\HeaderA{is}{Is an Object from a Class}{is}
\aliasA{extends}{is}{extends}
\aliasA{setIs}{is}{setIs}
\keyword{programming}{is}
\keyword{classes}{is}
\keyword{methods}{is}
\begin{Description}\relax
Functions to test inheritance relationships between an object and a
class (\code{is}) or between two classes (\code{extends}), and to
establish such relationships (\code{setIs},  an explicit alternative to the \code{contains=} argument to \code{\LinkA{setClass}{setClass}}).
\end{Description}
\begin{Usage}
\begin{verbatim}
is(object, class2)

extends(class1, class2, maybe=TRUE, fullInfo = FALSE)

setIs(class1, class2, test=NULL, coerce=NULL, replace=NULL,
      by = character(), where = topenv(parent.frame()), classDef =,
      extensionObject = NULL, doComplete = TRUE)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{object}] any \R{} object.
\item[\code{class1, class2}] the names of the classes between which \code{is} relations are to be
examined defined, or (more efficiently) the class definition
objects for the classes.
\item[\code{maybe, fullInfo}] In a call to \code{extends}, \code{maybe} is the value returned if a
relation is conditional. In a call with \code{class2} missing, \code{fullInfo} is a
flag, which if \code{TRUE} causes a list of objects of class
\code{classExtension} to be returned, rather than just the
names of the classes.

\item[\code{test, coerce, replace}] In a call to \code{setIs}, functions optionally supplied to test whether the relation is
defined, to coerce the object to \code{class2}, and to alter the
object so that \code{is(object, class2)} is identical to
\code{value}. See the details section below.

The remaining arguments are for internal use and/or usually omitted.
\item[\code{extensionObject}] alternative to the \code{test, coerce,
    replace, by} arguments; an object from class
\code{SClassExtension} describing the relation.  (Used in internal calls.)

\item[\code{doComplete}] when \code{TRUE}, the class definitions will be
augmented with indirect relations as well.  (Used in internal calls.)
\item[\code{by}] In a call to \code{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.)
\item[\code{where}] In a call to \code{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 name space or environment of the package.  Other uses are tricky and not usually a good idea, unless you really know what you are doing.
\item[\code{classDef}] Optional class definition for \code{class} , required internally
when \code{setIs} is called during the initial definition of the
class by a call to \code{\LinkA{setClass}{setClass}}. \emph{Don't} use this
argument, unless you really know why you're doing so.
\end{ldescription}
\end{Arguments}
\begin{Section}{Summary of Functions}
\describe{
\item[\code{is}:] With two arguments, tests whether \code{object} can be treated as from
\code{class2}.

With one argument, returns all the super-classes of this object's class.

\item[\code{extends}:] Does the first class extend the second class?
The call returns \code{maybe} if the extension includes a test.  

When called with one argument, the value is a vector of the
superclasses of \code{class1}.  If argument \code{fullInfo}  is
\code{TRUE}, the call returns a named list of objects of class \code{\LinkA{SClassExtension}{SClassExtension.Rdash.class}}; otherwise, just the names of the superclasses.

\item[\code{setIs}:] Defines \code{class1} to be an extension (subclass) of
\code{class2}.
If \code{class2} is an existing virtual class, such as a class
union, then only the two classes need to be supplied in the
call, if the implied inherited methods work for \code{class1}.
See the details section below.

Alternatively, arguments
\code{coerce} and \code{replace} should be supplied, defining
methods to coerce to the superclass and to replace the part
corresponding to the superclass. As discussed in the details and
other sections below, this form is often less recommended than the
corresponding call to \code{\LinkA{setAs}{setAs}}, to which it is an alternative. 

}
\end{Section}
\begin{Section}{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  \dQuote{simple} inheritance, the preferred form:
\Enumerate{

\item
By the \code{contains=} argument in a call to \code{\LinkA{setClass}{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 \code{simple}, with
important implications for method definition (see the section on
this topic below).

\item
Making \code{class1} a subclass of a virtual class
either by a call to \code{\LinkA{setClassUnion}{setClassUnion}} to make the
subclass a member of a new class union, or by a call to
\code{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.


\item
Supplying \code{coerce}  and \code{replace} arguments to \code{setAs}.
\R{} allows arbitrary inheritance relationships, using the same
mechanism for defining coerce methods by a call to
\code{\LinkA{setAs}{setAs}}.  The difference between the  two is simply
that \code{\LinkA{setAs}{setAs}} will require a call to \code{\LinkA{as}{as}}
for a conversion to take place, whereas after the call to
\code{\LinkA{setIs}{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 \code{\LinkA{setAs}{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
\code{coerce=} and \code{replace=} argument are supplied to \code{setIs}.


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

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

The value returned (invisibly) by
\code{setIs} is the revised class definition of \code{class1}.
\end{Section}
\begin{Section}{Coerce, replace, and test functions}
The  \code{coerce} argument is a function that turns a
\code{class1} object into a \code{class2} object.  The
\code{replace} argument is a function of two arguments that modifies a \code{class1}
object (the first argument) to replace the part of it that
corresponds to \code{class2} (supplied as \code{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 \code{as(object, class2) <- value}.

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

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

For additional discussion of these functions, see
the documentation of the
\code{\LinkA{setAs}{setAs}} function.  (Unfortunately, argument
\code{def} to that function corresponds to argument \code{coerce} here.) 

The inheritance relationship can also be conditional, if a function is supplied as the
\code{test} argument.  This should be a function of one argument
that returns \code{TRUE} or \code{FALSE} according to whether the
object supplied satisfies the relation \code{is(object, class2)}.
Conditional relations between
classes are slightly deprecated because they cannot be implemented
as efficiently as ordinary relations and because they sometimes can
lead to confusion (in thinking about what methods are dispatched for
a particular function, for example).  But they can correspond to
distinctions such as two classes that have the same representation,
but with only one of them obeying certain additional constraints.
\end{Section}
\begin{Section}{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 \dQuote{simple}, that
is, defined by one or more uses of the \code{contains=} argument in
a call to \code{\LinkA{setClass}{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
\code{setIs}, extra computations are required.  This form of
inheritance implies that the subclass does \emph{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 \code{\LinkA{as}{as}}
before the body of the method is evaluated.

The calls to \code{\LinkA{as}{as}} generated in this case have the
argument \code{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 \code{class2} is a specialized class
with just a few applicable methods, creating the inheritance
relation may have little effect on the behavior of \code{class1}.
But if \code{class2} is a class with many methods, you may
find that you now inherit some undesirable methods for
\code{class1}, in some cases, fail to inherit expected methods.
In the second example below, the non-simple inheritance from class
\code{"factor"} might be assumed to inherit S3 methods via that
class.  But the S3 class is ambiguous, and in fact is
\code{"character"} rather than \code{"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 \code{\LinkA{initialize}{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
\code{simpleInheritanceOnly} argument to \code{\LinkA{setGeneric}{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 \code{setIs} call and settle for explicit coercing
defined by a call to \code{\LinkA{setAs}{setAs}}; or, define explicit
methods involving \code{class1} to override the bad inherited
methods.  The first choice is the safer, when there are serious
problems.
\end{Section}
\begin{References}\relax
Chambers, John M. (2008)
\emph{Software for Data Analysis: Programming with R}
Springer.  (For the R version.)

Chambers, John M. (1998)
\emph{Programming with Data}
Springer (For the original S4 version.)
\end{References}
\begin{Examples}
\begin{ExampleCode}

## 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 setClass for class "track")
setClass("trackCurve", contains = "track",
         representation( smooth = "numeric"))
## A class similar to "trackCurve", but with different structure
## allowing matrices for the "y" and "smooth" slots
setClass("trackMultiCurve",
         representation(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", representation(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", representation(stamp="POSIXt"))

fd = new("factorDated", factor(ll), stamp = Sys.time())

identical(levels(fd), levels(as(fd, "factor")))


\end{ExampleCode}
\end{Examples}

