//[[Rcpp::export]] Rcpp::List collapse_single_cpp( Rcpp::IntegerVector ances, Rcpp::IntegerVector desc, Rcpp::NumericVector elen, Rcpp::NumericVector nnode, Rcpp::LogicalVector show_progress) { int n_singles = n_singletons(ances); std::vector<int> tab_node = tabulate_tips(ances); Rcpp::IntegerVector tab_node_rcpp(tab_node.size()); tab_node_rcpp = tab_node; Rcpp::IntegerVector position_singleton = which_integer(tab_node_rcpp, Rcpp::IntegerVector::create(1)); Rcpp::IntegerVector position_singleton_orig = position_singleton; RProgress::RProgress pb("Progress [:bar] :current/:total (:percent) :eta", (double) n_singles, 60); if (show_progress) { pb.tick(0); } while (position_singleton.size() > 0) { // Rcpp::Rcout << "tabNode is "; // for (unsigned k = 0; k < tabNode.size(); ++k) // Rcpp::Rcout << " " << tabNode[k]; // Rcpp::Rcout << std::endl; // Rcpp::Rcout << "position singleton is "; // for (unsigned k = 0; k < positionSingleton.size(); ++k) // Rcpp::Rcout << " " << positionSingleton[k]; // Rcpp::Rcout << std::endl; int i = position_singleton[0]; Rcpp::IntegerVector iV(1); iV = i; //Rcpp::Rcout << "i is " << i << " and iV is " << iV << std::endl; Rcpp::IntegerVector prev_node = which_integer(desc, iV + 1); Rcpp::IntegerVector next_node = which_integer(ances, iV + 1); //Rcpp::Rcout << "prev_node is " << prev_node << " and next_node is " << next_node << std::endl; //Rcpp::Rcout << "before desc:"; //for (unsigned k = 0; k < desc.size(); ++k) // Rcpp::Rcout << " " << desc[k]; //Rcpp::Rcout << std::endl; desc[prev_node] = desc[next_node]; //Rcpp::Rcout << "after desc:"; //for (unsigned k = 0; k < desc.size(); ++k) // Rcpp::Rcout << " " << desc[k]; //Rcpp::Rcout << std::endl; Rcpp::IntegerVector to_rm = which_integer(ances, iV + 1); //Rcpp::Rcout << "to_rm is " << to_rm << std::endl; desc.erase(to_rm[0]); ances.erase(to_rm[0]); desc = match_and_substract(desc, iV); ances = match_and_substract(ances, iV); nnode = nnode - 1; if (elen.size() > 0) { elen[prev_node] = elen[prev_node] + elen[next_node]; elen.erase(next_node[0]); } tab_node = tabulate_tips(ances); tab_node_rcpp(tab_node.size()); tab_node_rcpp = tab_node; position_singleton = which_integer(tab_node_rcpp, Rcpp::IntegerVector::create(1)); if (show_progress) { pb.tick(); } } Rcpp::List res = Rcpp::List::create( Rcpp::Named("ances") = ances, Rcpp::Named("desc") = desc, Rcpp::Named("Nnode") = nnode, Rcpp::Named("edge.length") = elen, Rcpp::Named("position_singletons") = position_singleton_orig); return res; }