Overload log function - r

Question

I am trying to overload some functions in the context of S4-classes. Here is a sample code:
foo <- setClass(
Class = "foo",
slots = c("name" = "character", "value" = "numeric")
)
setMethod(f = "exp",
signature = c(x = "foo"),
definition = function(x) {
exp(x#value)
}
)
setMethod(f = "round",
signature = c(x = "foo", digits = "foo"),
definition = function(x, digits) {
round(x#value, digits#value)
}
)
setMethod(f = "log",
signature = c(x = "foo", base = "foo"),
definition = function(x, base) {
log(x#value, base#value)
}
)
While the exp and round functions work just fine, the log function does not with the following error:
Error in match.call(definition, call, expand.dots, envir) :
unused argument (base = c("foo", ""))
This is confusing as the args function states that the name of the second (optional) argument is indeed base.
Would you know what the issue is? Thanks.

Answer 1

From the help page for log,
"Note that this means that the S4 generic for log has a signature with only one argument, x, but that base can be passed to methods (but will not be used for method selection). On the other hand, if you only set a method for the Math group generic then base argument of log will be ignored for your class."
So, you can't use "base" in your signature. If you really need dispatch on the base argument, you will have to write a second generic:
myLog <- function(x,base) log(x,base)
setGeneric(myLog,signature=c("x","base"))
On a separate issue, you don't need to write separate definitions for every function like this, you can use group generics. In your example, you could write
setMethod("Math","foo",function(x)callGeneric(x#value))
or possibly
setMethod("Math","foo",function(x,...)callGeneric(x#value,...))
And this single line of code will make all of
[1] "abs" "sign" "sqrt" "ceiling" "floor" "trunc" "cummax" "cummin"
[9] "cumprod" "cumsum" "exp" "expm1" "log" "log10" "log2" "log1p"
[17] "cos" "cosh" "sin" "sinh" "tan" "tanh" "acos" "acosh"
[25] "asin" "asinh" "atan" "atanh" "cospi" "sinpi" "tanpi" "gamma"
[33] "lgamma" "digamma" "trigamma"
work as desired (by operating on the #value slot of foo). You might also want to do something similar for math2, which includes round.
A third way to achieve what you want is to have your "foo" class extend the numeric class:
setClass("foo",
slots = c("name" = "character"),
contains="numeric"
) -> foo
Then everything works as if the objects are actually numeric. If you need to get at the "data part" of an object x of class foo, then you can use foo#.Data.