[R] Computing sums of the columns of an array

[Uwe Ligges]

Duncan Murdoch wrote:

> 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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