On Thu, Apr 14, 2011 at 7:02 PM,
<rcpp-devel-requ...@r-forge.wu-wien.ac.at> wrote:
> I was able to write a very short C++ function using the Rcpp package
> that provided about a 1000-fold increase in speed relative to the best
> I could do in R. I don't have the script on this computer so I will
> post it tomorrow when I am back on the computer at the office.
>
> Apologies for cross-posting to the Rcpp-devel list but I am doing so
> because this might make a good example of the usefulness of Rcpp and
> inline.
And RcppArmadillo, as the case may be.
This is a cool little problem. In the examples given, I'd caution
people against comparing apples and durian. The sort(x) is a cost
that should be considered *within* each implementation. I used
Armadillo to sort (src, f4), and get another 100% worth of speedup
that I can't reproducing using R's sort (src1, f1-f3). If i modify
SEXP in-place (and this always confuses me, so I tend to avoid it),
I'm seeing an additional ~5-10% speed gain (src2, f5) -- the advantage
of this last seems to be primarily in memory-constrained applications.
On to the code!
src = '
NumericVector xx_(clone(x)), yy_(clone(y));
int nxx = xx_.size();
int nyy = yy_.size();
arma::vec xx(xx_), yy(yy_);
yy = sort(yy);
xx = sort(xx);
//
//
int j = 0; //gt index for yy
for (int i=0; i < nxx; i++) {
while ((j < nyy) && ( xx(i) > yy(j) ) ) {
j++;
}
xx_(i) = j;
}
return (xx_);
'
src1 = '
NumericVector xx_(clone(x)), yy_(clone(y));
// assumes x & y are already sorted
arma::vec xx(xx_), yy(yy_);
int nxx = xx.n_elem;
int nyy = yy.n_elem;
int j = 0; //gt index for yy
for (int i=0; i < nxx; i++) {
while ((j < nyy) && ( xx(i) > yy(j) ) ) {
j++;
}
xx_(i) = j;
}
return (xx_);
'
src2 = '
NumericVector xx_(x), yy_(y); //kinda scary
int nxx = xx_.size();
int nyy = yy_.size();
arma::vec xx(xx_.begin(), nxx, false), yy(yy_.begin(), nyy, false);
//really kinda scary
yy = sort(yy);
xx = sort(xx);
//
//
int j = 0; //gt index for yy
for (int i=0; i < nxx; i++) {
while ((j < nyy) && ( xx(i) > yy(j) ) ) {
j++;
}
xx_(i) = j;
}
return (xx_);
'
require(inline)
require(RcppArmadillo)
f1 <- function(x, y) { sort(length(y) - findInterval(-x, rev(-sort(y))));}
f2 <- function(x, y) {x = sort(x); length(y) - findInterval(-x, rev(-sort(y)))}
f3.a <- cxxfunction(signature(x="numeric", y="numeric"), src1,
plugin='RcppArmadillo')
f3 <- function(x,y) {
x <- sort(x)
y <- sort(y)
return(f3.a(x,y))
}
f4 <- cxxfunction(signature(x="numeric", y="numeric"), src,
plugin='RcppArmadillo')
## danger -- violates R semantics
f5 <- cxxfunction(signature(x="numeric", y="numeric"), src2,
plugin='RcppArmadillo')
## this is a really ugly test. ygwypf, i suppose :)
for (i in 1:5) {
x1 <- x <- rnorm(5e6)
y1 <- y <- rnorm(5e6)
print( cbind(
r1=system.time(r1 <- f1(x,y)),
r2=system.time(r2 <- f2(x,y)), r3=system.time(r3 <- f3(x1,y1)),
r4 = system.time(r4 <- f4(x,y)), r5 = system.time(r5 <- f5(x,y))
))
}
print(all.equal(r1, r2))
print(all.equal(r1, r3))
print(all.equal(r1, r4))
print(all.equal(r1, r5))
best,
Christian Gunning
University of New Mexico Biology Department
--
A man, a plan, a cat, a ham, a yak, a yam, a hat, a canal – Panama!
______________________________________________
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
and provide commented, minimal, self-contained, reproducible code.
