[R] Speeding up

[ONKELINX, Thierry]

Dear Bjorn,

Do you know that mean(xy*ind)+mean(xy*!ind) yields the same value for
all i? Maybe you meant mean(xy[ind]) + mean(xy[!ind])

sapply(xord, function(xordi, xy = x){
  ind <- xy < xordi
  mean(xy*ind)+mean(xy*!ind)
})

Cheers,

Thierry

------------------------------------------------------------------------
----
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature
and Forest
Cel biometrie, methodologie en kwaliteitszorg / Section biometrics,
methodology and quality assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium
tel. + 32 54/436 185
Thierry.Onkelinx op inbo.be
www.inbo.be 

Do not put your faith in what statistics say until you have carefully
considered what they do not say.  ~William W. Watt
A statistical analysis, properly conducted, is a delicate dissection of
uncertainties, a surgery of suppositions. ~M.J.Moroney

 

> -----Oorspronkelijk bericht-----
> Van: r-help-bounces op stat.math.ethz.ch 
> [mailto:r-help-bounces op stat.math.ethz.ch] Namens Van Campenhout Bjorn
> Verzonden: maandag 9 juli 2007 15:12
> Aan: r-help op stat.math.ethz.ch
> Onderwerp: [R] Speeding up
> 
> Hi R-helpers,
> 
> I am new in programming and R, so this may be basic.  I need 
> to speed up a procedure where I minimize some function on 
> different partitions of the data. I can do this with a loop, 
> as for instance in:
> 
> i<-1
> meanmin<-Inf
> while (i<length(x)) {
> 	ind<-x<xord[i]
> 	if (some function to be minimized<meanmin) {
> 		meanmin<-some function to be minimized
> 		indmin<-xord[i]
> 	}
> i<-i+1
> }
> print(indmin)
> 
> I learned that I should avoid loops, so I found the following
> alternative:
> 
> dmat<-outer(x,xord,"<")*1
> ss<-apply(dmat,2,function (z) some function to be minimized) 
> indmin<-xord[which.min(ss)]
> print(indmin)
> 
> But this does not lead to spectacular improvements 
> (obviously, this is dependent on the function and the length 
> of x, and this dmat does not seem to be an elegant solution 
> to me).  Is there scope for substantial improvement? Any 
> pointers will be greatly appreciated.  Below an example with 
> some timings.
> 
> 
> > set.seed(12345)
> > x <- rnorm(1000, mean = 5, sd = 2)
> > xord<-x[order(x)]
> > 
> > system.time({i<-1
> + meanmin<-Inf
> + while (i<length(x)) {
> + ind<-x<xord[i]
> + if ((mean(x*ind)+mean(x*!ind))<meanmin) {
> + meanmin<-mean(x*ind)+mean(x*!ind)
> + indmin<-xord[i]
> + }
> + i<-i+1
> + }
> + print(indmin)})
> [1] 3.826595
>    user  system elapsed 
>    0.14    0.00    0.14 
> > 
> > 
> > 
> > system.time({dmat<-outer(x,xord,"<")*1
> + ss<-apply(dmat,2,function (z) mean(x*z)+mean(x*!z)) 
> + indmin<-xord[which.min(ss)]
> + print(indmin)})
> [1] 3.826595
>    user  system elapsed 
>    0.42    0.06    0.49 
> > 
> >
> 
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