Return a list of NumericVectors from Rcpp function

Question

I am trying to calculate Gower's similarity between a set of items. Using Rcpp package I am writing my own function to calculate the similarity value as with larger data the daisy function throws an error.

The function is :

#include <Rcpp.h>
using namespace Rcpp;

// [[Rcpp::export]]
List gowerSim(CharacterMatrix inp) {

  int n_row = inp.nrow(), n_col = inp.ncol();
  int sumRow = 0, colLen;
  List out(n_row);

  //double sim[n_row];
  NumericVector sim(n_row);

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

    for (int j = 0; j < n_row; j++) {

      sumRow = 0; 
      colLen = n_col;

      for (int k = 0; k < n_col; k++) {
        if (inp(i,k) != "NA" && inp(j,k) != "NA") {

          if (inp(i,k) != inp(j,k)) {
            sumRow = sumRow + 1;
          }
        } else {
          colLen = colLen - 1;
        }
      }
      if (colLen > 0) {
        sim[j] = (double) sumRow/colLen;
        //printf("%f",sim[j]);
      } else {
        sim[j] = NA_INTEGER;
      }
    }

    out[i] = sim;

    if (i < 3) {
      print(out);
    }
  }

  return out;
}

/*** R
clust<-gowerSim(inp)
*/

The returned list has the last vector copied to all the other elements, i.e, suppose if clust has length 250, clust[[1]] and clust[[250]] have all the values same. However, while printing (for top 3 elements) each vector out[1], out[2], out[3] is different.

Can anybody please tell what is the issue here?

Answer 1

The solution for this problem is to define the vector sim after the first for command, like this:

List gowerSim(CharacterMatrix inp) {

  int n_row = inp.nrow(), n_col = inp.ncol();
  int sumRow=0,colLen;
  List out(n_row);

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

    NumericVector sim(n_row);

    for(int j=0;j<n_row;j++){
      sumRow=0; 
      colLen=n_col;
      for(int k=0; k<n_col;k++){
        if(inp(i,k)!="NA" && inp(j,k)!="NA"){
          if(inp(i,k)!=inp(j,k)){
            sumRow=sumRow+1;
          }
        }else{
          colLen=colLen-1;
        }
      }
      if(colLen>0){
        sim[j] = (double) sumRow/colLen;
        //printf("%f",sim[j]);
      }else{
        sim[j] = NA_INTEGER;
      }
    }
    out[i] = sim;
    if(i<3){
      print(out);
    }
  }

  return out;
}

A little example:

mat <- matrix( as.character(c(rep(1,5),sample(3,15,repl=TRUE),rep(5,5))),5)
clust <- gowerSim(mat)
clust

Or you can define the vector as you did it and reset it in the first for-loop.

Why exactly this approach works and your not: I don't really know, but I think it is referred to the list structure in C++.

My first approach to solve your problem was the following one: Instead filling up a list, we are filling a Matrix, and this works fine, see here:

NumericMatrix gowerSim(CharacterMatrix inp) {

  int n_row = inp.nrow(), n_col = inp.ncol();
  int sumRow=0,colLen;
  NumericMatrix out(n_row, n_col);
  NumericVector sim(n_row);

  for(int i=0;i<n_row;i++);

    for(int j=0;j<n_row;j++){
      sumRow=0; 
      colLen=n_col;
      for(int k=0; k<n_col;k++){
        if(inp(i,k)!="NA" && inp(j,k)!="NA"){
          if(inp(i,k)!=inp(j,k)){
            sumRow=sumRow+1;
          }
        }else{
          colLen=colLen-1;
        }
      }
      if(colLen>0){
        sim[j] = (double) sumRow/colLen;
        //printf("%f",sim[j]);
      }else{
        sim[j] = NA_INTEGER;
      }
    }
    out(_,i) = sim;
    if(i<3){
      print(out);
    }
  }

  return out;
}