I need to increment cells of a matrix (collusionM). The indexes to increment are in an index (matchIndex). This is sample code
library(seqinr) library(Matrix) x <- "abcabcabc" mx <- s2c(x) collisionM <- Matrix(0,nrow=10, ncol=10, sparse=TRUE) matchIndex <- list() rows <- length(mx) for (j in 1:(rows)) matchIndex[[j]] <- which(mx[j]==mx) for (j in 1:(rows)) collisionM[j,matchIndex[[j]]] <- collisionM[j,matchIndex[[j]]] + 1 Works fine, except with my data (rows=32000) it is too slow. The problem is the second for loop, where it increments the index of the sparse matrix; this needs to be rewritten so it is more efficient. Any ideas? ______________________________________________ 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.
