Re: [R] [Rcpp-devel] Find number of elements less than some number: Elegant/fastsolution needed

From: Christian Gunning <xian_at_unm.edu>
Date: Thu, 14 Apr 2011 21:47:22 -0700


On Thu, Apr 14, 2011 at 7:02 PM,
<rcpp-devel-request_at_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!

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Received on Fri 15 Apr 2011 - 06:53:56 GMT

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