[R] Making routine faster by using apply instead of for-loop

[William Dunlap]

> -----Original Message-----
> From: r-help-bounces at r-project.org 
> [mailto:r-help-bounces at r-project.org] On Behalf Of Etienne Stockhausen
> Sent: Tuesday, January 12, 2010 10:59 AM
> To: r-help at r-project.org
> Subject: [R] Making routine faster by using apply instead of for-loop
> 
> Hey everybody,
> 
> I have a small problem with a routine, which prepares some data for
> plotting.
> I've made a small example:
> 
>     c=10
>     mat=data.frame(matrix(1:(c*c),c,c))
>     row.names(mat)=seq(c,1,length=c)
>     names(mat)=c(seq(2,c,length=c/2),seq(c,2,length=c/2))
>     v=as.numeric(row.names(mat))
>     w=as.numeric(names(mat))
>     for(i in 1:c)
>     { for(j in 1:c)
>     {
>     if(v[j]+w[i]<=c)(mat[i,j]=NA)
>     }}
> 
> This produces exactly the data I need to go on, but if I increase the
> constant c ,to for instance 500 , it takes a very long time 
> to set the NA's.

The first problem is that random (element-by-element)
access to a data.frame is much slower than the equivalent
access to a matrix.  Rewriting your code a bit to
use a matrix speeds up the c=500 case by a factor of 750.
f0 <- function (c = 10)  {
    mat = matrix(1:(c * c), c, c)
    rownames(mat) = seq(c, 1, length = c)
    colnames(mat) = c(seq(2, c, length = c/2), seq(c, 2, length = c/2))
    v = as.numeric(rownames(mat))
    w = as.numeric(colnames(mat))
    for (i in 1:c) {
        for (j in 1:c) {
            if (v[j] + w[i] <= c) {
                mat[i, j] = NA
            }
        }
    }
    mat
}
Rewriting that to insert the NA's one operation speeds it up by
another factor of 10 (in the c=500 case)
f1 <- function (c = 10) {
    v <- seq(c, 1, length = c)
    w <- c(seq(2, c, length = c/2), seq(c, 2, length = c/2))
    mat <- matrix(1:(c * c), nrow = c, ncol = c, dimnames = list(v, 
        w))
    mat[outer(w, v, `+`) <= c] <- NA
    mat
}

If you really want a matrix, pass the output of these functions
into data.frame (with check.names=FALSE since the column
names are not considered legal on data.frame: the contain
duplicates and look numeric).

By the way, it is generally a bad idea to use apply() on
a data.frame.  It is meant for matrices.

Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com 

> I've heard there is a much faster way to set the NA's using 
> the command
> apply( ), but I don't know how.
> I'm looking forward for any ideas or hints, that might help me.
> 
> Best regards
> 
> Etienne
> 
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