[R] S4 pass-by-value work-around?

[Martin Morgan]

Hi Jeff --

two different scenarios are to overwrite the current object, along the
lines of

y <- uniquify(y)

where uniquify is a method like createUniqueName but returns the
(modified) instance rather than unique name

setMethod('uniquify', 'MyMatrix', function(x) {
    x at uniqueCount <- # something unique
    x
})

The second is a replacement method, along the lines of

setGeneric("uniqueCount<-",
    function(x, ..., value) standardGeneric("uniqueCount<-"))

setReplaceMethod("uniqueCount",
    signature=c(x="MyMatrix", value="numeric"),
    function(x, ..., value) {
        x at uniqueCount <- value
        x
    })

uniqueCount(x) <- uniqueCount(x) + 1
x # now modified

This is untested psuedo-code, so I hope it's right enough to get you
going.

Martin

Jeffrey Spies <jspies2008 at gmail.com> writes:

> Howdy all,
>
> I have a problem that I'd like some advice/help in solving---it has to do
> with R's pass-by-value system.  I understand the issue, but am wondering if
> anyone has found a working solution in dealing with it for cases when one
> wants to modify an object inside of a method, specifically when working with
> S4.  I'm aware that R.oo is able to deal with this using S3, but I'd really
> rather stick to S4.
>
> The basics of what I would like to do are coded below:
>
> setClass("MyMatrix",
> 	representation(
> 		parameters="matrix",
> 		uniqueCount="numeric"
> 	),
> 	prototype(
> 		parameters=matrix(numeric(0),0,0),
> 		uniqueCount=1	
> 	)
> )
>
> setGeneric("createUniqueName", function(object)
> standardGeneric("createUniqueName"))
>
> setMethod("createUniqueName", "MyMatrix", function(object){
> 	retval <- paste("unique_", object at uniqueCount, sep="")
> 	object at uniqueCount <- object at uniqueCount + 1
> 	return(retval)
> })
>
> x <- new("MyMatrix", parameters=matrix(0, 2, 2))
> createUniqueName(x) # returns "unique_1"
> x # x at uniqueCount is still 1
>
> I understand why this is happening, but am wondering how people in the
> community have dealt with it, specifically when using S4.  Any advice would
> be appreciated.  Also, I am aware that this is somewhat of a silly example,
> but it should allow you to see what I'm trying to accomplish.
>
> Thank you,
>
> Jeff.
>
>
> -- 
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>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

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Phone: (206) 667-2793