mEdit <- setRefClass("mEdit",
      fields = list( data = "matrix",
        edits = "list"))

## The basic edit, undo methods
mEdit$methods(
     edit = function(i, j, value) {
       ## the following string documents the edit method
       'Replaces the range [i, j] of the
        object by value.
        '
         backup <-
             list(i, j, data[i,j])
         data[i,j] <<- value
         edits <<- c(edits, list(backup))
         invisible(value)
     },
     undo = function() {
       'Undoes the last edit() operation
        and update the edits field accordingly.
        '
         prev <- edits
         if(length(prev)) prev <- prev[[length(prev)]]
         else stop("No more edits to undo")
         edit(prev[[1]], prev[[2]], prev[[3]])
         ## trim the edits list
         length(edits) <<- length(edits) - 2
         invisible(prev)
     })

## A method to automatically print objects
mEdit$methods(
     show = function() {
       'Method for automatically printing matrix editors'
       cat("Reference matrix editor object of class",
          classLabel(class(.self)), "\n")
       cat("Data: \n")
       methods::show(data)
       cat("Undo list is of length", length(edits), "\n")
     }
     )

xMat <- matrix(1:12,4,3)
xx <- mEdit(data = xMat)
xx$edit(2, 2, 0)
xx
xx$undo()
mEdit$help("undo")
stopifnot(all.equal(xx$data, xMat))

utils::str(xx) # show fields and names of methods

## A method to save the object
mEdit$methods(
     save = function(file) {
       'Save the current object on the file
        in R external object format.
       '
         base::save(.self, file = file)
     }
)

tf <- tempfile()
xx$save(tf)


## Not run: 
## Inheriting a reference class:  a matrix viewer
mv <- setRefClass("matrixViewer",
    fields = c("viewerDevice", "viewerFile"),
    contains = "mEdit",
    methods = list( view = function() {
        dd <- dev.cur(); dev.set(viewerDevice)
        devAskNewPage(FALSE)
        matplot(data, main = paste("After",length(edits),"edits"))
        dev.set(dd)},
        edit = # invoke previous method, then replot
          function(i, j, value) {
            callSuper(i, j, value)
            view()
          }))

## initialize and finalize methods
mv$methods( initialize =
  function(file = "./matrixView.pdf", ...) {
    viewerFile <<- file
    pdf(viewerFile)
    viewerDevice <<- dev.cur()
    dev.set(dev.prev())
    callSuper(...)
  },
  finalize = function() {
    dev.off(viewerDevice)
  })

## debugging an object: call browser() in method $edit()
xx$trace(edit, browser)

## debugging all objects from class mEdit in method $undo()
mEdit$trace(undo, browser)

## End(Not run)