Computing sums of the columns of an array

On 8/5/2005 12:16 PM, Martin C. Martin wrote:

Hi,

I have a 5x731 array A, and I want to compute the sums of the columns.  
Currently I do:

apply(A, 2, sum)

But it turns out, this is slow: 70% of my CPU time is spent here, even 
though there are many complicated steps in my computation.

Is there a faster way?

You'd probably do better with matrix multiplication:

rep(1, nrow(A)) %*% A
No, better use colSums(), which has been optimized for this purpose:

  A <- matrix(seq(1, 10000000), ncol=10000)
  system.time(colSums(A))
  # ~ 0.1 sec.
  system.time(rep(1, nrow(A)) %*% A)
  # ~ 0.5 sec.

Uwe Ligges
Duncan Murdoch

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Computing sums of the columns of an array

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