// [[Rcpp::export]]
Rcpp::NumericMatrix DistMatrixMinkowskiMAT(Rcpp::NumericMatrix dists, double p, bool testNA){
int ncols = dists.ncol();
double dist_value = 0.0;
Rcpp::NumericMatrix dist_matrix(ncols,ncols);
// http://stackoverflow.com/questions/23748572/initializing-a-matrix-to-na-in-rcpp
std::fill( dist_matrix.begin(), dist_matrix.end(), Rcpp::NumericVector::get_na() );
for (int i = 0; i < ncols; i++){
for (int j = 0; j < ncols; j++){
if(Rcpp::NumericVector::is_na(dist_matrix(i,j))){
dist_value = minkowski(dists(Rcpp::_, i),dists(Rcpp::_, j), p, testNA);
dist_matrix(i,j) = dist_value;
dist_matrix(j,i) = dist_value;
}
}
}
return dist_matrix;
}
// @export
// [[Rcpp::export]]
Rcpp::NumericMatrix DistMatrixWithoutUnitMAT(Rcpp::NumericMatrix dists, Rcpp::Function DistFunc, bool testNA){
// http://stackoverflow.com/questions/27391472/passing-r-function-as-parameter-to-rcpp-function
int ncols = dists.ncol();
double dist_value = 0.0;
Rcpp::NumericMatrix dist_matrix(ncols,ncols);
// http://stackoverflow.com/questions/23748572/initializing-a-matrix-to-na-in-rcpp
std::fill( dist_matrix.begin(), dist_matrix.end(), Rcpp::NumericVector::get_na() );
for (int i = 0; i < ncols; i++){
for (int j = 0; j < ncols; j++){
if(Rcpp::NumericVector::is_na(dist_matrix(i,j))){
dist_value = Rcpp::as<double>(DistFunc(dists(Rcpp::_, i),dists(Rcpp::_, j), testNA));
dist_matrix(i,j) = dist_value;
dist_matrix(j,i) = dist_value;
}
}
}
return dist_matrix;
}
// @export
// [[Rcpp::export]]
Rcpp::NumericMatrix DistMatrixWithoutUnitDF(Rcpp::DataFrame distsDF, Rcpp::Function DistFunc, bool testNA){
// http://stackoverflow.com/questions/27391472/passing-r-function-as-parameter-to-rcpp-function
Rcpp::NumericMatrix dists = as_matrix(distsDF);
int nrow = dists.nrow();
double dist_value = 0.0;
Rcpp::NumericMatrix dist_matrix(nrow,nrow);
// http://stackoverflow.com/questions/23748572/initializing-a-matrix-to-na-in-rcpp
std::fill( dist_matrix.begin(), dist_matrix.end(), Rcpp::NumericVector::get_na() );
for (int i = 0; i < nrow; i++){
for (int j = 0; j < nrow; j++){
if(Rcpp::NumericVector::is_na(dist_matrix(i,j))){
dist_value = Rcpp::as<double>(DistFunc(dists(i,Rcpp::_),dists(j,Rcpp::_), testNA));
dist_matrix(i,j) = dist_value;
dist_matrix(j,i) = dist_value;
}
}
}
return dist_matrix;
}
double average_neighbor_distance(const std::vector<std::vector<double> > * points, const unsigned int num_neigh) {
std::vector<std::vector<double> > dist_matrix( points->size(), std::vector<double>(points->size(), 0.0) );
for (unsigned int i = 0; i < points->size(); i++) {
for (unsigned int j = i + 1; j < points->size(); j++) {
double distance = euclidean_distance( &(*points)[i], &(*points)[j] );
dist_matrix[i][j] = distance;
dist_matrix[j][i] = distance;
}
std::sort(dist_matrix[i].begin(), dist_matrix[i].end());
}
double total_distance = 0.0;
for (unsigned int i = 0; i < points->size(); i++) {
for (unsigned int j = 0; j < num_neigh; j++) {
total_distance += dist_matrix[i][j + 1];
}
}
return total_distance / ( (double) num_neigh * (double) points->size() );
}
