dimitris_ps - 1 year ago 122

R Question

My problem is mostly that of efficiency.

I have a vector of patterns that i would like to match against a vector

`x`

The end result should return the pattern that is match to each element of the vector. A second criteria would be, if many patterns are matched for a specific element of the vector

`x`

For example, lets say the vector of patterns is:

`patterns <- c("[0-9]{2}[a-zA-Z]", "[0-9][a-zA-Z] ", " [a-zA-Z]{3} ")`

and the vector

`x`

`x <- c("abc 123ab abc", "abc 123 abc ", "a", "12a ", "1a ")`

The end result would be:

`customeRExp(patterns, x)`

[1] "[0-9]{2}[a-zA-Z]" " [a-zA-Z]{3} "

[3] NA "[0-9]{2}[a-zA-Z]"

[5] "[0-9][a-zA-Z] "

This is what i have so far:

`customeRExp <- function(pattern, x){`

m <- matrix(NA, ncol=length(x), nrow=length(pattern))

for(i in 1:length(pattern)){

m[i, ] <- grepl(pattern[i], x)}

indx <- suppressWarnings(apply(m, 2, function(y) min(which(y, TRUE))))

pattern[indx]

}

customeRExp(patterns, x)

Which correctly returns:

`[1] "[0-9]{2}[a-zA-Z]" " [a-zA-Z]{3} " NA`

[4] "[0-9]{2}[a-zA-Z]" "[0-9][a-zA-Z] "

The problem is that my dataset is huge, and the list of patterns quite big also.

Is there a more efficient way of doing the same?

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Answer Source

My default approach to speeding up loops like the above is generally to just rewrite in C++. Here's a quick attempt using Boost Xpressive:

```
// [[Rcpp::depends(BH)]]
#include <Rcpp.h>
#include <boost/xpressive/xpressive.hpp>
namespace xp = boost::xpressive;
// [[Rcpp::export]]
Rcpp::CharacterVector
first_match(Rcpp::CharacterVector x, Rcpp::CharacterVector re) {
R_xlen_t nx = x.size(), nre = re.size(), i = 0, j = 0;
Rcpp::CharacterVector result(nx, NA_STRING);
std::vector<xp::sregex> vre(nre);
for ( ; j < nre; j++) {
vre[j] = xp::sregex::compile(std::string(re[j]));
}
for ( ; i < nx; i++) {
for (j = 0; j < nre; j++) {
if (xp::regex_search(std::string(x[i]), vre[j])) {
result[i] = re[j];
break;
}
}
}
return result;
}
```

The point of this approach is to save unnecessary calculations by `break`

ing as soon as we find a matching regular expression.

The performance increase isn't earth-shattering (~40%), but it is an improvement over your current function. Here is a test using larger versions of your sample data:

```
x2 <- rep(x, 5000)
p2 <- rep(patterns, 100)
all.equal(first_match(x2, p2), customeRExp(p2, x2))
#[1] TRUE
microbenchmark::microbenchmark(
first_match(x2, p2),
customeRExp(p2, x2),
times = 50
)
# Unit: seconds
# expr min lq mean median uq max neval
# first_match(x2, p2) 1.743407 1.780649 1.900954 1.836840 1.931783 2.544041 50
# customeRExp(p2, x2) 2.368621 2.459748 2.681101 2.566717 2.824887 3.553025 50
```

Another option would be to look into using the `stringi`

package which generally outperforms base R by a good margin.

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