[R] help:too slow

[detlef.steuer@unibw-hamburg.de]

Hi!

Using your original function on some dummy data I get:
(700MHz PIII Linux 2.2.18)

w  <-  as.matrix(floor(runif(100000,100,999)))
unix.time(m  <- time(col2mat(w)))
[1] 22.67  0.69 50.48  0.00  0.00

50 seconds to generate the whole matrix.

If I comment out the print(s) it reduces to:
unix.time(m  <- time(col2mat(w)))
[1] 21.03  0.64 21.86  0.00  0.00

But if I change the function definition to

"col2mat" <-
    function(x, sampsz=220, qsamp=2000) {
        m<-matrix(nr=qsamp, nc=sampsz)
        for(s in 1:qsamp){ 
###            print(s)
###            for(i in 1:sampsz){
                m[s,(1:sampsz)] <- x[s+(1:sampsz),1]
###            }
        }
        m
    }

which I consider functional equivalent I can go down to:
> unix.time(m  <- time(col2mat(w)))
[1] 0.52 0.06 0.59 0.00 0.00

Probably you can get rid of the outer loop in a similar fashion.
Hope that helps,

detlef



On 20-Mar-01 Valery A.Khamenya wrote:
> here is a script I use to make overlapping cut of my input "col.dat"
> file into a matrix:
> 
>#----------------------------------
> col2mat<-function(x, sampsz=220, qsamp=2000) {
>   m<-matrix(nr=qsamp, nc=sampsz)
>   for(s in 1:qsamp){ 
>     print(s)
>     for(i in 1:sampsz){
>       m[s,i] <- x[s+i,1]
>     }
>   }
>   m
> }
> w<-read.table("col.dat", check.names=FALSE)
> m<-col2mat(w)
>#----------------------------------
> 
> the input file "col.dat" looks like this:
>#-----------------------
> 118
> 118
> 122
> .
> .
> .
> -90
> -84
> -120
> -108
>#------------
> contains about 380000 numbers and has a size of 1.5Mb. Not a small
> file I understand, but not too large! However I do not use the whole
> file at _this_ stage of my task, I use no more than 10% (no more than
> 150Kb) if it is matter. Well. 
> 
> Problem: m<-col2mat(w) works toooo slow. One row (that is 220 numbers)
> of such a matrix is being formed in ~5 sec! (5*2000 = 10000 sec). it
> is slowed in thousands times comparing to analogical C-code, too much
> I think. 
> 
> Q1: is there a better way to create my matrix? (maybe I do some
>     mistake)
> 
> Q2(for developers): if this slowdown is a problem of R's engine, may
>                     we hope the problem will be corrected?
> 
> thank you.
> 
> Valery A.Khamenya (please reply-to:<news_vkhamenya at chat.ru>)
> 
> 
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Detlef Steuer ** Universität der Bw ** 22043 Hamburg
Tel: (0049) (0)40/6541-2819
steuer at unibw-hamburg.de

There is more to life than increasing its speed.  - Mahatma Gandhi

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