On Jun 26, 2011, at 2:56 AM, Alexander Engelhardt wrote:
Hey,
I just read another post about calling R from C. Someone on
stackoverflow (DWin makes me suspect its David W.?) referenced this: http://www.math.univ-montp2.fr/~pudlo/R_files/call_R.pdf
Which made me think: Why is a loop in R bad, but in C not?
I do not think the cited authority provides any support to that
notion. It rather suggests that things which might benefit from using
a compiler can be fairly easily passed to C.
And where exactly does looping cost the most? I wrote a piece of
code for my bachelor's thesis where I loop from 1 to 500, and
estimate a boosted model in every iteration. The procedure takes 2-6
minutes. In this example the loop (instead of some kind of apply())
shouldn't cost too much time, right?
I suspect it's way worse if someone would loop from 1 to 10000 and
perform only a small task (a mean(), for example) in each loop. Can
someone confirm this?
_You_ can investigate it. I cannot determine from your statements what
expectations you have for an apply-vs-loop test, so I am not sure if
this is confirming or disproving:
z2 <- z <- vector("numeric", 10000)
x <- matrix(1:100, 10000,20)
aloop1 <- Sys.time(); z<-apply(x,1, mean); difftime( Sys.time(),
aloop1)
aloop2 <- Sys.time(); for (i in 1:10000) {z2[i] <- mean(x[i,]) } ;
difftime( Sys.time(), aloop2)
identical(z, z2)
Probably not in line with your current understanding. I wonder whether
the trivial advantage offered by apply (due to the single assignment I
suspect) is in line with you understanding. Most of the efficiency in
apply operations are at the level of clarity of the code and ease of
use. The maximal efficiency gains are to use the proper vectorized
operations that can be 50-100 times faster:
> aloop3 <- Sys.time(); z3 <- rowMeans(x) ; difftime( Sys.time(),
aloop3)
Time difference of 0.01409197 secs
> identical(z, z3)
[1] TRUE
Other efficincy strategies are to pre-allocate structures of known
size and avoid using c, cbind or rbind operatiosn to accumulate
results in a loop
--
David Winsemius, MD
West Hartford, CT
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
