[R] Timings of function execution in R [was Re: R in Industry]

[Thomas Lumley]

On 2/9/07, Prof Brian Ripley <ripley at stats.ox.ac.uk> wrote:
>> The other reason why pmin/pmax are preferable to your functions is that
>> they are fully generic.  It is not easy to write C code which takes into
>> account that <, [, [<- and is.na are all generic.  That is not to say that
>> it is not worth having faster restricted alternatives, as indeed we do
>> with rep.int and seq.int.
>>
>> Anything that uses arithmetic is making strong assumptions about the
>> inputs.  It ought to be possible to write a fast C version that worked for
>> atomic vectors (logical, integer, real and character), but is there
>> any evidence of profiled real problems where speed is an issue?


I had an example just last month of an MCMC calculation where profiling showed that pmax(x,0) was taking about 30% of the total time.  I used

     function(x) {z <- x<0; x[z] <- 0; x}

which was significantly faster. I didn't try the arithmetic solution. Also, I didn't check if a solution like this would still be faster when both arguments are vectors (but there was a recent mailing list thread where someone else did).


      -thomas

Thomas Lumley			Assoc. Professor, Biostatistics
tlumley at u.washington.edu	University of Washington, Seattle