Hi Gabor, Thanks. I will try to figure out the solution you suggest. I found out about melt() from a discussion forum; it seems to me that "melt()$value" is similar to "c()", and when I modified the script as below it 'seems' to be running faster. Anyway in the end I only needed to use a smaller network so the computation went ok.
y_s <- melt(y_s)[c(upper.tri(y_s)),] #new code y_s <- melt(y_s)[melt(upper.tri(y_s))$value,] #old code The reason I needed three columns was for later statistical analysis for which such a format was necessary. Best regards, Joe. On Thu, Aug 18, 2011 at 12:47 PM, Gábor Csárdi <csa...@rmki.kfki.hu> wrote: > Joe, > > what is melt() supposed to do here? > > What's wrong with the simple solution of creating a data.frame first, > and then filling it with values through a loop? Actually, keeping the > matrix is just as good, indexing is just as fast, and takes the same > amount of memory as your three column matrix, doesn't it? > > Gabor > > On Fri, Aug 5, 2011 at 10:40 AM, joe j <joe.st...@gmail.com> wrote: >> Using Igraph, I create shortest paths, then convert the matrix into >> three column vectors - "vertex1", "vertex2", "shortestpath" - as the >> code below shows. >> >> #code for generating shortest path matrix and creating a 3 columns >> from an igraph graph object "y" >> y_s<-shortest.paths(y, weights = NULL) >> y_s <- melt(y_s)[melt(upper.tri(y_s))$value,] #Step 2: this is where >> the trouble with memory occurs >> y_s[,1] <- V(y)$name[y_s[,1]] >> y_s[,2] <- V(y)$name[y_s[,2]] >> names(y_s)<-c("vertex1", "vertex2", "shortestpath") >> >> However I am looking for an alternative way of doing this becase at >> the second step I run into a fight with my machine's memory. I know I >> can create vectors using as.vector(), c(), etc, but I am not able to >> create the two other columns with vertex names. >> >> Best regards, >> Joe. >> >> ______________________________________________ >> 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. >> > > > > -- > Gabor Csardi <csa...@rmki.kfki.hu> MTA KFKI RMKI > ______________________________________________ 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.