Here's a possible solution to avoid the loop k <- as.matrix(expand.grid(1:ncol(x),1:ncol(x))) a1 <- as.data.frame(matrix(sapply(1:nrow(k), function(n) agree(x[,k[n,]])$value), nrow=ncol(x))) colnames(a1) <- colnames(x) rownames(a1) <- colnames(x)
> identical(a, a1) [1] TRUE Or if you want to avoid double calculation, a2 <- as.data.frame(matrix(0, nrow=ncol(x), ncol=ncol(x))) colnames(a2) <- colnames(x) rownames(a2) <- colnames(x) k <- t(combn(1:ncol(x), 2)) a2[lower.tri(a2)] <- sapply(1:nrow(k), function(n) agree(x[,k[n,]])$value) a2 <- a2+diag(100,ncol(x)) a2[upper.tri(a2)] <- t(a2)[upper.tri(a2)] > identical(a, a2) [1] TRUE Best, Nello -----Original Message----- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Kulupp Sent: Montag, 24. Juni 2013 11:02 To: r-help@r-project.org Subject: [R] Avoiding loops using 'for' and pairwise comparison of columns Dear R-experts, I'd like to avoid the use of very slow 'for'-loops but I don't know how. My data look as follows (the original data has 1600 rows and 30 columns): # data example c1 <- c(1,1,1,0.25,0,1,1,1,0,1) c2 <- c(0,0,1,1,0,1,0,1,0.5,1) c3 <- c(0,1,1,1,0,0.75,1,1,0.5,0) x <- data.frame(c1,c2,c3) I need to compare every column with each other and want to know the percentage of similar values for each column pair. To calculate the percentage of similar values I used the function 'agree' from the irr-package. I solved the problem with a loop that is very slow. library(irr) # required for the function 'agree' # empty data frame for the results a <- as.data.frame(matrix(data=NA, nrow=3, ncol=3)) colnames(a) <- colnames(x) rownames(a) <- colnames(x) # the loop to write the data for (j in 1:ncol(x)){ for (i in 1:ncol(x)){ a[i,j] <- agree(cbind(x[,j], x[,i]))$value } } I would be very pleased to receive your suggestions how to avoid the loop. Furthermore the resulting data frame could be displayed as a diagonal matrix without duplicates of each pairwise comparison, but I don't know how to solve this problem. Kind regards Thomas ______________________________________________ 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.
