[R] speeding up loop and dealing wtih memory problems
jim holtman
jholtman at gmail.com
Mon Jul 28 15:43:37 CEST 2008
If your matrix is 835353x86, then if it is numeric, then it will take
about 550MB for a single copy. You should therefore have at least 2GB
(so you can have a couple of copies as part of some processing) of
real memory on your system. If you want to replace NAs with zero,
then this is how you might do it with 'vectorization':
> x
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 1 NA NA 2 1 2
[2,] 2 2 2 NA 2 2
[3,] 2 2 NA NA 1 2
[4,] NA 1 2 1 2 1
[5,] 1 1 NA 2 NA NA
[6,] NA 1 NA 1 2 NA
> x[is.na(x)] <- 0
> x
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 1 0 0 2 1 2
[2,] 2 2 2 0 2 2
[3,] 2 2 0 0 1 2
[4,] 0 1 2 1 2 1
[5,] 1 1 0 2 0 0
[6,] 0 1 0 1 2 0
Maybe you should read the Intro To R to understand how vectorization works.
Same way with your last loop:
x[is.na(x[,4]), 4] <- 0
On Mon, Jul 28, 2008 at 9:15 AM, Denise Xifara
<dionysia-kiara.xifaras at st-hildas.ox.ac.uk> wrote:
> Dear All and Mark,
>
> Given a dataset that I have called dat, I was hoping to speed up the
> following loop:
>
> for(i in 1:835353){
> for(j in 1:86){
> if (is.na(dat[i,j])==TRUE){dat[i,j]<-0 }}}
> Actually I am also having a memory problem. I get the following:
>
> Error: cannot allocate vector of size 3.2 Mb
> In addition: Warning messages:
> 1: In dat[i, j] <- 0 :
> Reached total allocation of 1535Mb: see help(memory.size)
> 2: In dat[i, j] <- 0 :
> Reached total allocation of 1535Mb: see help(memory.size)
> 3: In dat[i, j] <- 0 :
> Reached total allocation of 1535Mb: see help(memory.size)
> 4: In dat[i, j] <- 0 :
> Reached total allocation of 1535Mb: see help(memory.size)
>
> If I try and apply the loop just to a particular column, rather than the
> whole dataset, so that I dont have the memory problem, ie
>
> for(i in 1:835353){
> if (is.na(dat[i,4])==TRUE){dat[i,4]<-0 }}
>
> it takes ridiculously long to process, so I was hoping that there would be a
> quicker way to do this.
>
> Thank you all very much for the help,
> Denise
>
> [[alternative HTML version deleted]]
>
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>
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
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