FW: [R] Optimising code

[Crispin Miller]

Yup, my mistake for not being very clear! Alas the computer is already very fast - looks like it's C for me...

> -----Original Message-----
> From: Patrick Burns [mailto:pburns at pburns.seanet.com]
> Sent: 07 October 2003 12:00
> Cc: Crispin Miller
> Subject: Re: FW: [R] Optimising code
> 
> 
> I had misunderstood also.  I agree with Uwe either move
> to C or buy a faster computer -- or at least another one.
> 
> Pat
> 
> Uwe Ligges wrote:
> 
> > Crispin Miller wrote:
> >
> >>>> I have a function that applies a wilcoxon test to 12 
> sets of about 
> >>>> a quarter of a million pairs
> >>>
> >>
> >>
> >>> ... and let me guess: everything is significiant to an almost 
> >>> arbitrary value of \alpha?
> >>
> >>
> >>
> >> :-) For each of quarter of a million sets, I do a wilcoxon between 
> >> two pairs each containing twenty numbers...
> >> I do this 12 times...
> >
> >
> > Ah. Sorry for misunderstanding.
> >
> >
> >>>> (and takes about 3 hours). I've replaced the inner loop I 
> >>>
> >>>
> >>> had originally with a function call via mapply, and also 
> considered 
> >>> different approximations  of the wilcoxon, rather than 
> that which is 
> >>> implemented in wilcox.test, but that makes little 
> difference 9and if 
> >>> anything slows things down :-).
> >>>
> >>> Are you using wilcox.test(), or a self written function?
> >>>
> >>
> >>
> >> I started off with wilcox.test, and tried to speed it up 
> by hacking 
> >> out as much from the original function as possible, since a fair 
> >> proportion of the code being executed was logic deciding 
> between the 
> >> different flavours of the test (I didn't expect that to make much 
> >> difference, but tried it anyway), there was also a call to pnorm() 
> >> which I replaced with a numeric approximation. This is not inlined 
> >> into the original function.
> >
> >
> >
> > In that case you cannot do very much except for writing it in a 
> > language like C / Fortran, if you really need the speed.
> >
> > Uwe Ligges
> >
> >> Crispin
> >>  
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> >>
> >>  
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> >>
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> >
> >
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> >
> >
> 
> 
> 
>
 
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