From mtmorgan at fhcrc.org  Wed Apr  2 18:54:22 2008
From: mtmorgan at fhcrc.org (Martin Morgan)
Date: Wed, 02 Apr 2008 09:54:22 -0700
Subject: [Rd] "[<-" plus drop-type extra argument
In-Reply-To: <1A68FCB28DE72F4BA3B967E6506CCE4302294808@mildnpexmb01.maninvestments.ad.man.com>
References: <6E7FF74C-4FBE-4AEA-B8D7-8C4F27CD47C0@noc.soton.ac.uk>
	<1A68FCB28DE72F4BA3B967E6506CCE4302294808@mildnpexmb01.maninvestments.ad.man.com>
Message-ID: <47F3BA3E.7050200@fhcrc.org>


Sklyar, Oleg (MI London) wrote:
> Robin:
> 
> two points:

> Second, your setReplaceMethod seems to be wrong in the definition, try the following adding signature for value and ... in the function call. You cannot simply drop the ... . Probably you will also need to include j="missing" in the signature. There is also no need to construct a new object on return and I do not think drop is a part of generic for replacement, it is for extraction though
> 
> setReplaceMethod("[", signature(x="foo", value="ANY"),
>   function(x, i,j, ..., recalculate=FALSE, value) {
>     x at .Data[i] = value
>     if (recalculate) x at NC = sum(x at .Data)
>     x
>   })

Informative to investigate this a bit further. Without the ... we have

 > showMethods("[<-", class="foo", includeDef=TRUE)
Function: [<- (package base)
x="foo"
function (x, i, j, ..., value)
{
     .local <- function (x, i, j, recalculate = FALSE, value)
     x
     .local(x, i, j, ..., value)
}

.local maps between the generic and the method signature; the map is 
incorrect when there are additional arguments but no .... An 
indiscretion, perhaps, on the part of the methods package. This is in 
contrast to a method with ...

 > showMethods("[<-", class="foo", includeDef=TRUE)
Function: [<- (package base)
x="foo"
function (x, i, j, ..., value)
{
     .local <- function (x, i, j, ..., recalculate = FALSE, value)
     x
     .local(x, i, j, ..., value = value)
}

here .local plays the same role, but value is named explicitly and the 
problem avoided.

With respect to use of 'new' and slot assignments,  it might be delving 
too much into implementation but I think (a) using 'initialize' is 
better than 'new' when you're doing a copy construction and (b) 
'initialize' is more memory efficient than slot assignment when doing 
multiple assignments (at least tracemem says so):

setGeneric("up1", function(x) standardGeneric("up1"))
setGeneric("up2", function(x) standardGeneric("up2"))

setMethod("up1", signature(x="foo"), function(x) {
     x at x <- 1
     x at NC <- NA_real_
     x
})
setMethod("up2", signature(x="foo"), function(x) {
     initialize(x, x=1, NC=NA_real_)
})

 > a1 <- up1(a) # 2 copies
tracemem[0x6d08d60 -> 0x7fa4628]: up1 up1
tracemem[0x7fa4628 -> 0x9b45518]: up1 up1
 > a2 <- up2(a) # just 1
tracemem[0x6d08d60 -> 0x6cad360]: initialize initialize up2 up2
 > identical(a1, a2)
[1] TRUE

This also provides object validation, which may or may not be desirable.

Martin

> Here is the output:
>> a = new("foo", 1:15)
>> a
> An object of class ???foo???
>  [1]  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15
> Slot "NC":
> [1] NA
> 
>> a[5,recalculate=TRUE] = 25
>> a
> An object of class ???foo???
>  [1]  1  2  3  4 25  6  7  8  9 10 11 12 13 14 15
> Slot "NC":
> [1] 140
> 
> 
> Dr Oleg Sklyar
> Technology Group
> Man Investments Ltd
> +44 (0)20 7144 3803
> osklyar at maninvestments.com 
> 
>> -----Original Message-----
>> From: r-devel-bounces at r-project.org 
>> [mailto:r-devel-bounces at r-project.org] On Behalf Of Robin Hankin
>> Sent: 02 April 2008 09:51
>> To: R-devel at r-project.org
>> Subject: [Rd] "[<-" plus drop-type extra argument
>>
>> Hello
>>
>> I am writing a replacement method for an S4 class and want to 
>> pass an additional argument to  "[<-"() along the lines of  
>> "["()'s  "drop"  
>> argument.
>>
>> Specifically, I have an S4  class, call it "foo", with a slot  'x'  
>> that is a
>> vector and a slot  'NC' that  is a scalar.
>>
>> I want to be able to pass a Boolean argument to the 
>> replacement method which specifies whether or not to 
>> recalculate  NC (which is time-consuming and often not 
>> needed).  I want the default behaviour to be "don't recalculate NC".
>>
>> Toy example follows, in which 'NC' is the sum of x (in my 
>> application, calculating NC is an expensive multidimensional 
>> integral).
>>
>>
>> setClass("foo",
>>           representation = representation(x="numeric" , NC="numeric"),
>>           prototype      = list(x=double() , NC=NA_real_)
>>           )
>>
>> setReplaceMethod("[",signature(x="foo"),
>>                   function(x,i,j,recalculate=FALSE,value){
>>                     jj <- x at x
>>                     jj[i] <- value
>>                     if(recalculate){
>>                       return(new("foo" , x=jj , NC=sum(jj)))
>>                     } else {
>>                       return(new("foo" , x=jj , NC=NA_real_))
>>                     }
>>                   }
>>                   )
>>
>>
>>
>>
>> Then
>>
>>
>>
>>  >
>>  > a <- new("foo", x=1:10,NC=45)
>>
>>
>>  > a[4,recalculate=FALSE] <- 10000
>>  > a
>> An object of class ?foo?
>> Slot "x":
>>   [1]     1     2     3 10000     5     6     7     8     9    10
>>
>> Slot "NC":
>> [1] NA
>>
>> #  Desired behaviour: NC not recalculated
>>
>>
>>  >
>>  > a[4,recalculate=TRUE] <- 10000
>>  > a
>> An object of class ?foo?
>> Slot "x":
>>   [1]     1     2     3 10000     5     6     7     8     9    10
>>
>> Slot "NC":
>> [1] 10051
>>
>>
>> # Desired behaviour: NC recalculated
>>
>>  >
>>  > a[4] <- 10000
>> Error in .local(x, i, j, ..., value) :
>>    argument "value" is missing, with no default  >
>>
>> # Undesired behaviour:  I wanted 'recalculate' to take its 
>> default value of FALSE, and 'NC' not be recalculated.
>>
>>
>> How to do this?
>>
>>
>>
>>
>>
>> --
>> Robin Hankin
>> Uncertainty Analyst and Neutral Theorist, National 
>> Oceanography Centre, Southampton European Way, Southampton 
>> SO14 3ZH, UK
>>   tel  023-8059-7743
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
> 
> 
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M2 B169
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[Rd] "[<-" plus drop-type extra argument
Martin Morgan