Computing sums of the columns of an array

-----Original Message-----
From: r-help-bounces at stat.math.ethz.ch 
[mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of Uwe Ligges
Sent: Friday, August 05, 2005 12:44 PM
To: Duncan Murdoch
Cc: r-help at stat.math.ethz.ch
Subject: Re: [R] Computing sums of the columns of an array


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.

A <- matrix(runif(5 * 731), 5)
system.time(replicate(1e4, rep(1, nrow(A)) %*% A), gcFirst=TRUE)

system.time(replicate(1e4, rep(1, nrow(A)) %*% A), gcFirst=TRUE)

system.time(replicate(1e4, rep(1, nrow(A)) %*% A), gcFirst=TRUE)

system.time(replicate(1e4, rep(1, nrow(A)) %*% A), gcFirst=TRUE)

system.time(replicate(1e4, colSums(A)), gcFirst=TRUE)

system.time(replicate(1e4, colSums(A)), gcFirst=TRUE)

system.time(replicate(1e4, colSums(A)), gcFirst=TRUE)

system.time(replicate(1e4, colSums(A)), gcFirst=TRUE)

Uwe Ligges

Duncan Murdoch