| 1 | #include <Rcpp.h> |
| 2 | |
| 3 | // [[Rcpp::depends(BH, bigmemory)]] |
| 4 | #include <bigmemory/MatrixAccessor.hpp> |
| 5 | |
| 6 | #include <numeric> |
| 7 | #include <cfloat> |
| 8 | |
| 9 | using namespace Rcpp; |
| 10 | |
| 11 | //' computeMedoidsIndices |
| 12 | //' |
| 13 | //' Compute medoids indices |
| 14 | //' |
| 15 | //' @param pMedoids External pointer |
| 16 | //' @param ref_series reference series |
| 17 | //' |
| 18 | //' @return A map serie number -> medoid index |
| 19 | // [[Rcpp::export]] |
| 20 | IntegerVector computeMedoidsIndices(SEXP pMedoids, NumericMatrix ref_series) |
| 21 | { |
| 22 | XPtr<BigMatrix> pMed(pMedoids); |
| 23 | MatrixAccessor<double> medoids = MatrixAccessor<double>(*pMed); |
| 24 | int nb_series = ref_series.ncol(), |
| 25 | K = pMed->ncol(), |
| 26 | L = pMed->nrow(); |
| 27 | IntegerVector mi(nb_series); |
| 28 | |
| 29 | for (int i=0; i<nb_series ; i++) |
| 30 | { |
| 31 | // mi[i] <- which.min( rowSums( sweep(medoids, 2, ref_series[i,], '-')^2 ) ) |
| 32 | mi[i] = 0; |
| 33 | double best_dist = DBL_MAX; |
| 34 | for (int j=0; j<K; j++) |
| 35 | { |
| 36 | double dist_ij = 0.; |
| 37 | for (int k=0; k<L; k++) |
| 38 | { |
| 39 | double delta = ref_series(k,i) - *(medoids[j]+k); |
| 40 | dist_ij += delta * delta; |
| 41 | } |
| 42 | if (dist_ij < best_dist) |
| 43 | { |
| 44 | mi[i] = j+1; //R indices start at 1 |
| 45 | best_dist = dist_ij; |
| 46 | } |
| 47 | } |
| 48 | } |
| 49 | |
| 50 | return mi; |
| 51 | } |