I suspect the vast majority of time is because of growing objects. Preallocate 'iv', 'jv', 'rho_sv' and 'rho_pv' to be their final length and then subscript into them with their values.
Patrick Burns [EMAIL PROTECTED] +44 (0)20 8525 0696 http://www.burns-stat.com (home of S Poetry and "A Guide for the Unwilling S User") jim holtman wrote: >First thing to do is to use Rprof (?Rprof) on a subset of your data to >see where time is being spent. My guess is that most of it is in the >calls to 'cor' and if this is the case, they you have to figure out >some other algorithm. > >Also if these dataframes all contain numeric information, convert them >to matrices intially because the subsetting that you are doing on the >dataframe (e.g., alist[[p]][i,"v"]) can be very expensive. The output >from Rprof will help determine what course of action you should take. > >On 10/16/07, Dieter Best <[EMAIL PROTECTED]> wrote: > > >>Hi there, >> >> I have a multiple for loop over a list of data frames >> >> for ( i in 1:(N-1) ) { >> for ( j in (i+1):N ) { >> for ( p in 1:M ) { >> v_i[p] = alist[[p]][i,"v"] >> v_j[p] = alist[[p]][j,"v"] >> } >> rho_s = cor(v_i, v_j, method = "spearman") >> rho_p = cor(v_i, v_j, method = "pearson" ) >> iv = c( iv, min(i, j) ) >> jv = c( jv, max(i, j) ) >> rho_sv = c( rho_sv, rho_s) >> rho_pv = c( rho_pv, rho_p) >> } >>} >> >> N is of the order of 400, M about 800. >> >> This takes me an entire day basically. Is there anything I could do to speed >> things up or is cor really that slow? >> >> -- D >> >> >> >>--------------------------------- >> >> >> [[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.
