From rdpeng at gmail.com  Fri Mar  2 20:43:07 2007
From: rdpeng at gmail.com (Roger D. Peng)
Date: Fri, 02 Mar 2007 14:43:07 -0500
Subject: [Rd] extracting rows from a data frame by looping over the row
 names: performance issues
In-Reply-To: <45E86F69.80507@fhcrc.org>
References: <45E86F69.80507@fhcrc.org>
Message-ID: <45E87E4B.6070803@gmail.com>

Extracting rows from data frames is tricky, since each of the columns could be 
of a different class.  For your toy example, it seems a matrix would be a more 
reasonable option.

R-devel has some improvements to row extraction, if I remember correctly.  You 
might want to try your example there.

-roger

Herve Pages wrote:
> 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_ADDRESS=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 at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
> 

-- 
Roger D. Peng  |  http://www.biostat.jhsph.edu/~rpeng/



[Rd] extracting rows from a data frame by looping over the row names: performance issues
Roger D. Peng