AFAICS, the problem is that you have not (carefully?) read the docs and are approaching R as a C programmer and not taking a whole object point of view. The loop is completely unnecessary! PLEASE READ AN INTRO TO R (again,perhaps) before posting.
So, unless I misunderstand (and my apologies if I do), what you want is simply: ix <- seq(from=2,to=40, by=2) averagedResults <- (zz[,ix] + zz[,ix+1])/2 This was instantaneous on my computer for a 95000 x 40 matrix. So if I got it right, this is a pretty impressive example of why doing your homework by first reading the docs is important. Bert Gunter Genentech nonclinical Statistics -----Original Message----- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Jorge Ivan Velez Sent: Monday, June 08, 2009 9:03 AM To: Amit Patel Cc: r-help@r-project.org Subject: Re: [R] help to speed up loops in r Dear Amit, The following should get you started: # Some data set.seed(123) X <- matrix(rnorm(20*10), ncol=10) X # Group of replicates g <- rep(1:(ncol(X)/2), each=2) g # Mean of replicate variables t(apply(X, 1, tapply, g, mean, na.rm = TRUE)) I created a grouping variable (g) and then calculate the mean by row ( apply(X, 1,...) ) for each level of g (that's why I included tapply). I have not checked timing but I guess it is faster than the script you already have. HTH, Jorge On Mon, Jun 8, 2009 at 11:45 AM, Amit Patel <amitrh...@yahoo.co.uk> wrote: > > Hi > i am using a script which involves the following loop. It attempts to > reduce a data frame(zz) of 95000 * 41 down to a data frame > (averagedreplicates) of 95000 * 21 by averaging the replicate values as you > can see in the script below. This script however is very slow (2days). Any > suggestions to speed it up. > > NB I have also tried using rowMeans rather than adding the 2 values and > dividing by 2. (same problem) > > > > > #SCRIPT STARTS > for (i in 1:length(averagedreplicates[,1])) > #for (i in 1:dim(averagedreplicates)[1]) > { > cat(i,'\n') > > > #calculates Meanss > #Sample A > averagedreplicates[i,2] <- (zz[i,2] + zz[i,3])/2 > averagedreplicates[i,3] <- (zz[i,4] + zz[i,5])/2 > averagedreplicates[i,4] <- (zz[i,6] + zz[i,7])/2 > averagedreplicates[i,5] <- (zz[i,8] + zz[i,9])/2 > averagedreplicates[i,6] <- (zz[i,10] + zz[i,11])/2 > > #Sample B > averagedreplicates[i,7] <- (zz[i,12] + zz[i,13])/2 > averagedreplicates[i,8] <- (zz[i,14] + zz[i,15])/2 > averagedreplicates[i,9] <- (zz[i,16] + zz[i,17])/2 > averagedreplicates[i,10] <- (zz[i,18] + zz[i,19])/2 > averagedreplicates[i,11] <- (zz[i,20] + zz[i,21])/2 > > #Sample C > averagedreplicates[i,12] <- (zz[i,22] + zz[i,23])/2 > averagedreplicates[i,13] <- (zz[i,24] + zz[i,25])/2 > averagedreplicates[i,14] <- (zz[i,26] + zz[i,27])/2 > averagedreplicates[i,15] <- (zz[i,28] + zz[i,29])/2 > averagedreplicates[i,16] <- (zz[i,30] + zz[i,31])/2 > > #Sample D > averagedreplicates[i,17] <- (zz[i,32] + zz[i,33])/2 > averagedreplicates[i,18] <- (zz[i,34] + zz[i,35])/2 > averagedreplicates[i,19] <- (zz[i,36] + zz[i,37])/2 > averagedreplicates[i,20] <- (zz[i,38] + zz[i,39])/2 > averagedreplicates[i,21] <- (zz[i,40] + zz[i,41])/2 > } > > > > ______________________________________________ > 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. > [[alternative HTML version deleted]] ______________________________________________ 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. ______________________________________________ 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.
