Re: [R] Using vectorization instead of for loop for performing a calculation efficiently
Thanks, Ok so I feel silly now ... I think I need to get a more thorough text and work through some examples. 'replace' does what I was trying to do manually. Thanks for the tip, this really is MUCH faster. -Original Message- From: Gabor Grothendieck [mailto:[EMAIL PROTECTED] Sent: Saturday, April 01, 2006 7:58 PM To: Peter Wilkinson Cc: r-help@stat.math.ethz.ch Subject: Re: [R] Using vectorization instead of for loop for performing a calculation efficiently Try this: > set.seed(1) > mat <- matrix(rnorm(2 * 10), 2) > system.time(mat2 <- replace(mat, rowSums(mat > 0) == 10, NA)) [1] 0.04 0.01 0.05 NA NA > R.version.string # Windows XP [1] "R version 2.2.1, 2005-12-20" On 4/1/06, Peter Wilkinson <[EMAIL PROTECTED]> wrote: > I am trying to write an efficient function that will do the following: > > Given an nxm matrix, 10 rows (observations) by 10 columns (samples) > for each row, test of all values in the row are greater than a value k > If all values are greater than k, then set all values to NA (or > something), Return an nxm matrix with the modified rows. > > If I do this with a matrix of 20,000 rows, I will be waiting until > Christmas for it to finish: > > For rows in Matrix: >if rows < filter >set all elements in rows to NA (or something) >else >do nothing > Return the matrix with the modified rows > > > I don't know how to code this properly. The following: > > If (sum(ifelse(nvector>filter,1,0) == 0 ) ) > > Tells me if any row has at least 1 value above the filter. How do I > get rid of the 'outer' loop? > > Peter > > -> > > Peter Wilkinson > Senior Bioinformatician / Programmer-Analyst National Immune > Monitoring Laboratory > tel: (514)-343-7876 > > __ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! > http://www.R-project.org/posting-guide.html > __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Using vectorization instead of for loop for performing a calculation efficiently
Try this: > set.seed(1) > mat <- matrix(rnorm(2 * 10), 2) > system.time(mat2 <- replace(mat, rowSums(mat > 0) == 10, NA)) [1] 0.04 0.01 0.05 NA NA > R.version.string # Windows XP [1] "R version 2.2.1, 2005-12-20" On 4/1/06, Peter Wilkinson <[EMAIL PROTECTED]> wrote: > I am trying to write an efficient function that will do the following: > > Given an nxm matrix, 10 rows (observations) by 10 columns (samples) > for each row, test of all values in the row are greater than a value k > If all values are greater than k, then set all values to NA (or something), > Return an nxm matrix with the modified rows. > > If I do this with a matrix of 20,000 rows, I will be waiting until Christmas > for it to finish: > > For rows in Matrix: >if rows < filter >set all elements in rows to NA (or something) >else >do nothing > Return the matrix with the modified rows > > > I don't know how to code this properly. The following: > > If (sum(ifelse(nvector>filter,1,0) == 0 ) ) > > Tells me if any row has at least 1 value above the filter. How do I get rid > of the 'outer' loop? > > Peter > > -> > > Peter Wilkinson > Senior Bioinformatician / Programmer-Analyst > National Immune Monitoring Laboratory > tel: (514)-343-7876 > > __ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html > __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Using vectorization instead of for loop for performing a calculation efficiently
I am trying to write an efficient function that will do the following: Given an nxm matrix, 10 rows (observations) by 10 columns (samples) for each row, test of all values in the row are greater than a value k If all values are greater than k, then set all values to NA (or something), Return an nxm matrix with the modified rows. If I do this with a matrix of 20,000 rows, I will be waiting until Christmas for it to finish: For rows in Matrix: if rows < filter set all elements in rows to NA (or something) else do nothing Return the matrix with the modified rows I dont know how to code this properly. The following: If (sum(ifelse(nvector>filter,1,0) == 0 ) ) Tells me if any row has at least 1 value above the filter. How do I get rid of the 'outer' loop? Peter -> Peter Wilkinson Senior Bioinformatician / Programmer-Analyst National Immune Monitoring Laboratory tel: (514)-343-7876 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
