Convert your 'targets' matrix into a 2 column matrix with the 1st column representing the row and the 2nd the column where you want your values, then change the values to a single vector and you can just use the targets matrix as the subsetting in 1 step without (explicit) looping, for example:
library(Matrix) adjM <- Matrix(0,nrow=10,ncol=10) locs <- cbind( sample(1:10), sample(1:10) ) vals <- rnorm(10) adjM[ locs ] <- vals I would expect this to be faster than looping (but have not tested). On Thu, Apr 24, 2014 at 9:45 AM, Tom Wright <[email protected]> wrote: > I need to generate a sparse matrix. Currently I have the data held in two > regular matrices. One 'targets' holds the column subscripts while the other > 'scores' holds the values. I have written a 'toy' sample below. Using this > approach takes about 90 seconds to populate a 30000 x 30000 element matrix. > I'm going to need to scale this up by a factor of about 1000 so I really > need a faster way of populating the sparse matrix. > Any advice received gratefully. > > # toy code starts here > > require('Matrix') > set.seed(0) > > adjM<-Matrix(0,nrow=10,ncol=10) > > #generate the scores for the sparse matrix, with the target locations > targets<-matrix(nrow=10,ncol=5) > scores<-matrix(nrow=10,ncol=5) > for(iloc in 1:10) > { > targets[iloc,]<-sample(1:10,5,replace=FALSE) > scores[iloc,]<-rnorm(5) > } > > #populate the sparse matrix > for(iloc in 1:10) > { > adjM[iloc,targets[iloc,!is.na(targets[iloc,])]]<-scores[iloc,!is.na > (targets[iloc,])] > } > > [[alternative HTML version deleted]] > > ______________________________________________ > [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 > and provide commented, minimal, self-contained, reproducible code. -- Gregory (Greg) L. Snow Ph.D. [email protected] ______________________________________________ [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 and provide commented, minimal, self-contained, reproducible code.
