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, ...)$obs
mean <- mean(m)
std <- sd(m)
res <- list(mean = mean, std = std)
}
return(res)
}
bias.dres <- sapply(bias, DRes)
I run this code and after 3 hours is still running. I am on Windows XP
and this is my sessionInfo()
> sessionInfo()
R version 2.7.0 Patched (2008-05-02 r45580)
i386-pc-mingw32
locale:
LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
Kingdom.1252;LC_MONETARY=English_United
Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] analogue_0.5-1 vegan_1.11-4 ade4_1.4-7
Any help will be very much appreciated.
Marc.
first preallocate 'm' to the max (m <- numeric(nr)) and then run Rprof to see where time is being spent. Since there was not reproducible data provided, it is hard to analyze beyond this point. Time is probably being spent in one of the functions On Tue, Jun 10, 2008 at 4:49 AM, Marc <marc.moragues@gmail.com> wrote:> Hi, > > I have the following function that I want to apply to a list of 14 matrices > (1536 x 170) of binary data: > > DRes <- function(x, nr = 10000, metric = "mixed", ...) { > require(analogue) > require(ade4) > m <- c() > for (i in 1:nr) { > set.seed(i) > x1 <- x[, sample(dimnames(x)[[2]], length(x[1,])/2)] > x2 <- x[, !dimnames(x)[[2]] %in% dimnames(x1)[[2]]] > d1 <- as.dist(distance(as.data.frame(x1), method = metric)) > d2 <- as.dist(distance(as.data.frame(x2), method = metric)) > m[i] <- mantel.rtest(d1, d2, ...)$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? [[alternative HTML version deleted]]
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? [[alternative HTML version deleted]]