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){new...@bar <- 10})
>
>
>
> z <- new('foo')
>
>
>
> z...@stuff$x <- new('foo')
>
>
>
> doit(z,z...@stuff$x)
>
>
>
> z...@stuff$x@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
>
> [email protected]
>
>
>
>
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>
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