Methods               package:methods               R Documentation

_G_e_n_e_r_a_l _I_n_f_o_r_m_a_t_i_o_n _o_n _M_e_t_h_o_d_s

_D_e_s_c_r_i_p_t_i_o_n:

     This documentation section covers some general topics on how
     methods work and how the 'methods' package interacts with the rest
     of R.  The information is usually not needed to get started with
     methods and classes, but may be helpful for moderately ambitious
     projects, or when something doesn't work as expected.

     The section *How Methods Work* describes the underlying mechanism;
     *Dispatch and Method Selection* provides more details on how class
     definitions determine which methods are used. For additional
     information specifically about class definitions, see '?Classes'.

_H_o_w _M_e_t_h_o_d_s _W_o_r_k:

     A generic function is a function that has associated with it a
     collection of other functions (the methods), all of which agree in
     formal arguments with the generic.

     Each R package will include  methods metadata objects
     corresponding to each generic function  for which methods have
     been defined in that package. When the package is loaded into an R
     session, the methods for each generic function are _cached_, that
     is, stored in the environment of the generic function along with
     the methods from previously loaded packages.  This merged table of
     methods is used to dispatch or select methods from the generic,
     using class inheritance and possibly group generic functions (see
     'S4groupGeneric') to find an applicable method. See the *Dispatch*
     section below. The caching computations ensure that only one
     version of each generic function is visible globally; although
     different attached packages may contain a copy of the generic
     function, these are in fact identical.

     The methods for a generic are stored according to the
     corresponding 'signature' for which the method was defined, in a
     call to 'setMethod'.  The signature associates one class name with
     each of a subset of the formal arguments to the generic function. 
     Which formal arguments are available, and the order in which they
     appear, are determined by the '"signature"' slot of the generic
     function.  By default, the signature of the generic consists of
     all the formal arguments except ..., in the order they appear in
     the function definition.

     Trailing arguments in the signature will be _inactive_  if no
     method has yet been specified that included those arguments.
     Inactive arguments are not needed or used in labeling the cached
     methods.  (The distinction does not change which methods are
     dispatched, but ignoring inactive arguments does improve the
     efficiency of dispatch.  Thus, defining the generic signature to
     contain the most useful arguments first can help efficiency
     somewhat.)

     All arguments in the signature of the generic function will be
     evaluated when the function is called, rather than using the
     traditional lazy evaluation rules of S.  Therefore, it's important
     to _exclude_ from the signature any arguments that need to be
     dealt with symbolically (such as the first argument to function
     'substitute').  Note that only actual arguments are evaluated, not
     default expressions. A missing argument enters into the method
     selection as class '"missing"' and non-missing arguments according
     to their actual class.

     As of version 2.4.0 of R, the cached methods are stored in an
     environment object.  The names used for assignment are a
     concatenation of the class names for the arguments in the active
     signature.

_D_i_s_p_a_t_c_h _a_n_d _M_e_t_h_o_d _S_e_l_e_c_t_i_o_n:

     When a call to a generic function is evaluated, a method is
     selected corresponding to the classes of the actual arguments in
     the signature. First, the cached methods table is searched for a
     _direct_ match; that is, a method stored under the direct class
     names. The direct class is the value of 'class(x)' for each
     non-missing argument, and class '"missing"' for each missing
     argument. If no method is found directly for the actual arguments
     in a call to a generic function, an attempt is made to match the
     available methods to the arguments by using _inheritance_.

     Each class definition potentially includes the names of one or
     more classes that the new class contains.  (These are sometimes
     called the _superclasses_ of the new class.) The S language has an
     additional, explicit mechanism for defining superclasses, the
     'setIs' mechanism. Also, a call to 'setClassUnion' makes the union
     class a superclass of each of the members of the union. All three
     mechanisms are treated equivalently for purposes of inheritance: 
     they define the _direct_ superclasses of a particular class.

     The direct superclasses themselves may contain other classes. 
     Putting all this information together produces the full list of
     superclasses for this class. The superclass list is included in
     the definition of the class that is cached during the R session.
     Each element of the list describes the nature of the relationship
     (see SClassExtension-class for details). Included in the element
     is a 'distance' slot giving a numeric distance between the two
     classes. The distance currently is the path length for the
     relationship: '1' for direct superclasses (regardless of which
     mechanism defined them), then '2' for the direct superclasses of
     those classes, and so on. In addition, any class implicitly has
     class '"ANY"' as a superclass.  The distance to '"ANY"' is treated
     as larger than the distance to any actual class. The special class
     '"missing"' corresponding to missing arguments has only '"ANY"' as
     a superclass, while '"ANY"' has no superclasses.

     The information about superclasses is summarized when a class
     definition is printed.

     When a method is to be selected by inheritance, a search is made
     in the table for all methods directly corresponding to a
     combination of either the direct class or one of its superclasses,
     for each argument in the active signature. For an example, suppose
     there is only one argument in the signature and that the class of
     the corresponding object was '"dgeMatrix"' (from the 'Matrix'
     package on CRAN). This class has two direct superclasses and
     through these 4 additional superclasses. Method selection finds
     all the methods in the table of directly specified methods labeled
     by one of these classes, or by '"ANY"'.

     When there are multiple arguments in the signature, each argument
     will generate a similar  list of inherited classes. The possible
     matches are now all the combinations of classes from each argument
     (think of the function 'outer' generating an array of all possible
     combinations). The search now finds all the methods matching any
     of this combination of classes. The computation of distances also
     has to combine distances for the individual arguments. There are
     many ways to combine the distances; the current implementation
     simply adds them. The result of the search is then a list of zero,
     one or more methods, and a parallel vector of distances between
     the target signature and the available methods.

     If the list has more than one matching method,  only those
     corresponding to the minimum distance are considered. There may
     still be multiple best methods. The dispatch software considers
     this an ambiguous case and warns the user (only on the first call
     for this selection). The method occurring first in the list of
     superclasses is selected.  By the mechanism of producing the
     extension information, this orders the direct superclasses by the
     order they appeared in the original call to 'setClass', followed
     by classes specified in 'setIs' calls, in the order those calls
     were evaluated, followed by classes specified in unions. Then the
     superclasses of those classes are appended (note that only the
     ordering of classes within a particular generation of superclasses
     counts, because only these will have the same distance). For
     further discussion of method selection, see the document  <URL:
     http://developer.r-project.org/howMethodsWork.pdf>.

     All this detail about selection is less important than the
     realization that having ambiguous method selection usually means
     that you need to be more specific about intentions. It is likely
     that some consideration other than the ordering of superclasses in
     the class definition is more important in determining which method
     _should_  be selected, and the preference may well be different
     for different generic functions.  Where ambiguities arise, the
     best approach is usually to provide a specific method for the
     subclass.

     When the inherited method has been selected, the selection is
     cached in the generic function so that future calls with the same
     class will not require repeating the search.  Cached non-direct
     selections are not themselves used in inheritance searches, since
     that could result in invalid selections.

     Besides being initiated through calls to the generic function,
     method selection can be done explicitly by calling the function
     'selectMethod'.

_R_e_f_e_r_e_n_c_e_s:

     The R package 'methods' implements, with a few exceptions, the
     programming interface for classes and methods in the book
     _Programming with Data_ (John M. Chambers, Springer, 1998), in
     particular sections 1.6, 2.7, 2.8, and chapters 7 and 8.

     While the programming interface for the 'methods' package follows
     the reference, the R software is an original implementation, so
     details in the reference that reflect the S4 implementation may
     appear differently in R.  Also, there are extensions to the
     programming interface developed more recently than the reference.

_S_e_e _A_l_s_o:

     'setGeneric', 'setClass' and the document  <URL:
     http://developer.r-project.org/howMethodsWork.pdf>.

