S4groupGeneric {methods}R Documentation

S4 Group Generic Functions

Description

Methods can be defined for groups of functions known as group generic functions. These exist in both S3 (see S3groupGeneric) and S4 flavours, with different groups.

Methods are defined for the group of functions as a whole. A method defined for an individual member of the group takes precedence over a method defined for the group as a whole.

When package methods is attached there are objects visible with the names of the group generics: these functions should never be called directly (a suitable error message will result if they are).

Usage

## S4 group generics:
Arith(e1, e2)
Compare(e1, e2)
Ops(e1, e2)
Logic(e1, e2)
Math(x)
Math2(x, digits)
Summary(x, ..., na.rm = FALSE)
Complex(z)

Arguments

x, z, e1, e2 objects.
digits number of digits to be used in round or signif.
... further arguments passed to or from methods.
na.rm logical: should missing values be removed?

Details

When package methods is attached (which it is by default), formal (S4) methods can be defined for the group generic functions (which are R objects which should never be called directly – a suitable error message will result if they are). There are also S3 groups Math, Ops, Summary and Complex, see ?S3groupGeneric, with no corresponding R objects.

The functions belonging to the various groups are as follows:

Arith
"+", "-", "*", "^", "%%", "%/%", "/"
Compare
"==", ">", "<", "!=", "<=", ">="
Logic
"&", "|", but not "!" since that has only one argument. Note that this is contrary to Chambers(1998), on purpose.
Ops
"Arith", "Compare", "Logic"
Math
"log", "sqrt", "log10", "cumprod", "abs", "acos", "acosh", "asin", "asinh", "atan", "atanh", "ceiling", "cos", "cosh", "cumsum", "exp", "floor", "gamma", "lgamma", "sin", "sinh", "tan", "tanh", "trunc"
Math2
"round", "signif"
Summary
"max", "min", "range", "prod", "sum", "any", "all"
Complex
"Arg", "Conj", "Im", "Mod", "Re"

Note that "Ops" merely consists of three sub groups. Functions with the group names exist in the methods package but should not be called directly.

All the functions in these groups (other than the group generics themselves) are basic functions in R. They are not by default S4 generic functions, and many of them are defined as primitives, meaning that they do not have formal arguments. However, you can still define formal methods for them. The effect of doing so is to create an S4 generic function with the appropriate arguments, in the environment where the method definition is to be stored. It all works more or less as you might expect, admittedly via a bit of trickery in the background.

Note: currently those members which are not primitive functions must have been converted to S4 generic functions (preferably before setting an S4 group generic method) as it only sets methods for known S4 generics. This can be done by a call to setGeneric, for example setGeneric("round", group="Math2").

References

Appendix A, Classes and Methods of
Chambers, J. M. and Hastie, T. J. eds (1992) Statistical Models in S. Wadsworth & Brooks/Cole.

Chambers, J. M. (1998) Programming with Data. Springer, pp. 352–4.

See Also

S3groupGeneric for S3 group generics.

Examples

setClass("testComplex", representation(zz = "complex"))
## method for whole group "Complex"
setMethod("Complex", "testComplex",
          function(z) c("groupMethod", callGeneric(z@zz)))
## exception for Arg() :
setMethod("Arg", "testComplex",
          function(z) c("ArgMethod", Arg(z@zz)))
z1 <- 1+2i
z2 <- new("testComplex", zz = z1)
stopifnot(identical(Mod(z2), c("groupMethod", Mod(z1))))
stopifnot(identical(Arg(z2), c("ArgMethod", Arg(z1))))

[Package methods version 2.5.0 Index]