(Extremely sorry, disregard previous email as I hit send before pasting the latest version of the example; this one is smaller too) Dear R users,
I want to apply a function that takes two vectors as input to all pairs (combinations (nrow(X), 2))of matrix rows in a matrix. I know that ideally, one should avoid loops in R, but after reading the docs for do.call, apply, etc, I still don't know how to write the nested loop in a vectorized way. Example data: x = matrix(rnorm(100), 10, 10) # this is actually a very large sparse matrix, but it doesn't matter for the # example library(Matrix) x = as(x,"CsparseMatrix") # cosine function cosine = function (x, y){ if (is.vector(x) && is.vector(y)) { return(crossprod(x, y)/sqrt(crossprod(x) * crossprod(y))) } else {stop("cosine: argument mismatch. Two vectors needed as input.")} } # The loop-based solution I have is: if (is(x, "Matrix") ) { cos = array(NA, c(ncol(x), ncol(x))) for (i in 2:ncol(x)) { for (j in 1:(i - 1)) { cos[i, j] = cosine(x[, i], x[, j]) } } } This solution seems inneficient. Is there an easy way of achieving this with a clever do.call + apply combination? Also, I have noticed that getting a row from a Matrix object produces a normal array (i.e., it does not inherit Matrix class). However, selecting >1 rows, does produce a same-class matrix. If I convert with as() the output of selecting one row, am I losing performance? Is there any way to make the resulting vector be a 1-D Matrix object? This solution seems inneficient. Is there an easy way of achieving this with a clever do.call + apply combination? -- Thanks in advance, -Jose -- Jose Quesada, PhD Research fellow, Psychology Dept. Sussex University, Brighton, UK http://www.andrew.cmu.edu/~jquesada ______________________________________________ R-help@stat.math.ethz.ch 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.