From Troy.Robertson at aad.gov.au  Fri Jul  3 01:19:39 2009
From: Troy.Robertson at aad.gov.au (Troy Robertson)
Date: Fri, 3 Jul 2009 09:19:39 +1000
Subject: [Rd] V2.9.0 changes [Sec=Unclassified]
In-Reply-To: <4A4CAEF4.3070008@fhcrc.org>
Message-ID: <42C7503E0B99F248B06BC65E7D2B4E020122C50FB30A@EX2K7-CCR.AAD.GOV.AU>


> -----Original Message-----
> From: Martin Morgan [mailto:mtmorgan at fhcrc.org]
> Sent: Thursday, 2 July 2009 10:58 PM
> To: Troy Robertson
> Cc: 'r-devel at R-project.org'
> Subject: Re: [Rd] V2.9.0 changes [Sec=Unclassified]
>
> Troy Robertson wrote:
> > Well...
> >
> > My performance problems were in the pass-by-value semantics of R.
> >
> > I have just changed my classes to inherit from .environment and then
> moved data members from S4 slots to the .xData objects as Martin
> suggested.
>
> Actually, I had hoped the take-home message would be in the final
> paragraph:
>
> >> 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.
>

Yes, it just takes a little time and playing around to work out the rules of R (and S4) though, and how to use them to your advantage rather than be limited by them.  I know I am still probably not using this functional language in the best way, but there you go.


>
> > That meant I could remove all my returns and assignments on all method
> calls.
> >
> > This has sped execution time for my model up by more than an order of
> magnitude. Eg one test simulation from 1931 secs down to 175 secs.
> >
> > Not bad seeing as though the class structure, functionality and logic
> has not been touched.
> >
> > I really do think S4 could benfit from having its slots stored in
> environment when the class enherits from .environment.  It would be a lot
> more sensible if my data members were still declared as S4 slots instead
> of having to hide them in .xData
> >
> > 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
> >
> >
> >> -----Original Message-----
> >> From: Martin Morgan [mailto:mtmorgan at fhcrc.org]
> >> Sent: Tuesday, 23 June 2009 11:25 PM
> >> To: Troy Robertson
> >> Cc: 'r-devel at R-project.org'
> >> Subject: Re: [Rd] V2.9.0 changes [Sec=Unclassified]
> >>
> >> 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
> >>>
> >>>
> >>>
> >>>
> >>>
> >>
> __________________________________________________________________________
> >> _
> >>>     Australian Antarctic Division - Commonwealth of Australia
> >>> IMPORTANT: This transmission is intended for the addressee only. If
> you
> >> are not the
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> >>> strictly prohibited by Commonwealth law. If you have received this
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> >>> please notify the sender immediately by e-mail or by telephoning +61 3
> >> 6232 3209 and
> >>> DELETE the message.
> >>>         Visit our web site at http://www.antarctica.gov.au/
> >>>
> >>
> __________________________________________________________________________
> >> _
> >>>       [[alternative HTML version deleted]]
> >>>
> >>> ______________________________________________
> >>> R-devel at r-project.org mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/r-devel
> >
> >
> __________________________________________________________________________
> _
> >
> >     Australian Antarctic Division - Commonwealth of Australia
> > IMPORTANT: This transmission is intended for the addressee only. If you
> are not the
> > intended recipient, you are notified that use or dissemination of this
> communication is
> > strictly prohibited by Commonwealth law. If you have received this
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> 6232 3209 and
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> __________________________________________________________________________
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___________________________________________________________________________

    Australian Antarctic Division - Commonwealth of Australia
IMPORTANT: This transmission is intended for the addressee only. If you are not the
intended recipient, you are notified that use or dissemination of this communication is
strictly prohibited by Commonwealth law. If you have received this transmission in error,
please notify the sender immediately by e-mail or by telephoning +61 3 6232 3209 and
DELETE the message.
        Visit our web site at http://www.antarctica.gov.au/
___________________________________________________________________________



[Rd] V2.9.0 changes [Sec=Unclassified]
Troy Robertson