Your 2 examples have 2 differences and they are therefore confounded in
their effects.
What are your results for:
system.time(for (i in 1:100) {row <- dat[i, ] })
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
[EMAIL PROTECTED]
(801) 408-8111
> -----Original Message-----
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of Herve Pages
> Sent: Friday, March 02, 2007 11:40 AM
> To: r-devel@r-project.org
> Subject: [Rd] extracting rows from a data frame by looping
> over the row names: performance issues
>
> Hi,
>
>
> I have a big data frame:
>
> > mat <- matrix(rep(paste(letters, collapse=""), 5*300000), ncol=5)
> > dat <- as.data.frame(mat)
>
> and I need to do some computation on each row. Currently I'm
> doing this:
>
> > for (key in row.names(dat)) { row <- dat[key, ]; ... do
> some computation on row... }
>
> which could probably considered a very natural (and R'ish)
> way of doing it (but maybe I'm wrong and the real idiom for
> doing this is something different).
>
> The problem with this "idiomatic form" is that it is _very_
> slow. The loop itself + the simple extraction of the rows (no
> computation on the rows) takes 10 hours on a powerful server
> (quad core Linux with 8G of RAM)!
>
> Looping over the first 100 rows takes 12 seconds:
>
> > system.time(for (key in row.names(dat)[1:100]) { row <-
> dat[key, ] })
> user system elapsed
> 12.637 0.120 12.756
>
> But if, instead of the above, I do this:
>
> > for (i in nrow(dat)) { row <- sapply(dat, function(col) col[i]) }
>
> then it's 20 times faster!!
>
> > system.time(for (i in 1:100) { row <- sapply(dat,
> function(col) col[i]) })
> user system elapsed
> 0.576 0.096 0.673
>
> I hope you will agree that this second form is much less natural.
>
> So I was wondering why the "idiomatic form" is so slow?
> Shouldn't the idiomatic form be, not only elegant and easy to
> read, but also efficient?
>
>
> Thanks,
> H.
>
>
> > sessionInfo()
> R version 2.5.0 Under development (unstable) (2007-01-05
> r40386) x86_64-unknown-linux-gnu
>
> locale:
> LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_
> MONETARY=en_US;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_A
> DDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] "stats" "graphics" "grDevices" "utils"
> "datasets" "methods"
> [7] "base"
>
> ______________________________________________
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
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