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POR - vectorizing a which operation
 

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  1. POR - vectorizing a which operation
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    <p>Hi I have a function in R that I'm trying to optimize for performance. I need to vectorize a for loop. My problem is the slightly convoluted data structure and the way I need to perform lookups using the 'which' command.</p> <p>Lets say we are dealing with 5 elements (1,2,3,4,5), the 10x2 matrix pairs is a combination of all unique pairs the 5 elements (i.e. (1,2), (1,3),(1,4) ....(4,5)). all_prods is a 10x1 matrix that I need to look up using the pairs while iterating through all the 5 elements. </p> <p>So for 1, I need to index rows 1, 2, 3, 4 (pairs 1,2 1,3 1,4 and 1,5) from all_prods and so on for 1, 2, 3, 4, 5.</p> <p>I have only recently switched to R from matlab so would really appreciate any help.</p> <pre><code>foo &lt;- function(AA , BB , CC ){ pa &lt;- AA*CC; pairs &lt;- t(combn(seq_len(length(AA)),2)); all_prods &lt;- pa[pairs[,1]] * pa[pairs[,2]]; result &lt;- matrix(0,1,length(AA)); # WANT TO VECTORIZE THIS BLOCK for(st in seq(from=1,to=length(AA))){ result[st] &lt;- sum(all_prods[c(which(pairs[,1]==st), which(pairs[,2]==st))])*BB[st]; } return(result); } AA &lt;- seq(from=1,to=5); BB&lt;-seq(from=11,to=15); CC&lt;-seq(from=21,to=25); results &lt;- foo(AA,BB,CC); #final results is [7715 164208 256542 348096 431250] </code></pre> <p>I want to convert the for loop into a vectorised version. Instead of looping through every element st, I'd like to do it in one command that gives me a results vector (rather than building it up element by element)</p> <p>Thanks in advance.</p>
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    1. USuser1480926
    1. USuser1480926
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    1. COI suggest you provide some sample data to play with. See http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example
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      1. POR - vectorizing a which operation
      1. USRoman Luštrik
    2. COI'm not sure that's your bottle neck. You pre-allocate a matrix which is good, but `combn` and `t` are pretty greedy. Have you tried profiling your code?
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      1. POR - vectorizing a which operation
      1. USRoman Luštrik
    3. COI want to convert the for loop into a vectorised version. Instead of looping through every element st, I'd like to do it in one command that gives me a results vector (rather than building it up one by one). My apologies for not making this clearer. I have updated the post.
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      1. POR - vectorizing a which operation
      1. USuser1480926
 

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