Large loops in R

Without a reproducible example it's hard to tell for certain, but what
about simply (assuming nrows2 is actually columns):

sum((mat1/d1 - mat2/d2)^2)

R is smart enough to understand elementwise manipulation of a matrix:
you shouldn't need a loop at all.

Sarah

On Tue, Dec 4, 2012 at 2:27 PM, Charles Novaes de Santana
<charles.santana at gmail.com> wrote:

Dear Michael,

Thank you for your answer.

I have 2 matrices. Each position of the matrices is a weight. And I
need to calculate the following sum of differences:

Considering:
mat1 and mat2 - two matrices (each of them 48000 x 48000).
d1 and d2 - two constant values.

sum<-0;
for(i in 1:nrows1){
                        for(j in 1:nrows2){
                                        sum<-sum+ ( ( (mat1(i,j)/d1) -
(mat2(i,j)/d2) )^2 )
                                }
                        }
                }

I was wondering if there is a better way to do this sum.

Thank you for your attention!

Best,

Charles

On Tue, Dec 4, 2012 at 7:54 PM, R. Michael Weylandt
<michael.weylandt at gmail.com> <michael.weylandt at gmail.com> wrote:

On Dec 4, 2012, at 6:47 PM, Charles Novaes de Santana <charles.santana at gmail.com> wrote:

Dear all,

I need to access data from a large matrix (48000 x 48000) and to do it
I am trying to run two loops using "for" command. Surely it is been a
very slow job.

I heard that "for" is not the best option to perform large loops in R,
but I don't really know what would be the best (fast) option. sapply?
vapply? Could anyone help me with this issue, please?

What exactly are you trying to do? It's likely doable with a few vectorized operations.

Michael

--
Sarah Goslee
http://www.functionaldiversity.org