From mtmorgan at fhcrc.org  Tue Jun 23 15:25:22 2009
From: mtmorgan at fhcrc.org (Martin Morgan)
Date: Tue, 23 Jun 2009 06:25:22 -0700
Subject: [Rd] V2.9.0 changes [Sec=Unclassified]
In-Reply-To: <42C7503E0B99F248B06BC65E7D2B4E020122C50FB1FD@EX2K7-CCR.AAD.GOV.AU>
References: <42C7503E0B99F248B06BC65E7D2B4E020122C50FB1FD@EX2K7-CCR.AAD.GOV.AU>
Message-ID: <4A40D7C2.7050307@fhcrc.org>

Troy Robertson wrote:
> Hi all,
> 
> 
> 
> Prefix: I am a frustrated Java coder in R.

ah good, if you're frustrated with Java you'll find R very different ;)

> 
> 
> 
> I am coding a medium sized ecosystem modelling program in R.  I have changed to using S4 objects and it has cost me an order of magnitude in execution speed over the functional model.  I cannot afford this penalty and have found that it is the result of all the passing-by-value of objects.
> 
> 
> 
> I see that you can now safely inherit from environment in V2.9.0.
> 
> That got me all excited that I would now be able to pass objects by reference.
> 
> 
> 
> But...
> 
> That doesn't seem to be the case.
> 
> It only seem that passing an environment which holds the object allows for pass-by-reference and that passing an object which inherits from environment doesn't.
> 
> Why is this the case, either an object inherits the properties of its parent or it doesn't.

The object inherits slots from it's parent, and the methods defined on
the parent class. Maybe this example helps?

setClass("Ticker", contains=".environment")

## initialize essential, so each instance gets its own environment
setMethod(initialize, "Ticker",
          function(.Object, ..., .xData=new.env(parent=emptyenv()))
{
    .xData[["count"]] <- 0
    callNextMethod(.Object, ..., .xData=.xData)
})

## tick: increment (private) counter by n
setGeneric("tick", function(reference, n=1L) standardGeneric("tick"),
           signature="reference")

setMethod(tick, "Ticker", function(reference, n=1L) {
    reference[["count"]] <- reference[["count"]] + n
})

## tock: report current value of counter
setGeneric("tock", function(reference) standardGeneric("tock"))

setMethod(tock, "Ticker", function(reference) {
    reference[["count"]]
})

and then

> e <- new("Ticker")
> tock(e)
[1] 0
> tick(e); tick(e, 10); tock(e)
[1] 11
> f <- e
> tock(f); tick(e); tock(f)
[1] 11
[1] 12

The data inside .environment could be structured, too, using S4.
Probably it would be more appropriate to have the environment as a slot,
rather the class that is being extended. And in terms of inherited
'properties', e.g., the "[[" function as defined on environments is
available

> e[["count"]]

Of course I haven't seen your code, but a different interpretation of
your performance issues is that, within the rules of S4, you've chosen
to implement functionality in an inefficient way. So it might be
instructive to step back a bit and try to reformulate your data
structures and methods. This is hard to do.

Martin

> 
> Has anyone else had a play with this?  Or have I got it all wrong.
> 
> 
> 
> I tried the below:
> 
> -----------------------------------------------------------------------------------------
> 
> setClass('foo', representation=representation(stuff='list', bar='numeric'),
> 
>                      prototype=list(stuff=list(), bar=0),
> 
>                      contains='.environment')
> 
> 
> 
> setGeneric('doit', function(.Object, newfoo='environment') standardGeneric('doit'))
> 
> 
> 
> setMethod('doit', 'foo', function(.Object, newfoo){newfoo at bar <- 10})
> 
> 
> 
> z <- new('foo')
> 
> 
> 
> z at stuff$x <- new('foo')
> 
> 
> 
> doit(z,z at stuff$x)
> 
> 
> 
> z at stuff$x at bar
> 
> 
> 
> [1] 0
> 
> ------------------------------------------------------------------------------------------
> 
> 
> 
> Can anyone help with a better way of doing this.
> 
> I'm trying to avoid all the indirection of packing and unpacking environments for passing.
> 
> 
> 
> 
> 
> Thanks heaps
> 
> 
> 
> Troy
> 
> 
> 
> 
> 
> Troy Robertson
> 
> Database and Computing Support Provider
> 
> Southern Ocean Ecosystems, ERM/Fish
> 
> Australian Antarctic Division
> 
> Channel Highway, Kingston 7050
> 
> PH: 03 62323571
> 
> Troy.Robertson at aad.gov.au
> 
> 
> 
> 
> ___________________________________________________________________________
> 
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[Rd] V2.9.0 changes [Sec=Unclassified]
Martin Morgan