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Removed printouts from proposal func
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@jameshay218
jameshay218 committed May 13, 2024
1 parent 4bd3acd commit 4197b2e
Showing 1 changed file with 3 additions and 41 deletions.
44 changes: 3 additions & 41 deletions src/proposal.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -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;

Expand All @@ -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?
Expand All @@ -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
///////////////////////////////////////////////////////
Expand Down Expand Up @@ -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;
Expand All @@ -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;
Expand All @@ -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,
Expand Down Expand Up @@ -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;
Expand All @@ -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 =============== //
Expand All @@ -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);
Expand Down Expand Up @@ -787,7 +756,6 @@ List inf_hist_prop_prior_v2_and_v4(
log_prob = std::min<double>(0.0, (new_prob+prior_new) - (old_prob+prior_old));
} else {
log_prob = std::min<double>(0.0, (new_prob+prior_new) - (old_prob+prior_old));
//Rcpp::Rcout << log_prob << std::endl;
}

rand1 = R::runif(0,1);
Expand All @@ -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);
Expand All @@ -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
Expand All @@ -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;
}
}
}
Expand Down

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