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    <p>For the purpose of setting the "diagonal" elements to zero you have already been given an answer but I wonder if you were hoping for something more general. The reasons for lack of success with that code were two-fold: the construction of your indices were flawed and the indexing was wrong. This would have succeeded:</p> <pre><code>for(i in 1:(rowCount - 1)){ # need an expression that retruns a sequence for (j in 1:rowCount) # ditto if (i == j){ similMatrix[i,j] &lt;- 0; # need to index the matrix with two element if using i,j } } #---------- &gt; show(similMatrix) [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [1,] 0 NA NA NA NA NA NA NA NA [2,] NA 0 NA NA NA NA NA NA NA [3,] NA NA 0 NA NA NA NA NA NA [4,] NA NA NA 0 NA NA NA NA NA [5,] NA NA NA NA 0 NA NA NA NA [6,] NA NA NA NA NA 0 NA NA NA [7,] NA NA NA NA NA NA 0 NA NA [8,] NA NA NA NA NA NA NA 0 NA </code></pre> <p>But resorting to loops in R is generally considered a last resort (sometimes for the wrong reasons.) There is a much more compact way of doing the same "loop" operation and it generalizes more widely than just setting the diagonal.</p> <pre><code>similMatrix[ row(similMatrix) == col(similMatrix) ] &lt;- 0 &gt; similMatrix [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [1,] 0 NA NA NA NA NA NA NA NA [2,] NA 0 NA NA NA NA NA NA NA [3,] NA NA 0 NA NA NA NA NA NA [4,] NA NA NA 0 NA NA NA NA NA [5,] NA NA NA NA 0 NA NA NA NA [6,] NA NA NA NA NA 0 NA NA NA [7,] NA NA NA NA NA NA 0 NA NA [8,] NA NA NA NA NA NA NA 0 NA </code></pre> <p>If you wanted to set the subdiagonal to zero you could just use:</p> <pre><code>similMatrix[ row(similMatrix)-1 == col(similMatrix) ] &lt;- 0 </code></pre> <p>You can avoid generating the extra row and col matrices using this:</p> <pre><code> mind &lt;- min( dim(similMatrix) ) # avoid going outside dimensions if not symmetric similMatrix[ cbind( seq(maxd),seq(maxd) ) &lt;- 0 </code></pre>
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    1. COthis is perfect, thank you a lot!
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