diff --git a/src/proposal.cpp b/src/proposal.cpp index 2ac5ebf..6b7eb3c 100644 --- a/src/proposal.cpp +++ b/src/proposal.cpp @@ -405,8 +405,6 @@ List inf_hist_prop_prior_v2_and_v4( // ######################################################################## // For each individual for(int i = 0; i < n_sampled; ++i){ - //Rcpp::Rcout << "Indiv: " << i << std::endl; - //usleep(10); // Which proposal step to take and do we need to calculate the likelihood swap_step_option = R::runif(0,1) < proposal_inf_hist_indiv_swap_ratio; @@ -421,20 +419,14 @@ List inf_hist_prop_prior_v2_and_v4( // Birth group is [i-1, 1] birth_group = indiv_group_indices[(number_possible_exposures+1)*(indiv)]; - //Rcpp::Rcout << "Indiv (prop): " << indiv << std::endl; - //Rcpp::Rcout << "Groups (prop): " << groups << std::endl; - //Rcpp::Rcout << "Birth group (prop): " << birth_group << std::endl; } else { // Otherwise, the individual's group is unchanged group = indiv_group_indices[indiv]; } - //Rcpp::Rcout << "indiv: " << indiv+1 << std::endl << std::endl; - popn_group_id = popn_group_id_vec(indiv); old_prob = likelihoods_pre_proposal(indiv); - //Rcpp::Rcout << "Old prob: " << old_prob << std::endl << std::endl; - + // Time sampling control n_times_samp = n_times_samp_vec(indiv); // How many times are we intending to resample for this individual? n_samp_length = sample_mask(indiv) - age_mask(indiv) + 1; // How many times maximum can we sample from? @@ -456,20 +448,15 @@ List inf_hist_prop_prior_v2_and_v4( tmp_loc_sample_probs = time_sample_probs[samps_shifted]; // Re-normalise tmp_loc_sample_probs = tmp_loc_sample_probs/sum(tmp_loc_sample_probs); - //Rcpp::Rcout << "Possible time samples: " << samps << std::endl; locs = RcppArmadillo::sample(samps, n_samp_max, false, tmp_loc_sample_probs); - //Rcpp::Rcout << "Sampled locations: " << locs << std::endl; - // For each selected infection history entry for(int j = 0; j < n_samp_max; ++j){ - //Rcpp::Rcout << "Updating infection history entry: " << j << std::endl; // Assume that proposal hasn't changed likelihood until shown otherwise lik_changed = false; // Infection history to update new_infection_history = new_infection_history_mat(indiv,_); - //Rcpp::Rcout << "Infection history before: " << new_infection_history<< std::endl; - + /////////////////////////////////////////////////////// // OPTION 1: Swap contents of a year for an individual /////////////////////////////////////////////////////// @@ -513,8 +500,7 @@ List inf_hist_prop_prior_v2_and_v4( // Number of infections in that group in that time m_1_old = n_infections(popn_group_id,loc1); m_2_old = n_infections(popn_group_id,loc2); - //Rcpp::Rcout << "popn_group_id: " << popn_group_id << "; loc2: " << loc2<< "; popn_group_id: 1" << std::endl; - + // Swap contents new_infection_history(loc1) = new_infection_history(loc2); new_infection_history(loc2) = loc1_val_old; @@ -527,16 +513,10 @@ List inf_hist_prop_prior_v2_and_v4( m_1_new = m_1_old - loc1_val_old + loc2_val_old; m_2_new = m_2_old - loc2_val_old + loc1_val_old; - //Rcpp::Rcout << "Prior lookup" << std::endl; - //Rcpp::Rcout << "m_1_old: " << m_1_old << "; loc1: " << loc1<< "; popn_group_id: 1" << std::endl; - //Rcpp::Rcout << "m_2_old: " << m_2_old << "; loc2: " << loc2<< "; popn_group_id: 1" << std::endl; - prior_1_old = prior_lookup(m_1_old, loc1, popn_group_id); prior_2_old = prior_lookup(m_2_old, loc2, popn_group_id); prior_old = prior_1_old + prior_2_old; - //Rcpp::Rcout << "m_1_new: " << m_1_new << "; loc1: " << loc1<< "; popn_group_id: 1" << std::endl; - //Rcpp::Rcout << "m_2_new: " << m_2_new << "; loc2: " << loc2<< "; popn_group_id: 1" << std::endl; prior_1_new = prior_lookup(m_1_new, loc1, popn_group_id); prior_2_new = prior_lookup(m_2_new, loc2, popn_group_id); prior_new = prior_1_new + prior_2_new; @@ -553,15 +533,11 @@ List inf_hist_prop_prior_v2_and_v4( /////////////////////////////////////////////////////// } else { - // Rcpp::Rcout << "Age mask: " << age_mask(indiv) << std::endl; - //Rcpp::Rcout << "Sample mask: " << sample_mask(indiv) << std::endl; year = locs(j) + age_mask(indiv) - 1; old_entry = new_infection_history(year); overall_add_proposals(indiv,year)++; - // Rcpp::Rcout << "Old entry: " << old_entry << std::endl; - //Rcpp::Rcout << "Year: " << year << std::endl; //usleep(10); if(!prior_on_total){ // Get number of individuals that were alive and/or infected in that year, @@ -615,8 +591,6 @@ List inf_hist_prop_prior_v2_and_v4( //////////////////////// if(solve_likelihood && lik_changed){ - //if(TRUE){ - //Rcpp::Rcout << "Infection history after change: " << new_infection_history<< std::endl; // Calculate likelihood! indices = new_infection_history > 0; @@ -628,14 +602,11 @@ List inf_hist_prop_prior_v2_and_v4( if(timevarying_groups){ groups_subset = groups[use_indices]; } - //Rcpp::Rcout << infection_times_indices_tmp << std::endl; // Start end end location of the type_data matrix type_start = type_data_start(indiv); type_end = type_data_start(indiv+1)-1; - //Rcpp::Rcout << "Type start: " << type_start << std::endl; - //Rcpp::Rcout << "Type end: " << type_end << std::endl << std::endl; // ====================================================== // // =============== CHOOSE MODEL TO SOLVE =============== // @@ -644,8 +615,6 @@ List inf_hist_prop_prior_v2_and_v4( new_prob = 0; for(int index = type_start; index <= type_end; ++index){ - //Rcpp::Rcout << "index: " << index << std::endl; - //usleep(10); biomarker_group = biomarker_groups(index)-1; data_type = data_types(biomarker_group); obs_weight = obs_weights(biomarker_group); @@ -787,7 +756,6 @@ List inf_hist_prop_prior_v2_and_v4( log_prob = std::min(0.0, (new_prob+prior_new) - (old_prob+prior_old)); } else { log_prob = std::min(0.0, (new_prob+prior_new) - (old_prob+prior_old)); - //Rcpp::Rcout << log_prob << std::endl; } rand1 = R::runif(0,1); @@ -798,7 +766,6 @@ List inf_hist_prop_prior_v2_and_v4( // Carry out the swap if(swap_step_option){ - //Rcpp::Rcout <<"Swap step" << std::endl; accepted_swap(indiv) += 1; tmp = new_infection_history_mat(indiv,loc1); new_infection_history_mat(indiv,loc1) = new_infection_history_mat(indiv,loc2); @@ -808,15 +775,11 @@ List inf_hist_prop_prior_v2_and_v4( if(!prior_on_total){ n_infections(popn_group_id, loc1) = m_1_new; n_infections(popn_group_id, loc2) = m_2_new; - //if(m_1_new < 0) Rcpp::Rcout << "m_1_new < 0!" << std::endl; - //if(m_2_new < 0) Rcpp::Rcout << "m_2_new < 0!" << std::endl; } // Don't need to update group infections if prior_on_total, as infections // only move within an individual (so number in group stays same) } else { - //Rcpp::Rcout <<"Add/remove step" << std::endl; - accepted_iter(indiv) += 1; new_infection_history_mat(indiv,year) = new_entry; // Update total number of infections in group/time @@ -827,7 +790,6 @@ List inf_hist_prop_prior_v2_and_v4( n_infected_group(popn_group_id) = n_infected_group(popn_group_id) - old_entry + new_entry; } - //Rcpp::Rcout << n_infections(popn_group_id, 44) << std::endl; } } }