2013-01-08-strings_with_rcpp.md

title	author	license	tags	summary	layout	src
Handling Strings with Rcpp	Kevin Ushey	GPL (>= 2)	string vector	Demonstrates how one might handle a vector of strings with `Rcpp`, in addition to returning output.	post	2013-01-08-strings_with_rcpp.Rmd

This is a quick example of how you might use Rcpp to send and receive R 'strings' to and from R. We'll demonstrate this with a few operations.

Sort a String with R

Note that we can do this in R in a fairly fast way:

{% highlight r %} my_strings <- c("apples", "and", "cranberries") R_str_sort <- function(strings) { sapply( strings, USE.NAMES=FALSE, function(x) { intToUtf8( sort( utf8ToInt( x ) ) ) }) } R_str_sort( my_strings ) {% endhighlight %}

[1] "aelpps"      "adn"         "abceeinrrrs"

Sort a String with C++/Rcpp

Let's see if we can re-create the output with Rcpp.

{% highlight cpp %} #include <Rcpp.h> using namespace Rcpp;

// [[Rcpp::export]] std::vector< std::string > cpp_str_sort( std::vector< std::string > strings ) {

int len = strings.size();

for( int i=0; i < len; i++ ) { std::sort( strings[i].begin(), strings[i].end() ); }

return strings; } {% endhighlight %}

Note the main things we do here:

• Rcpp's attributes handle any as-ing and wrap-ing of vectors; we even just specify our return type as std::vector< std::string >.
• We then call the void method std::sort, which can sort a string in place,
• ... and we return that vector of strings.

Now, let's test it, and let's benchmark it as well.

{% highlight r %} cpp_str_sort( my_strings ) {% endhighlight %}

[1] "aelpps"      "adn"         "abceeinrrrs"

{% highlight r %} long_strings <- rep( paste( collapse="", sample( letters, 1E5, replace=TRUE ) ), times=100 )

rbenchmark::benchmark( cpp_str_sort(long_strings), R_str_sort(long_strings), replications=3 ) {% endhighlight %}

                        test replications elapsed relative user.self
1 cpp_str_sort(long_strings)            3   0.898    1.000     0.883
2   R_str_sort(long_strings)            3   2.356    2.624     2.350
  sys.self user.child sys.child
1    0.014          0         0
2    0.007          0         0

Note that the C++ implementation is quite a bit faster (on my machine). However, std::sort will not handle UTF-8 encoded vectors.

Now, let's do something crazy -- let's see if we can use Rcpp to perform an operation that takes a vector of strings, and returns a list of vectors of strings. (Or, in R parlance, a list of vectors of type character).

We'll do a simple 'split', such that each string is split every n indices.

Split a string at consecutive indices n

{% highlight cpp %} #include <Rcpp.h> using namespace Rcpp;

// [[Rcpp::export]] List cpp_str_split( std::vector< std::string > strings, int n ) {

int num_strings = strings.size();

List out(num_strings);

for( int i=0; i < num_strings; i++ ) {

int num_substr = strings[i].length() / n;
std::vector< std::string > tmp;

for( int j=0; j < num_substr; j++ ) {
  
  tmp.push_back( strings[i].substr( j*n, n ) );
  
}

out[i] = tmp;

}

return out; } {% endhighlight %}

Main things to notice:

• We declare the output to be a List,
• We form a List container of size num_strings,
• We construct the split strings one by one, then place them back into our output container (note how with out[i] = tmp, we can assign our vector of strings directly as an element of the list),
• We return the list we constructed.

{% highlight r %} cpp_str_split( c("abcd", "efgh", "ijkl"), 2 ) {% endhighlight %}

[[1]]
[1] "ab" "cd"

[[2]]
[1] "ef" "gh"

[[3]]
[1] "ij" "kl"

{% highlight r %} cpp_str_split( c("abc", "de"), 2 ) {% endhighlight %}

[[1]]
[1] "ab"

[[2]]
[1] "de"

My solution is perhaps a bit deficient (bug or feature?) in that it truncates any strings not long enough; ideally, we'd either improve the C++ code or form an appropriate wrapper to the function in R (and warn the user if truncation might occur).

Hopefully this gives you a better idea how you might use Rcpp to perform more extensive string manipulation with R character vectors.