[R] counting the occurrences of vectors
Gabor Grothendieck
ggrothendieck at myway.com
Sat Jul 3 18:12:10 CEST 2004
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
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