Hello,
We don't know your function f, so this is hard to say. Anyway, this
below implements something similar to apply(.,1,paste0) in rcpp (current
devl version):
#include <Rcpp.h>
using namespace Rcpp ;
// [[Rcpp::export]]
CharacterVector pasteColumns(CharacterMatrix m){
String buffer ;
int nc = m.ncol(), nr = m.nrow() ;
CharacterVector out(nr) ;
for( int i=0; i<nr; i++){
CharacterMatrix::Row row = m(i,_) ;
buffer = "" ;
for( int j=0; j<nc; j++){
buffer += row[j] ;
}
out[i] = buffer ;
}
return out ;
}
With this, I get these timings:
nc <- 100; nr <- 2e4
M <- matrix( sample(letters, nc*nr, replace = TRUE) , ncol = nc )
require(microbenchmark)
microbenchmark(
pasteColumns(M),
apply(M, 1, paste0)
)
Unit: milliseconds
expr min lq median uq max
1 apply(M, 1, paste0) 451.39975 484.41435 495.92757 501.58728 714.1418
2 pasteColumns(M) 67.91322 68.29269 70.34704 77.09383 145.9161
Le 10/12/12 23:43, [email protected] a écrit :
I preface this by stating that I'm very much a Rcpp beginner who is
comfortable in R but I've never before used C++. I'm working through the
Rcpp documentation but haven't been able to answer my question.
I've written an Rcpp (v0.10.1) function f that takes as input a
CharacterMatrix X. X has 20 million rows and 100 columns. For each row
of X the function alters certain entries of that row according to rules
governed by some other input variables. f returns the updated version of
X. This function works as I'd like it to:
# a toy example with nrow = 2, ncol = 2
> X <- matrix('A', ncol = 2, nrow = 2)
> X
[,1] [,2]
[1,] "A" "A"
[2,] "A" "A"
> X <- f(X, other_input_variables)
> X
[,1] [,2]
[1,] "Z" "A"
[2,] "z" "A"
However, instead of f returning a CharacterMatrix as it currently does,
I'd like to return a CharacterVector Y, where each element of Y is a
"collapsed" row of the updated X.
I can achieve the desired result in R by using:
Y <- apply(X=X, MARGIN = 1, FUN = function(x){paste0(x, collapse = '')})
> Y
[1] "ZA" "zA"
but I wondered whether this "joining" is likely to be more efficiently
performed within my function f? If so, how do I join the 100 individual
character entries of a row of the CharacterMatrix X into a single string
that will then comprise an element of the returned CharacterVector Y?
Many thanks,
Pete
--------------------------------
Peter Hickey,
PhD Student/Research Assistant,
Bioinformatics Division,
Walter and Eliza Hall Institute of Medical Research,
1G Royal Parade, Parkville, Vic 3052, Australia.
Ph: +613 9345 2324
[email protected] <mailto:[email protected]>
http://www.wehi.edu.au
--
Romain Francois
Professional R Enthusiast
+33(0) 6 28 91 30 30
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blog: http://romainfrancois.blog.free.fr
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