Computing sums of the columns of an array

On 8/5/2005 12:43 PM, Uwe Ligges wrote:

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.

I didn't claim my solution was the best, only better. :-)

One point of interest:  I think your example exaggerates the difference 
by using a matrix of integers.  On my machine I get a ratio something 
like yours with the same example

 > A <- matrix(seq(1, 10000000), ncol=10000)
 >   system.time(colSums(A))

[1] 0.08 0.00 0.08   NA   NA

 >   system.time(rep(1, nrow(A)) %*% A)

[1] 0.25 0.01 0.23   NA   NA

but if I make A floating point, there's much less difference:

 > A <- matrix(as.numeric(seq(1, 10000000)), ncol=10000)
 >   system.time(colSums(A))

[1] 0.09 0.00 0.09   NA   NA

 >   system.time(rep(1, nrow(A)) %*% A)

[1] 0.11 0.00 0.12   NA   NA

Still, colSums is the winner in both cases.

Duncan Murdoch