> -----Original Message----- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Uwe Ligges > Sent: Friday, August 05, 2005 12:44 PM > To: Duncan Murdoch > Cc: [email protected] > Subject: Re: [R] Computing sums of the columns of an array > > > Duncan Murdoch wrote: > > > On 8/5/2005 12:16 PM, Martin C. Martin wrote: > > > >>Hi, > >> > >>I have a 5x731 array A, and I want to compute the sums of > the columns. > >>Currently I do: > >> > >>apply(A, 2, sum) > >> > >>But it turns out, this is slow: 70% of my CPU time is spent > here, even > >>though there are many complicated steps in my computation. > >> > >>Is there a faster way? > > > > > > You'd probably do better with matrix multiplication: > > > > rep(1, nrow(A)) %*% A > > > No, better use colSums(), which has been optimized for this purpose: > > A <- matrix(seq(1, 10000000), ncol=10000) > system.time(colSums(A)) > # ~ 0.1 sec. > system.time(rep(1, nrow(A)) %*% A) > # ~ 0.5 sec.
With the dimension that Martin stated, I don't see much difference: > A <- matrix(runif(5 * 731), 5) > system.time(replicate(1e4, rep(1, nrow(A)) %*% A), gcFirst=TRUE) [1] 5.28 0.13 5.46 NA NA > system.time(replicate(1e4, rep(1, nrow(A)) %*% A), gcFirst=TRUE) [1] 1.99 0.20 2.22 NA NA > system.time(replicate(1e4, rep(1, nrow(A)) %*% A), gcFirst=TRUE) [1] 1.97 0.25 2.28 NA NA > system.time(replicate(1e4, rep(1, nrow(A)) %*% A), gcFirst=TRUE) [1] 1.90 0.20 2.16 NA NA > system.time(replicate(1e4, colSums(A)), gcFirst=TRUE) [1] 1.53 0.22 1.75 NA NA > system.time(replicate(1e4, colSums(A)), gcFirst=TRUE) [1] 1.53 0.19 1.72 NA NA > system.time(replicate(1e4, colSums(A)), gcFirst=TRUE) [1] 1.51 0.19 1.70 NA NA > system.time(replicate(1e4, colSums(A)), gcFirst=TRUE) [1] 1.49 0.25 1.79 NA NA However, I don't understand why the first try took so much longer. Andy > Uwe Ligges > > > > > Duncan Murdoch > > > > ______________________________________________ > > [email protected] mailing list > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide! > http://www.R-project.org/posting-guide.html > > > ______________________________________________ > [email protected] mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! > http://www.R-project.org/posting-guide.html > > > ______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
