I have no idea of what your data looks like, so using random numbers and
only going for nr=1, after about a minute I stopped it.  Here is what Rprof
showed:

/cygdrive/c/perf: perl c:/perf/bin/readRprof.pl Rprof.out 1
  0  75.8 root
  1.   75.7 sapply
  2. .   75.7 lapply
  3. . .   75.7 FUN
  4. . . .   75.6 as.dist
  5. . . . .   75.6 distance
  6. . . . . .   75.6 distance.default
  7. . . . . . .   75.4 apply
  8. . . . . . . .   73.8 FUN
  9. . . . . . . . .   73.8 switch
 10. . . . . . . . . .   73.8 apply
 11. . . . . . . . . . .   63.4 FUN
 12. . . . . . . . . . . .    6.6 !
 12. . . . . . . . . . . .    2.8 -
 12. . . . . . . . . . . .    2.5 any
 12. . . . . . . . . . . .    2.2 /
 12. . . . . . . . . . . .    1.7 sum
 12. . . . . . . . . . . .    1.6 *
 11. . . . . . . . . . .    2.3 aperm
 11. . . . . . . . . . .    1.0 unlist
  8. . . . . . . .    1.5 join

This says almost all the time is in the 'distance' function.  Try running
your data with 'nr' very small and see what happens.

On Tue, Jun 10, 2008 at 4:49 AM, Marc <marc.moragues@gmail.com> wrote:

> Hi,
>
> I have the following function that I want to apply to a list of 14 matrices
> (1536 x 170) of binary data:
>
> DRes <- function(x, nr = 10000, metric = "mixed", ...) {
>  require(analogue)
>  require(ade4)
>  m <- c()
>  for (i in 1:nr) {
>   set.seed(i)
>   x1 <- x[, sample(dimnames(x)[[2]], length(x[1,])/2)]
>   x2 <- x[, !dimnames(x)[[2]] %in% dimnames(x1)[[2]]]
>   d1 <- as.dist(distance(as.data.frame(x1), method = metric))
>   d2 <- as.dist(distance(as.data.frame(x2), method = metric))
>   m[i] <- mantel.rtest(d1, d2, ...)$obs
>   mean <- mean(m)
>   std <- sd(m)
>   res <- list(mean = mean, std = std)
>  }
>  return(res)
> }
> bias.dres <- sapply(bias, DRes)
>
> I run this code and after 3 hours is still running. I am on Windows XP and
> this is my sessionInfo()
> > sessionInfo()
> R version 2.7.0 Patched (2008-05-02 r45580)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
> Kingdom.1252;LC_MONETARY=English_United
> Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> other attached packages:
> [1] analogue_0.5-1 vegan_1.11-4   ade4_1.4-7
> Any help will be very much appreciated.
> Marc.
>
> ______________________________________________
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html<http://www.r-project.org/posting-guide.html>
> and provide commented, minimal, self-contained, reproducible code.
>



-- 
Jim Holtman
Cincinnati, OH
+1 513 646 9390

What is the problem you are trying to solve?

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