From: Gabor Grothendieck <ggrothendieck_at_myway.com>

Date: Sun 04 Jul 2004 - 02:12:10 EST

[1] 0.03 0.00 0.03 NA NA

[1] 0.1 0.0 0.1 NA NA

R-help@stat.math.ethz.ch mailing list

https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Sun Jul 04 02:16:27 2004

Date: Sun 04 Jul 2004 - 02:12:10 EST

Ravi Varadhan <rvaradha <at> jhsph.edu> writes:

*> Hi:
**>
*

> I have two matrices, A and B, where A is n x k, and B is m x k, where n >> m

>> k. Is there a computationally fast way to

> count the number of times each row (a k-vector) of B occurs in A? Thanks

for any suggestions.

*>
*

> Best,

> Ravi.

Here are two approaches. The first one is an order of magnitude faster than the second.

R> # test matrices R> set.seed(1) R> a <- matrix(sample(3,1000,rep=T),nc=5) R> b <- matrix(sample(3,100,rep=T),nc=5)

R> f1 <- function(a,b) {

+ a2 <- apply(a, 1, paste, collapse=":") + b2 <- apply(b, 1, paste, collapse=":") + c(table(c(a2,unique(b2)))[b2] - 1) + }

R> f2 <- function(a,b) {

+ ta <- t(a) + apply(b,1,function(x)sum(apply(ta == x,2,all))) + } R> gc(); system.time(ans1 <- f1(a,b)) used (Mb) gc trigger (Mb) Ncells 458311 12.3 818163 21.9 Vcells 124264 1.0 786432 6.0

[1] 0.03 0.00 0.03 NA NA

R> gc(); system.time(ans2 <- f2(a,b))

used (Mb) gc trigger (Mb) Ncells 458312 12.3 818163 21.9 Vcells 124270 1.0 786432 6.0

[1] 0.1 0.0 0.1 NA NA

R> all.equal(ans1, ans2)

**[1] TRUE
**

R-help@stat.math.ethz.ch mailing list

https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Sun Jul 04 02:16:27 2004

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