Did not see a simple way to make it faster. However, this is a piece of
code which can be made to run much faster in C. See below.
I don't know if you are familiar with running c-code from R. If not, the
official documentation is in the R Extensions manual. However, this is
not the most easy documentation for a first read. If you want to use the
c-code and have problems getting it running, let me/us know your
operating system and I/we will try to walk you through it.
HTH,
Jan
=== c-code ===
void foo(double* m, int* pn, int* r) {
int n = *pn;
double* pm1 = m;
double* pm2 = m + n;
int* pr = r;
for (int i = 0; i < n; ++i, ++pm1, ++pm2, ++pr) {
*pr = 1;
double* qm1 = m;
double* qm2 = m + n;
for (int j = 0; j < n; ++j, ++qm1, ++qm2) {
if ((*qm1 > *pm1) && (*qm2 > *pm2)) {
*pr = 0;
break;
}
}
}
}
=== r-code ===
dyn.load("rtest.so")
foo <- function(m) {
n <- dim(m)[1]
.C("foo",
as.double(m),
as.integer(n),
r = logical(n))$r
}
x <- runif(32000)
y <- runif(32000)
xy <- cbind(x,y)
t1 <- system.time({
outer <- function(z){
!any(x > z[1] & y > z[2])
}
j <- apply(xy,1, outer)
})
t2 <- system.time({
j2 <- foo(xy)
})
=== results ===
> all(j == j2)
[1] TRUE
> t1
user system elapsed
35.462 0.028 35.549
> t2
user system elapsed
0.008 0.000 0.008
>
On 10/10/2012 12:15 PM, [email protected] wrote:
Hi all,
I wrote a function that actually does what I want it to do, but it tends to be
very slow for large amount of data. On my computer it takes 5.37 seconds for
16000 data points and 21.95 seconds for 32000 data points. As my real data
consists of 18000000 data points it would take ages to use the function as it
is now.
Could someone help me to speed up the calculation?
Thank you, Tonja
system.time({
x <- runif(32000)
y <- runif(32000)
xy <- cbind(x,y)
outer <- function(z){
!any(x > z[1] & y > z[2])}
j <- apply(xy,1, outer)
plot(x,y)
points(x[j],y[j],col="green")
})
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
______________________________________________
[email protected] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
