Serves me right, I suppose. Timing seems also very dependent on the dimensions of the matrix. Here's what I got with my inadequate test:
> x <- matrix(rnorm(3e5),ncol=3) ## via apply > system.time(apply(x,1,max)) user system elapsed 2.09 0.02 2.10 ## via pmax > system.time(do.call(pmax,data.frame(x))) user system elapsed 0.10 0.02 0.11 > Draw your own conclusions! Cheers, Bert Bert Gunter Genentech Nonclinical Biostatistics 650-467-7374 -----Original Message----- From: Wacek Kusnierczyk [mailto:waclaw.marcin.kusnierc...@idi.ntnu.no] Sent: Monday, March 30, 2009 2:33 AM To: Rolf Turner Cc: Bert Gunter; 'Ana M Aparicio Carrasco'; r-help@r-project.org Subject: Re: [R] Matrix max by row Rolf Turner wrote: > I tried the following: > > m <- matrix(runif(100000),1000,100) > junk <- gc() > print(system.time(for(i in 1:100) X1 <- do.call(pmax,data.frame(m)))) > junk <- gc() > print(system.time(for(i in 1:100) X2 <- apply(m,1,max))) > > and got > > user system elapsed > 2.704 0.110 2.819 > user system elapsed > 1.938 0.098 2.040 > > so unless there's something that I am misunderstanding (always a serious > consideration) Wacek's apply method looks to be about 1.4 times > *faster* than > the do.call/pmax method. hmm, since i was called by name (i'm grateful, rolf), i feel obliged to check the matters myself: # dummy data, presumably a 'large matrix'? n = 5e3 m = matrix(rnorm(n^2), n, n) # what is to be benchmarked... waku = expression(matrix(apply(m, 1, max), nrow(m))) bert = expression(do.call(pmax,data.frame(m))) # to be benchmarked library(rbenchmark) benchmark(replications=10, order='elapsed', columns=c('test', 'elapsed'), waku=matrix(apply(m, 1, max), nrow(m)), bert=do.call(pmax,data.frame(m))) takes quite a while, but here you go: # test elapsed # 1 waku 11.838 # 2 bert 20.833 where bert's solution seems to require a wonder to 'be considerably faster for large matrices'. to have it fair, i also did # to be benchmarked library(rbenchmark) benchmark(replications=10, order='elapsed', columns=c('test', 'elapsed'), bert=do.call(pmax,data.frame(m)), waku=matrix(apply(m, 1, max), nrow(m))) # test elapsed # 2 waku 11.695 # 1 bert 20.912 take home point: a good product sells itself, a bad product may not sell despite aggressive marketing. rolf, thanks for pointing this out. cheers, vQ > cheers, > > Rolf Turner > > > On 30/03/2009, at 3:55 PM, Bert Gunter wrote: > >> If speed is a consideration,availing yourself of the built-in pmax() >> function via >> >> do.call(pmax,data.frame(yourMatrix)) >> >> will be considerably faster for large matrices. >> >> If you are puzzled by why this works, it is a useful exercise in R to >> figure >> it out. >> >> Hint:The man page for ?data.frame says: >> "A data frame is a list of variables of the same length with unique row >> names, given class 'data.frame'." >> >> Cheers, >> Bert >> >> Bert Gunter >> Genentech Nonclinical Statistics >> >> -----Original Message----- >> From: r-help-boun...@r-project.org >> [mailto:r-help-boun...@r-project.org] On >> Behalf Of Wacek Kusnierczyk >> Sent: Saturday, March 28, 2009 5:22 PM >> To: Ana M Aparicio Carrasco >> Cc: r-help@r-project.org >> Subject: Re: [R] Matrix max by row >> >> Ana M Aparicio Carrasco wrote: >>> I need help about how to obtain the max by row in a matrix. >>> For example if I have the following matrix: >>> 2 5 3 >>> 8 7 2 >>> 1 8 4 >>> >>> The max by row will be: >>> 5 >>> 8 >>> 8 >>> >> >> matrix(apply(m, 1, max), nrow(m)) >> >> vQ >> >> ______________________________________________ >> 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. > > > ###################################################################### > Attention:This e-mail message is privileged and confidential. If you > are not theintended recipient please delete the message and notify the > sender.Any views or opinions presented are solely those of the author. > > This e-mail has been scanned and cleared by > MailMarshalwww.marshalsoftware.com > ###################################################### ______________________________________________ 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.
