[R] Cacheing computationally expensive getter methods for S4 objects

[Steve Lianoglou]

Hi,

On Wed, Oct 14, 2009 at 4:23 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> Steve Lianoglou wrote:
>> Very clever, that looks to do the trick!
>
> I think though that all Square's then share the same environment
> (created in the prototype) and hence area.
>
>> area(new("Square", length=50, width=100))
> Accessing
> [1] 50
>
>
> Which is quite efficient at doing the calculation, but maybe not what is
> expected...

Hah! This rabbit hole is deep, indeed.

Thanks for the tip, I'm using some incantation of "initialize" to get
around this, as you suggested, though your "functional scope" approach
also looks like a good idea.

Cheers,
-steve

>
> The solution is to create the area environment in an 'initialize' method.
>
> A different approach, but along similar lines, might make 'area' a
> function that exploits lexical scope. Here's an area 'factory'
>
> areaf <- function() {
>    area <- NULL
>    function(x) {
>        if (is.null(area)) {
>            message("expensive")
>            area <<- x at length * x at width
>        }
>        area
>    }
> }
>
> that we use in the initialize method
>
> setMethod(initialize, "Rect",
>          function(.Object, ..., length=.Object at length,
>                   width=.Object at width)
> {
>    callNextMethod(.Object, area=areaf(), length=length,
>                   width=width, ...)
> })
>
> setMethod(area, "Rect", function(x) x at area(x))
>
> The signature of initialize is such that one could
>
> setReplaceMethod("length", c("Rect", "numeric"), function(x, value) {
>    initialize(x, length=value)
> })
>
>
> so
>
>> a <- new("Rect", length=10, width=5)
>> area(a)
> expensive
> [1] 50
>> area(a) # cheap
> [1] 50
>> b <- a
>> area(b)
> [1] 50
>> length(b) <- 20
>> area(a)
> [1] 50
>> area(b)
> expensive
> [1] 100
>
> Martin
>
>>
>> Thanks,
>>
>> -steve
>>
>> On Oct 14, 2009, at 2:57 PM, Benilton Carvalho wrote:
>>
>>> If you change 'area' to an environment, you may be able to get
>>> something close to what you want.
>>>
>>> For example:
>>>
>>> setClass("Square",
>>>         representation(
>>>                        length='numeric',
>>>                        width='numeric',
>>>                        area='environment'
>>>                        ),
>>>         prototype(
>>>                   length=0,
>>>                   width=0,
>>>                   area=new.env()
>>>                   )
>>>         )
>>>
>>> setGeneric("area", function(x) standardGeneric("area"))
>>> setMethod("area", "Square",
>>>          function(x){
>>>            if (length(ls(x at area)) == 0){
>>>              message("Computing")
>>>              assign("area", x at width * x at length, envir=x at area)
>>>            }
>>>            message("Accessing")
>>>            get("area", envir=x at area)
>>>          })
>>>
>>> tmp <- new("Square", length=5, width=10)
>>> area(tmp) ## This should show "computing" and "accessing"
>>> area(tmp) ## the 2nd call should show 'accessing' only
>>>
>>>
>>> b
>>>
>>>
>>>
>>> On Oct 14, 2009, at 3:31 PM, Steve Lianoglou wrote:
>>>
>>>> Hi,
>>>>
>>>> I was wondering if there was a way to store the results of a
>>>> computationally expensive "getter" call on an S4 object, so that it is
>>>> only calculated once for each object.
>>>>
>>>> Trivial example: let's say I want to cache the "expensive" area
>>>> calculation of a square object.
>>>>
>>>> setClass("Square",
>>>>  representation(
>>>>    length='numeric',
>>>>    width='numeric',
>>>>    area='numeric'
>>>>  ),
>>>>  prototype(
>>>>    length=0,
>>>>    width=0,
>>>>    area=-1
>>>>  )
>>>> )
>>>>
>>>> setGeneric("area", function(x) standardGeneric("area"))
>>>> setMethod("area", "Square",
>>>> function(x) {
>>>>  if (x at area == -1) {
>>>>    x at area <- x at width * x at height
>>>>  }
>>>>  x at area
>>>> })
>>>>
>>>> Now the first time I call ``area(my.square)`` it computes
>>>> ``my.square at width * my.square at height``, but each subsequent call
>>>> returns ``x at area`` since the area computation has already been calc'd
>>>> and set for this object.
>>>>
>>>> Is this possible? I'm guessing the R pass by value semantics is going
>>>> to make this one difficult ... is there some S4 reference I missed
>>>> that has this type of info from?
>>>>
>>>> Thanks,
>>>> -steve
>>>>
>>>> --
>>>> 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
>>>>
>>>> ______________________________________________
>>>> R-help at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>> PLEASE do read the posting guide
>>>> http://www.R-project.org/posting-guide.html
>>>> and provide commented, minimal, self-contained, reproducible code.
>>>
>>
>> --
>> 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
>>
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
>
> --
> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793
>



-- 
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