Using intersect in R with Rcpp [closed] - rcpp

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I am new to Rcpp and am trying to write a simple function that would take a list of character vectors (myList), and a separate character vector (vec1), and would return a list of intersections between each list vector and vec1.
I can do this in R easily enough:
myList <- list(
c('apple','banana','orange','pineapple'),
c('pear','pineapple','watermelon'),
c('orange','apple','pineapple'),
NA,
c('watermelon','lime','apple','banana'))
vec1 <- c('apple','pineapple','banana')
# R implementation
lapply(myList, function(x) intersect(x, vec1))
But I am confused as to how to implement this with Rcpp. Here is my attempt:
cppFunction('
List intersectList (List input, StringVector vec) {
int n = input.size();
List out(n);
for (int i = 0; i < n; i++) {
StringVector sp = Rcpp::as< std::vector<std::string> > (input[i]);
if (sp.length() > 0) {
out[i] = intersect(sp, vec);
}
}
return out;
}
')
...however this results in an error:
Error in sourceCpp(code = code, env = env, rebuild = rebuild, cacheDir = cacheDir, :
Error 1 occurred building shared library.
file1510d6dbd767c.cpp:14:17: error: no viable conversion from 'std::__1::vector<std::__1::basic_string<char>, std::__1::allocator<std::__1::basic_string<char> > >' to 'StringVector' (aka 'Vector<16>')
StringVector sp = Rcpp::as< std::vector<std::string> > (input[i]);
^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include/Rcpp/vector/Vector.h:65:5: note: candidate constructor not viable: no known conversion from 'std::__1::vector<std::__1::basic_string<char>, std::__1::allocator<std::__1::basic_string<char> > >' to 'const Rcpp::Vector<16, PreserveStorage> &' for 1st argument
Vector( const Vector& other){
^
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include/Rcpp/vector/Vector.h:73:5: note: candidate constructor not viable: no known conversion from 'std::__1::vector<std::__1::basic_string<char>, std::__1::allocator<std::__1::basic_string<char> > >' to 'SEXP' (aka 'SEXPREC *') for 1st argument
Vector( SEXP x ) {
^
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include/Rcpp/vector/Vector.h:101:5: note: candidate constructor not viable: no known conversion from 'std::__1::vector<std::__1::basic_string<char>, std::__1::allocator<std::__1::basic_string<char> > >' to 'const std::string &' (aka 'const basic_string<char, char_traits<char>, allocator<char> > &') for 1st argument
Vector( const std::string& st ){
^
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include/Rcpp/vector/Vector.h:107:5: note: candidate constructor not viable: no known conversion from 'std::__1::vector<std::__1::basic_string<char>, std::__1::allocator<std::__1::basic_string<char> > >' to 'const char *' for 1st argument
Vector( const char* st ) {
^
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include/Rcpp/vector/Vector.h:128:5: note: candidate constructor not viable: no known conversion from 'std::__1::vector<std::__1::basic_string<char>, std::__1::allocator<std::__1::basic_string<char> > >' to 'const int &' for 1st argument
Vector( const int& size ) {
^
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include/Rcpp/vector/Vector.h:133:5: note: candidate constructor not viable: no known conversion from 'std::__1::vector<std::__1::basic_string<char>, std::__1::allocator<std::__1::basic_string<char> > >' to 'const Rcpp::Dimension &' for 1st argument
Vector( const Dimension& dims) {
^
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include/Rcpp/vector/Vector.h:78:5: note: candidate template ignored: could not match 'GenericProxy' against 'vector'
Vector( const GenericProxy<Proxy>& proxy ){
^
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include/Rcpp/vector/Vector.h:123:42: note: candidate template ignored: disabled by 'enable_if' [with T = std::__1::vector<std::__1::basic_string<char>, std::__1::allocator<std::__1::basic_string<char> > >]
typename Rcpp::traits::enable_if<traits::is_arithmetic<T>::value, void>::type* = 0) {
^
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include/Rcpp/vector/Vector.h:146:45: note: candidate template ignored: disabled by 'enable_if' [with T = std::__1::vector<std::__1::basic_string<char>, std::__1::allocator<std::__1::basic_string<char> > >]
typename Rcpp::traits::enable_if<traits::is_bool<T>::value && RTYPE == LGLSXP, void>::type* = 0) {
^
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include/Rcpp/vector/Vector.h:162:5: note: candidate template ignored: could not match 'VectorBase' against 'vector'
Vector( const VectorBase<RTYPE,NA,VEC>& other ) {
^
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include/Rcpp/vector/Vector.h:176:5: note: candidate template ignored: could not match 'SingleLogicalResult' against 'vector'
Vector( const sugar::SingleLogicalResult<NA,T>& obj ) {
^
1 error generated.
make: *** [file1510d6dbd767c.o] Error 1
In this particular case, the R implementation is simple and fast, so Rcpp may not be necessary. But I would like to understand the Rcpp implementation, as it would give me a better understanding of how to work with vectors and lists with Rcpp.

Answer 1

Briefly:
The function is called intersect; your title talks about intercept. Not the same thing.
The unit test for intersect() is a one-liner (see below). If I were you I'd start from it and try it with StringVector types.
You are jumping bacl and forth between StringVector and std::vector<std::string>. Why? If you change StringVector sp = Rcpp::as< std::vector<std::string> > (input[i]); to use StringVector in the as<>() you might be good. [ Untested, no time right now. ]
The test function (included in every version of Rcpp in file unitTests/cpp/sugar.cpp is:
// [[Rcpp::export]]
IntegerVector runit_intersect( IntegerVector x, IntegerVector y){
return intersect( x, y ) ;
}

Answer 2

Thanks to Dirk Eddelbuettel for suggesting the following:
> cppFunction('
+ List intersectList (List input, StringVector vec) {
+
+ int n = input.size();
+ List out(n);
+
+ for (int i = 0; i < n; i++) {
+
+ StringVector sp = Rcpp::as< StringVector > (input[i]);
+
+ if (sp.length() > 0) {
+ out[i] = intersect(sp, vec);
+ }
+ }
+
+ return out;
+
+ }
+ ')
>
> myList <- list(
+ c('apple','banana','orange','pineapple'),
+ c('pear','pineapple','watermelon'),
+ c('orange','apple','pineapple'),
+ NA,
+ c('watermelon','lime','apple','banana'))
>
> vec1 <- c('apple','pineapple','banana')
>
> intersectList(myList, vec1)
[[1]]
[1] "pineapple" "banana" "apple"
[[2]]
[1] "pineapple"
[[3]]
[1] "pineapple" "apple"
[[4]]
character(0)
[[5]]
[1] "banana" "apple"