R help - Aug 2010 - Change value of a slot of an S4 object within a method.

Dear all,

I have an S4 class with a slot "extra" which is a list. I want to be
able to add an element called "name" to that list, containing the
object "value" (which can be a vector, a dataframe or another S4
object)

Obviously

setMethod("add.extra",signature=c("PM10Data","character","vector"),
  function(object,name,value){
             object at extra[[name]] <- value
  }
)

Contrary to what I would expect, the line :
eval(eval(substitute(expression(object at extra[[name]] <<- value))))

gives the error :
Error in object at extra[[name]] <<- value : object 'object' not
found

Substitute apparently doesn't work any more in S4 methods...

 I found a work-around by calling the initializer every time, but this
influences the performance. Returning the object is also not an
option, as I'd have to remember to assign that one each time to the
original name.

Basically I'm trying to do some call by reference with S4, but don't
see how I should do that. How would I be able to tackle this problem
in an efficient and elegant way?

Thank you in advance
Cheers
Joris

-- 
Joris Meys
Statistical consultant

Ghent University
Faculty of Bioscience Engineering
Department of Applied mathematics, biometrics and process control

tel : +32 9 264 59 87
Joris.Meys at Ugent.be
-------------------------------
Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php

Hi Joris,

On Wed, Aug 25, 2010 at 11:56 AM, Joris Meys <jorismeys at gmail.com>
wrote:
> Dear all,
>
> I have an S4 class with a slot "extra" which is a list. I want to
be
> able to add an element called "name" to that list, containing the
> object "value" (which can be a vector, a dataframe or another S4
> object)
>
> Obviously
>
>
setMethod("add.extra",signature=c("PM10Data","character","vector"),
> ?function(object,name,value){
> ? ? ? ? ? ? object at extra[[name]] <- value
> ?}
> )
>
> Contrary to what I would expect, the line :
> eval(eval(substitute(expression(object at extra[[name]] <<- value))))
>
> gives the error :
> Error in object at extra[[name]] <<- value : object 'object'
not found
>
> Substitute apparently doesn't work any more in S4 methods...
>
> ?I found a work-around by calling the initializer every time, but this
> influences the performance. Returning the object is also not an
> option, as I'd have to remember to assign that one each time to the
> original name.
>
> Basically I'm trying to do some call by reference with S4, but
don't
> see how I should do that. How would I be able to tackle this problem
> in an efficient and elegant way?
In lots of my own S4 classes I define a slot called ".cache" which is
an environment for this exact purpose.

Using this solution for your scenario might look something like this:

setMethod("add.extra",signature=c("PM10Data","character","vector"),
function(object, name, value) {
  object at .cache$extra[[name]] <- value
})

I'm not sure what your entire problem looks like, but to "get"
your
extra list, or a value form it, you could:

setMethod("extra", signature="PM10Data",
function(object, name=NULL) {
  if (!is.null(name)) {
    object at .cache$extra[[name]]
  } else {
    object at .cache$extra
})

... or something like that.

The last thing you have to be careful of is that you nave to make sure
that each new("PM10Data") object you have initializes its *own* cache:

setClass("PM10Data", representation(...,
.cache='environment'))
setMethod("initialize", "PM10Data",
function(.Object, ..., .cache=new.env()) {
  callNextMethod(.Object, .cache=.cache, ...)
})

Does that make sense?

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
?| Memorial Sloan-Kettering Cancer Center
?| Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact