\HeaderA{Classes}{Class Definitions}{Classes}
\aliasA{\_\_ClassMetaData}{Classes}{.Rul..Rul.ClassMetaData}
\keyword{programming}{Classes}
\keyword{classes}{Classes}
\keyword{methods}{Classes}
\begin{Description}\relax
Class definitions are objects that contain the formal definition of a
class of \R{} objects, usually referred to as an S4 class, to
distinguish them from the informal S3 classes.
This document gives an overview of S4 classes; for
details of the class representation objects, see help for the class
\code{\LinkA{classRepresentation}{classRepresentation.Rdash.class}}.
\end{Description}
\begin{Section}{Metadata Information}
When a class is defined, an object is stored that contains the
information about that class.  The object, known as the
\emph{metadata} defining the class, is not stored under the name of
the class (to allow programmers to write generating functions of
that name), but under a specially constructed name.
To examine the class definition, call \code{\LinkA{getClass}{getClass}}.  The
information in the metadata object includes:

\describe{
\item[Slots:] The data contained in an object from an S4 class is defined by
the \emph{slots} in the class definition.

Each slot in an object is a component of the object;
like components (that is, elements) of a
list, these may be extracted and set, using the
function \code{\LinkA{slot}{slot}()} or more often the operator
\code{"\LinkA{@}{@}"}.  However, they
differ from list components in important ways.
First, slots can only be referred to by name, not by position,
and there is no partial matching of names as with list elements.

All the objects from a particular class have the same set of slot
names; specifically, the slot names that are contained in the
class definition.  Each slot in each object always is an object
of  the
class specified for this slot in the definition of the current class.
The word \dQuote{is} corresponds to the \R{} function of the same
name (\code{\LinkA{is}{is}}), meaning that the class of the object in
the slot must be the same as the class specified in the
definition, or some class that extends the one in the
definition (a \emph{subclass}).

One class name is special, \code{.Data}.  This stands for the
\sQuote{data part} of the object.  Any class that contains one
of the basic object types in \R, has implicitly a corresponding
\code{.Data} slot of that type, allowing computations to extract
or replace the data part while leaving other slots
unchanged. The \code{.Data} slot also determines the type of the
object; if \code{x} has a \code{.Data} slot, the type of the
slot is the type of the object (that is, the value of
\code{\LinkA{typeof}{typeof}(x)}). Extending a basic type this way allows objects to
use old-style code for the corresponding type as well as S4
methods.  Any basic type can be used for \code{.Data}, with the
exception of a few that do not behave like ordinary objects;
namely, \code{"NULL"}, environments, and external pointers.

There is  one additional use of the data part, which is also an
exception to the correspondence with the object's type.  The exception
arises from the special treatment of \code{\LinkA{matrix}{matrix.Rdash.class}}
and \code{\LinkA{array}{array.Rdash.class}} \dQuote{classes} in \R.
Matrix and array objects are managed internally and recognized
without regard to any class attribute; therefore, they can be
used as the data part of a new class.  In this case, the object
type for the new class depends on the type of the data in the
matrix or array.

If the new class does not have a data part as described above,
the type of objects from the new class is
\code{"S4"}.  


\item[Superclasses:] The definition of a class includes the \emph{superclasses} ---the classes that this class extends.  A
class \code{Fancy}, say, extends a class \code{Simple} if an
object from the \code{Fancy} class has all the capabilities of
the \code{Simple} class (and probably some more as well).  In
particular, and very usefully, any method defined to work for a
\code{Simple} object can be applied to a \code{Fancy} object as
well.

This relationship is
expressed equivalently by saying that \code{Simple} is a superclass of
\code{Fancy}, or that \code{Fancy} is a subclass of
\code{Simple}.

The direct superclasses of a class are those superclasses
explicitly defined.   Direct superclasses can be defined in
three ways.  Most commonly, the superclasses are listed in the
\code{contains=} argument in the call to \code{\LinkA{setClass}{setClass}}
that creates the subclass.   In this case the subclass will
contain all the slots of the superclass, and the relation
between the class is called \emph{simple}, as it in fact is.
Superclasses can also be defined
explicitly by a call to \code{\LinkA{setIs}{setIs}}; in this case, the
relation requires methods to be specified to go from subclass to
superclass.   Thirdly, a class union is a superclass of all the
members of the union.  In this case too the relation is simple,
but notice that the relation is defined when the superclass is
created, not when the subclass is created as with the
\code{contains=} mechanism.

The definition of a superclass will also potentially contain
its own direct superclasses.  These are considered (and shown) as
superclasses at distance 2 from the original class; their direct
superclasses are at distance 3, and so on.  All these are
legitimate superclasses for purposes such as method selection.

When superclasses are defined  by including the names of
superclasses in the \code{contains=} argument to
\code{\LinkA{setClass}{setClass}},   an object from the class will have all the slots
defined for its own class \emph{and} all the slots defined for all
its superclasses as well.

The information about the relation between a class and a
particular superclass is encoded as an object of class
\code{\LinkA{SClassExtension}{SClassExtension.Rdash.class}}.  A list of such objects for
the superclasses (and sometimes for the subclasses) is included in
the metadata object defining the class.  If you need to compute
with these objects (for example, to compare the distances), call
the function \code{\LinkA{extends}{extends}} with argument \code{fullInfo=TRUE}.


\item[Prototype:] The objects from a class, typically created by a call to
\code{\LinkA{new}{new}} or by assigning another object from the class,
are defined by the \emph{prototype} object for the class and by
additional arguments in the call to \code{\LinkA{new}{new}}, which are
passed to a method for that class for the function
\code{\LinkA{initialize}{initialize}}.

Each class definition contains a prototype object
for the class.  This must have values for all the slots defined by
the class definition.
By default, these are the prototypes of all
the slot classes, if those are not virtual classes.  However, the
definition of the class can specify any valid object for any of
the slots.

}
\end{Section}
\begin{Section}{Virtual classes; Basic classes}
Classes exist for which there are no actual objects, the
\emph{virtual} classes, in fact a
very important programming tool.  They are used to group together
ordinary classes that want to share some programming behavior,
without necessarily restricting how the behavior is implemented.
Virtual class definitions may if you want include
slots (to provide some common behavior without fully defining
the object---see the class \code{\LinkA{traceable}{traceable.Rdash.class}} for an example).

A simple and useful form of virtual class is the \emph{class
union}, a virtual class that is defined in a call to
\code{\LinkA{setClassUnion}{setClassUnion}} by listing one or
more of subclasses (classes that extend the class union).  Class
unions can include as subclasses basic data types (whose
definition is otherwise sealed).

There are a number of \sQuote{basic} classes, corresponding to the
ordinary kinds of data occurring in R.  For example,
\code{"numeric"} is a class corresponding to numeric vectors.
The other vector basic classes are \code{"logical"}, \code{"integer"}, 
\code{"complex"}, \code{"character"},  \code{"raw"}, \code{"list"}
and \code{"expression"}.
The prototypes for
the vector classes are vectors of length 0 of the corresponding
type.  Notice that basic classes are unusual in that the
prototype object is from the class itself.

In addition to the vector classes there are also basic classes corresponding to objects in the
language, such as \code{"function"} and \code{"call"}.
These classes are subclasses of the virtual class \code{"language"}.
Finally, there are basic classes for
specialized objects, such as \code{"environment"} and \code{"externalptr"}.
The vector and language basic classes can be used as slots or as
superclasses for any other class definitions. 
The classes corresponding to other object types can be used as
slots but not always as superclasses, since many of them do not follow the
functional behavior of the language; in particular, they are not
copied and so cannot have attributes or slots defined locally.
\end{Section}
\begin{Section}{S3 Classes}
Earlier, informal classes of objects (usually referred to as
\sQuote{S3} classes) are used by many \R{} functions.  It is natural to
consider including them as the class for a slot in a formal class,
or even as a class to be extended by the new class.  This isn't
prohibited but there are some disadvantages, and if you do want to
include S3 classes, they should be declared by including them in a
call to \code{\LinkA{setOldClass}{setOldClass}}.  Here are some considerations:

\Itemize{
\item Using S3 classes somewhat defeats the purpose of defining a
formal class:  An important advantage to your users is that a formal
class provides guarantees of what the object contains (minimally,
the classes of the slots and therfore what data they contain;
optionally, any other requirements imposed by a validity method).

But there is no guarantee whatever about the data in an object from
an S3 class.  It's entirely up to the functions that create or
modify such objects.  If you want to provide guarantees to your
users, you will need a valdity method that explicitly checks the
contents of S3-class objects.

\item To get the minimal guarantee (that the object in a slot has, or
extends, the class for the slot) you should ensure that the S3
classes are known to \emph{be} S3 classes, possibly with S
inheritance.  To do this, include a call to
\code{\LinkA{setOldClass}{setOldClass}} for the S3 classes used.

Otherwise, the S3 class is undefined (and the code used by
\code{setClass} will issue a warning).  Slot assignments, for
example, will not then check for possible errors.

\item Current versions of \R{} (beginning with 2.8.0) try to
accommodate S4 classes that extend S3 classes, that is, those
including an S3 class in the \code{contains=} argument to
\code{\LinkA{setClass}{setClass}} . Specifically, objects from  such classes
will contain the S3 class as a slot, and some S3 computations will
recognize the S3 class,
including method dispatch and the function
\code{\LinkA{inherits}{inherits}}.  See  \code{\LinkA{S3Class}{S3Class}} for details.
The S3 classes \emph{must} have been registered by a call to  \code{\LinkA{setOldClass}{setOldClass}}.
The basic caution remains true however: There is no guarantee that all S3 computations will be
compatible, and some are known not to be.

\item These caveats apply to S3 classes; that is, objects with a
class assigned by some \R{} function but without a formal class
definition.  In contrast, the built-in vector types (\code{numeric},
\code{list}, etc.) are generally fine as slots or for
\code{contains=} classes.  These object
types don't have formal slots, but the base code in the system
essentially forces them to contain the type of data they claim to
have.

Objects with a \dQuote{class}  of \code{matrix} or \code{array} are somewhat in
between.  They do not have an explicit S3 class, but do have one or
two attributes.  There is no general problem in having these as
slots, but because there is no guarantee of a dimnames slot, they
don't work as formal classes.  The \code{ts} class, although also
ancient in the S language, is implemented in \R{} essentially as an
S3 class, with the implications noted above---not suitable for a
\code{contains=} argument---but with a few S4
methods defined.  See the documentation for class \code{\LinkA{structure}{structure.Rdash.class}} for more details.

}
\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.) 

Chambers, John M.  and Hastie, Trevor  J. eds (1992)
\emph{Statistical Models in S.}
Wadsworth \& Brooks/Cole (Appendix A for S3 classes.)

Becker, R. A., Chambers, J. M. and Wilks, A. R. (1988)
\emph{The New S Language}.
Wadsworth \& Brooks/Cole. (Out of print.) (The description of
vectors, matrix, array and time-series objects.)
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{Methods}{Methods}} for analogous discussion of methods,
\code{\LinkA{setClass}{setClass}} for details of specifying class definitions,
\code{\LinkA{is}{is}},
\code{\LinkA{as}{as}},
\code{\LinkA{new}{new}},
\code{\LinkA{slot}{slot}}
\end{SeeAlso}

