From andy_liaw at merck.com  Fri Aug 27 16:25:08 2010
From: andy_liaw at merck.com (Liaw, Andy)
Date: Fri, 27 Aug 2010 10:25:08 -0400
Subject: [Rd] Is it safe not to coerce matrices with as.double() in .C()?
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From: Prof Brian Ripley
> 
> On Fri, 27 Aug 2010, peter dalgaard wrote:
> 
> >
> > On Aug 27, 2010, at 2:44 PM, Liaw, Andy wrote:
> >
> >> I'd very much appreciate guidance on this.  A user 
> reported that the
> >> as.double() coercion used inside the .C() call for a function in my
> >> package (specifically, randomForest:::predict.randomForest()) is
> >> taking up significant amount of time when called repeatedly, and
> >> Removing some of these reduced run time by 30-40% in some cases.
> >> These arguments are components of the fitted model (thus do not
> >> change), and are matrices.  Some basic tests show no difference in
> >> The result when the coercions are removed (other than 
> faster run time).
> >> What I like to know is whether this is safe to do, or is 
> it likely to
> >> lead
> >> to trouble in the future?
> >
> > In a word: yes. It is safe as long as you are absolutely sure that 
> > the argument has the right mode. The unsafeness comes in 
> when people 
> > might unwittingly use, say, an integer vector where a double was 
> > expected, causing memory overruns and general mayhem.
> >
> > Notice, BTW, that if you switch to .Call or .External, then 
> you have 
> > much more scope for handling such details on the C-side. E.g. you 
> > could coerce only if the object has the wrong mode, avoid 
> > duplicating things you won't be modifying anyway, etc.
> 
> But as as.double is effectively .Call it has the same freedom, and it 
> does nothing if no coercion is required.  The crunch here is 
> likely to 
> be
> 
>       ?as.double? attempts to coerce its argument to be of 
> double type:
>       like ?as.vector? it strips attributes including names.  
> (To ensure
>       that an object is of double type without stripping 
> attributes, use
>       ?storage.mode?.)
> 
> I suspect the issue is the copying to remove attributes, in which case

I can certainly believe this.  I've tried replacing as.double() to c(), thinking attributes need to be stripped.  That actually increased run time very slightly instead of reducing it.
 
> storage.mode(x) <- "double"
> 
> should be a null op and so both fast and safe.

Will follow this advise.  Thanks to both of you for the help!

Best,
Andy

 
> -- 
> Brian D. Ripley,                  ripley at stats.ox.ac.uk
> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
> University of Oxford,             Tel:  +44 1865 272861 (self)
> 1 South Parks Road,                     +44 1865 272866 (PA)
> Oxford OX1 3TG, UK                Fax:  +44 1865 272595
> 
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[Rd] Is it safe not to coerce matrices with as.double() in .C()?
Liaw, Andy