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outputs.cpp
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//
// Created by Jamie Cohen on 11/29/17.
//
#include "outputs.h"
using namespace std;
const string extension = ".txt";
Output::Output(Inputs &Tables, int y) {
// 2Dmatrices: [age][simyear]
DALY.resize (y + 1);
YLL.resize (y + 1);
YLD.resize (y + 1);
cost.resize (y + 1);
discDALY = 0;
TotalDALY = 0;
discountrate = 0.03;
TotalCost = 0;
discCost = 0;
ageoHR = 0;
age16 = 0;
age18 = 0;
age31 = 0;
age33 = 0;
age45 = 0;
age52 = 0;
age58 = 0;
trace.resize(Tables.ModelStopAge + 1);
for (int i = 0; i <= Tables.ModelStopAge; i++) {
trace[i].resize(y);
for (int j = 0; j < y; ++j)
trace[i][j].resize(7);
}
inc.resize(Tables.ModelStopAge + 1);
for (int i = 0; i <= Tables.ModelStopAge; i++) {
inc[i].resize(y);
for(int j = 0; j < y; j++)
inc[i][j].resize(5);
}
hpvscreens.resize(Tables.ModelStopAge + 1);
for (int i = 0; i <= Tables.ModelStopAge; i++) {
hpvscreens[i].resize (y);
}
papscreens.resize(Tables.ModelStopAge + 1);
for (int i = 0; i <= Tables.ModelStopAge; i++) {
papscreens[i].resize (y);
}
vaccines.resize(Tables.ModelStopAge + 1);
for (int i = 0; i <= Tables.ModelStopAge; i++) {
vaccines[i].resize (y);
}
CaIncStandardized.resize(Tables.ModelStopAge + 1);
for (int i = 0; i <= Tables.ModelStopAge; i++) {
CaIncStandardized[i].resize (y);
}
prev.resize(Tables.ModelStopAge + 1);
for (int i = 0; i <= Tables.ModelStopAge; i++) {
prev[i].resize (y);
}
total_alive.resize (Tables.ModelStopAge+1);
for (int i = 0; i <= Tables.ModelStopAge; i++) {
total_alive[i].resize (y);
}
totaldeadcancer = 0;
TotalHPV.resize(Tables.ModelStopAge+1);
for (int i = 0; i <= Tables.ModelStopAge; i++) {
TotalHPV[i].resize (y);
}
totalcancer_mort.resize (Tables.ModelStopAge + 1);
for (int i = 0; i <= Tables.ModelStopAge; i++) {
totalcancer_mort[i].resize (y);
}
LE.resize (Tables.ModelStopAge + 1);
for (int i = 0; i <= Tables.ModelStopAge; i++) {
LE[i].resize (y);
}
TotalPrevCancer.resize(Tables.ModelStopAge + 1);
for (int i = 0; i <= Tables.ModelStopAge; i++) {
TotalPrevCancer[i].resize (y);
}
TotalCancer.resize(Tables.ModelStopAge + 1);
for (int i = 0; i <= Tables.ModelStopAge; i++) {
TotalCancer[i].resize (y);
}
TotalDetectedCancer.resize(Tables.ModelStopAge + 1);
for (int i = 0; i <= Tables.ModelStopAge; i++) {
TotalDetectedCancer[i].resize (y);
}
TotalDetectedCancer_byyear.resize(y);
CancerDenom_byyear.resize(y);
TotalCancer_1618.resize(Tables.ModelStopAge + 1);
for (int i = 0; i <= Tables.ModelStopAge; i++) {
TotalCancer_1618[i].resize (y);
}
TotalCancer_nonavalent.resize (Tables.ModelStopAge + 1);
for (int i = 0; i <= Tables.ModelStopAge; i++) {
TotalCancer_nonavalent[i].resize (y);
}
TotalCancer_allother.resize(Tables.ModelStopAge + 1);
for (int i = 0; i <= Tables.ModelStopAge; i++) {
TotalCancer_allother[i].resize (y);
}
TotalCancerDenom.resize(Tables.ModelStopAge + 1);
for (int i = 0; i <= Tables.ModelStopAge; i++) {
TotalCancerDenom[i].resize (y);
}
HPVcount.resize (Tables.ModelStopAge + 1);
for (int i = 0; i <= Tables.ModelStopAge; i++) {
HPVcount[i].resize (y);
}
HPV16count.resize (Tables.ModelStopAge + 1);
for (int i = 0; i <= Tables.ModelStopAge; i++) {
HPV16count[i].resize (y);
}
HPV18count.resize (Tables.ModelStopAge + 1);
for (int i = 0; i <= Tables.ModelStopAge; i++) {
HPV18count[i].resize (y);
}
CIN2count.resize (Tables.ModelStopAge + 1);
for (int i = 0; i <= Tables.ModelStopAge; i++) {
CIN2count[i].resize (y);
}
CIN3count.resize (Tables.ModelStopAge + 1);
for (int i = 0; i <= Tables.ModelStopAge; i++) {
CIN3count[i].resize (y);
}
CAcount.resize (Tables.ModelStopAge + 1);
for (int i = 0; i <= Tables.ModelStopAge; i++) {
CAcount[i].resize (y);
}
DetectedCAcount.resize (Tables.ModelStopAge + 1);
for (int i = 0; i <= Tables.ModelStopAge; i++) {
DetectedCAcount[i].resize (y);
}
CAdead.resize (Tables.ModelStopAge + 1);
for (int i = 0; i <= Tables.ModelStopAge; i++) {
CAdead[i].resize (y);
}
HPVdenom.resize (Tables.ModelStopAge + 1);
for (int i = 0; i <= Tables.ModelStopAge; i++) {
HPVdenom[i].resize (y);
}
NormalCyto = 0;
HPV16 = 0;
HPV18 = 0;
HPV16denom.resize (Tables.ModelStopAge + 1);
for (int i = 0; i <= Tables.ModelStopAge; i++) {
HPV16denom[i].resize (y);
}
HPV18denom.resize (Tables.ModelStopAge + 1);
for (int i = 0; i <= Tables.ModelStopAge; i++) {
HPV18denom[i].resize (y);
}
CIN2denom.resize (Tables.ModelStopAge + 1);
for (int i = 0; i <= Tables.ModelStopAge; i++) {
CIN2denom[i].resize (y);
}
CIN3denom.resize (Tables.ModelStopAge + 1);
for (int i = 0; i <= Tables.ModelStopAge; i++) {
CIN3denom[i].resize (y);
}
CAdenom.resize (Tables.ModelStopAge + 1);
for (int i = 0; i <= Tables.ModelStopAge; i++) {
CAdenom[i].resize (y);
}
CIN2HIVneg.resize (Tables.ModelStopAge + 1);
for (int i = 0; i <= Tables.ModelStopAge; i++) {
CIN2HIVneg[i].resize (y);
}
CIN3HIVneg.resize (Tables.ModelStopAge + 1);
for (int i = 0; i <= Tables.ModelStopAge; i++) {
CIN3HIVneg[i].resize (y);
}
causalHPV16ageMatrix.resize(Tables.ModelStopAge + 1);
for (int i = 0; i <= Tables.ModelStopAge; i++) {
causalHPV16ageMatrix[i].resize (y);
}
causalHPV18ageMatrix.resize(Tables.ModelStopAge + 1);
for (int i = 0; i <= Tables.ModelStopAge; i++) {
causalHPV18ageMatrix[i].resize (y);
}
causalHPVhi5ageMatrix.resize(Tables.ModelStopAge + 1);
for (int i = 0; i <= Tables.ModelStopAge; i++) {
causalHPVhi5ageMatrix[i].resize (y);
}
causalHPVallhrageMatrix.resize(Tables.ModelStopAge + 1);
for (int i = 0; i <= Tables.ModelStopAge; i++) {
causalHPVallhrageMatrix[i].resize (y);
}
cancer = 0;
CA16 = 0;
CA18 = 0;
CA31 = 0;
CA33 = 0;
CA45 = 0;
CA52 = 0;
CA58 = 0;
CIN316 = 0;
CIN318 = 0;
CIN331 = 0;
CIN333 = 0;
CIN345 = 0;
CIN352 = 0;
CIN358 = 0;
CIN3LR = 0;
CIN216 = 0;
CIN218 = 0;
CIN231 = 0;
CIN233 = 0;
CIN245 = 0;
CIN252 = 0;
CIN258 = 0;
CIN2LR = 0;
CAotherHR = 0;
CIN2otherHR = 0;
CIN3otherHR = 0;
CIN2total = 0;
CIN3total = 0;
DwellTime_HPV_CIN_16_num = 0;
DwellTime_HPV_CIN_18_num = 0;
DwellTime_HPV_CIN_hi5_num = 0;
DwellTime_HPV_CIN_allhr_num = 0;
DwellTime_CIN_CA_16_num = 0;
DwellTime_CIN_CA_18_num = 0;
DwellTime_CIN_CA_hi5_num = 0;
DwellTime_CIN_CA_allhr_num = 0;
DwellTime_CA_16_denom = 0;
DwellTime_CA_18_denom = 0;
DwellTime_CA_hi5_denom = 0;
DwellTime_CA_allhr_denom = 0;
DwellTime_CA_16_latent_denom = 0;
DwellTime_CA_18_latent_denom = 0;
DwellTime_CA_hi5_latent_denom = 0;
DwellTime_CA_allhr_latent_denom = 0;
DwellTime_CA_detected_denom = 0;
DwellTime_CA_detected_num = 0;
Dormancy_HPV_CIN_16_num = 0;
Dormancy_HPV_CIN_18_num = 0;
Dormancy_HPV_CIN_hi5_num = 0;
Dormancy_HPV_CIN_allhr_num = 0;
Latency_HPV_CIN_16_num = 0;
Latency_HPV_CIN_18_num = 0;
Latency_HPV_CIN_hi5_num = 0;
Latency_HPV_CIN_allhr_num = 0;
causalHPV16age = 0;
causalHPV18age = 0;
causalHPVhi5age = 0;
causalHPVallhrage = 0;
}
void Output::createTrace(Woman &Data, int y) {
// No Cancer, allhr, HPV16, HPV18, HPVhi5, HPVoHR, HPVLR, CIN+
if(!Data.cancer){
if(Data.CurrentAge >= 15){
TotalCancerDenom[Data.CurrentAge][y]++;
CancerDenom_byyear[y]++;
}
if(!Data.hpv16){
HPV16denom[Data.CurrentAge][y]++;
}
if(!Data.hpv18){
HPV18denom[Data.CurrentAge][y]++;
}
if(accumulate(Data.HPVinfectionTimer.begin(), Data.HPVinfectionTimer.end(), 0) == 0){
HPVdenom[Data.CurrentAge][y]++;
}
trace[Data.CurrentAge][y][0]++; // no cancer (prev DENOM)
CAdenom[Data.CurrentAge][y]++;
if (Data.hpv16 || Data.hpv18 || Data.hpv31 || Data.hpv33 ||Data.hpv45 || Data.hpv52 || Data.hpv58 || Data.hpvotherHR){
trace[Data.CurrentAge][y][1]++; // all prevalent hr-HPV
if(Data.hpv16){
trace[Data.CurrentAge][y][2]++; // all prevalent HPV16
}
if(Data.hpv18){
trace[Data.CurrentAge][y][3]++; // all prevalent HPV18
}
if(Data.hpv31 || Data.hpv33 ||Data.hpv45 || Data.hpv52 || Data.hpv58){
trace[Data.CurrentAge][y][4]++; // all prevalent high-5
}
if(Data.hpvotherHR){
trace[Data.CurrentAge][y][5]++; // all prevalent HPVotherHR
}
}
if(Data.hpvlo){
trace[Data.CurrentAge][y][6]++; // all prevalent HPVLR
}
}
}
void Output::createTypeDist(Woman &Data) {
if (!Data.CIN2Lesions.empty()){
CIN2total++;
if(Data.hpv16){
CIN216++;
}
if(Data.hpv18){
CIN218++;
}
if(Data.hpv31){
CIN231++;
}
if(Data.hpv33){
CIN233++;
}
if(Data.hpv45){
CIN245++;
}
if(Data.hpv52){
CIN252++;
}
if(Data.hpv58){
CIN258++;
}
if(Data.hpvotherHR){
CIN2otherHR++;
}
if(Data.hpvlo){
CIN2LR++;
}
}
if (!Data.CIN3Lesions.empty()){
CIN3total++;
if(Data.hpv16){
CIN316++;
}
if(Data.hpv18){
CIN318++;
}
if(Data.hpv31){
CIN331++;
}
if(Data.hpv33){
CIN333++;
}
if(Data.hpv45){
CIN345++;
}
if(Data.hpv52){
CIN352++;
}
if(Data.hpv58){
CIN358++;
}
if(Data.hpvotherHR){
CIN3otherHR++;
}
if(Data.hpvlo){
CIN3LR++;
}
}
}
void Output::createCalibOutput(int y) {
int HPVcalibnum;
int HPVcalibdenom;
HPVcalibnum = 0;
HPVcalibdenom = 0;
for(int i = 17; i < 20; i++){
HPVcalibnum += trace[i][y][1];
HPVcalibdenom += trace[i][y][0];
}
calib.push_back (static_cast<double>(HPVcalibnum)/HPVcalibdenom);
HPVcalibnum = 0;
HPVcalibdenom = 0;
for(int i = 20; i < 25; i++){
HPVcalibnum += trace[i][y][1];
HPVcalibdenom += trace[i][y][0];
}
calib.push_back (static_cast<double>(HPVcalibnum)/HPVcalibdenom);
HPVcalibnum = 0;
HPVcalibdenom = 0;
for(int i = 25; i < 30; i++){
HPVcalibnum += trace[i][y][1];
HPVcalibdenom += trace[i][y][0];
}
calib.push_back (static_cast<double>(HPVcalibnum)/HPVcalibdenom);
HPVcalibnum = 0;
HPVcalibdenom = 0;
for(int i = 30; i < 35; i++){
HPVcalibnum += trace[i][y][1];
HPVcalibdenom += trace[i][y][0];
}
calib.push_back (static_cast<double>(HPVcalibnum)/HPVcalibdenom);
HPVcalibnum = 0;
HPVcalibdenom = 0;
for(int i = 35; i < 40; i++){
HPVcalibnum += trace[i][y][1];
HPVcalibdenom += trace[i][y][0];
}
calib.push_back (static_cast<double>(HPVcalibnum)/HPVcalibdenom);
HPVcalibnum = 0;
HPVcalibdenom = 0;
for(int i = 40; i < 45; i++){
HPVcalibnum += trace[i][y][1];
HPVcalibdenom += trace[i][y][0];
}
calib.push_back (static_cast<double>(HPVcalibnum)/HPVcalibdenom);
HPVcalibnum = 0;
HPVcalibdenom = 0;
for(int i = 45; i < 50; i++){
HPVcalibnum += trace[i][y][1];
HPVcalibdenom += trace[i][y][0];
}
calib.push_back (static_cast<double>(HPVcalibnum)/HPVcalibdenom);
HPVcalibnum = 0;
HPVcalibdenom = 0;
for(int i = 50; i < 55; i++){
HPVcalibnum += trace[i][y][1];
HPVcalibdenom += trace[i][y][0];
}
calib.push_back (static_cast<double>(HPVcalibnum)/HPVcalibdenom);
HPVcalibnum = 0;
HPVcalibdenom = 0;
for(int i = 55; i < 65; i++){
HPVcalibnum += trace[i][y][1];
HPVcalibdenom += trace[i][y][0];
}
calib.push_back (static_cast<double>(HPVcalibnum)/HPVcalibdenom);
HPVcalibnum = 0;
HPVcalibdenom = 0;
for(int i = 16; i < 23; i++){
HPVcalibnum += trace[i][y][2];
HPVcalibdenom += trace[i][y][0];
}
calib.push_back (static_cast<double>(HPVcalibnum)/HPVcalibdenom);
HPVcalibnum = 0;
HPVcalibdenom = 0;
for(int i = 16; i < 23; i++){
HPVcalibnum += trace[i][y][3];
HPVcalibdenom += trace[i][y][0];
}
calib.push_back (static_cast<double>(HPVcalibnum)/HPVcalibdenom);
HPVcalibnum = 0;
HPVcalibdenom = 0;
for(int i = 16; i < 23; i++){
HPVcalibnum += trace[i][y][4];
HPVcalibdenom += trace[i][y][0];
}
calib.push_back (static_cast<double>(HPVcalibnum)/HPVcalibdenom);
HPVcalibnum = 0;
HPVcalibdenom = 0;
for(int i = 16; i < 23; i++){
HPVcalibnum += trace[i][y][5];
HPVcalibdenom += trace[i][y][0];
}
calib.push_back (static_cast<double>(HPVcalibnum)/HPVcalibdenom);
HPVcalibnum = 0;
HPVcalibdenom = 0;
for(int i = 16; i < 23; i++){
HPVcalibnum += trace[i][y][6];
HPVcalibdenom += trace[i][y][0];
}
calib.push_back (static_cast<double>(HPVcalibnum)/HPVcalibdenom);
calib.push_back(static_cast<double>(CIN216) / CIN2total );
calib.push_back(static_cast<double>(CIN218) / CIN2total );
calib.push_back(static_cast<double>(CIN231 + CIN233 + CIN245 + CIN252 + CIN258) / CIN2total);
calib.push_back(static_cast<double>(CIN2LR) / CIN2total );
calib.push_back(static_cast<double>(CIN316) / CIN3total );
calib.push_back(static_cast<double>(CIN318) / CIN3total );
calib.push_back(static_cast<double>(CIN331 + CIN333 + CIN345 + CIN352 + CIN358) / CIN3total);
calib.push_back(static_cast<double>(CIN3LR) / CIN3total );
calib.push_back(static_cast<double>(CA16) / cancer );
calib.push_back(static_cast<double>(CA18) / cancer );
calib.push_back(static_cast<double>(CA31 + CA33 + CA45 + CA52 + CA58) / cancer );
int CAnew;
int CAdenom;
CAnew = 0;
CAdenom = 0;
for(int i = 15; i < 20; i++){
CAnew += DetectedCAcount[i][y];
CAdenom += TotalCancerDenom[i][y];
}
calib.push_back (100000*static_cast<double>(CAnew)/CAdenom);
CAnew = 0;
CAdenom = 0;
for(int i = 20; i < 25; i++){
CAnew += DetectedCAcount[i][y];
CAdenom += TotalCancerDenom[i][y];
}
calib.push_back (100000*static_cast<double>(CAnew)/CAdenom);
CAnew = 0;
CAdenom = 0;
for(int i = 25; i < 30; i++){
CAnew += DetectedCAcount[i][y];
CAdenom += TotalCancerDenom[i][y];
}
calib.push_back (100000*static_cast<double>(CAnew)/CAdenom);
CAnew = 0;
CAdenom = 0;
for(int i = 30; i < 35; i++){
CAnew += DetectedCAcount[i][y];
CAdenom += TotalCancerDenom[i][y];
}
calib.push_back (100000*static_cast<double>(CAnew)/CAdenom);
CAnew = 0;
CAdenom = 0;
for(int i = 35; i < 40; i++){
CAnew += DetectedCAcount[i][y];
CAdenom += TotalCancerDenom[i][y];
}
calib.push_back (100000*static_cast<double>(CAnew)/CAdenom);
CAnew = 0;
CAdenom = 0;
for(int i = 40; i < 45; i++){
CAnew += DetectedCAcount[i][y];
CAdenom += TotalCancerDenom[i][y];
}
calib.push_back (100000*static_cast<double>(CAnew)/CAdenom);
CAnew = 0;
CAdenom = 0;
for(int i = 45; i < 50; i++){
CAnew += DetectedCAcount[i][y];
CAdenom += TotalCancerDenom[i][y];
}
calib.push_back (100000*static_cast<double>(CAnew)/CAdenom);
CAnew = 0;
CAdenom = 0;
for(int i = 50; i < 55; i++){
CAnew += DetectedCAcount[i][y];
CAdenom += TotalCancerDenom[i][y];
}
calib.push_back (100000*static_cast<double>(CAnew)/CAdenom);
CAnew = 0;
CAdenom = 0;
for(int i = 55; i < 60; i++){
CAnew += DetectedCAcount[i][y];
CAdenom += TotalCancerDenom[i][y];
}
calib.push_back (100000*static_cast<double>(CAnew)/CAdenom);
CAnew = 0;
CAdenom = 0;
for(int i = 60; i < 65; i++){
CAnew += DetectedCAcount[i][y];
CAdenom += TotalCancerDenom[i][y];
}
calib.push_back (100000*static_cast<double>(CAnew)/CAdenom);
CAnew = 0;
CAdenom = 0;
for(int i = 65; i < 70; i++){
CAnew += DetectedCAcount[i][y];
CAdenom += TotalCancerDenom[i][y];
}
calib.push_back (100000*static_cast<double>(CAnew)/CAdenom);
CAnew = 0;
CAdenom = 0;
for(int i = 70; i < 75; i++){
CAnew += DetectedCAcount[i][y];
CAdenom += TotalCancerDenom[i][y];
}
calib.push_back (100000*static_cast<double>(CAnew)/CAdenom);
}
void Output::writeCalibOutput(std::string *Outdir, std::string calib_targs_names) {
ofstream output;
string OutputFileName;
OutputFileName.append(*Outdir);
OutputFileName.append("/");
OutputFileName.append("_calib");
OutputFileName.append(extension);
output.open(OutputFileName.c_str (), ios::out);
if(output) {
output << calib_targs_names << endl;
for (int k = 0; k < calib.size(); k ++){
output << calib[k] << '\t';
}
}
else
cerr << "Warning: Unable to open " << OutputFileName << endl;
output.close();
output.clear();
}
void Output::writeCEA(std::string *Outdir, int ModelStopAge, int TotalSimYears) {
ofstream output;
string OutputFileName;
OutputFileName.append(*Outdir);
OutputFileName.append("/");
OutputFileName.append("_costbenefit");
OutputFileName.append(extension);
output.open(OutputFileName.c_str (), ios::out);
if(output){
output << " \tCost\tDALYs" << endl;
output << "Undiscounted" << '\t';
output << TotalCost << '\t';
output << TotalDALY << endl;
output << "Discounted" << '\t';
output << discCost << '\t';
output << discDALY << endl;
}
else
cerr << "Warning: Unable to open " << OutputFileName << endl;
output.close();
output.clear();
OutputFileName.clear();
OutputFileName.append(*Outdir);
OutputFileName.append("/");
OutputFileName.append("_totalalive");
OutputFileName.append(extension);
output.open(OutputFileName.c_str (), ios::out);
if(output){
output << "" << '\t';
for(int j = 0; j < ModelStopAge; j++) {
output << j << '\t';
}
output << endl;
for(int i = 0; i < TotalSimYears; i++) {
output << "SimYear" << i << '\t';
for(int j = 0; j < ModelStopAge; j++) {
output << total_alive[j][i] << '\t';
}
output << endl;
}
}
else
cerr << "Warning: Unable to open " << OutputFileName << endl;
output.close();
output.clear();
}
void Output::writeInc(std::string *Outdir, int ModelStartAge, int ModelStopAge, int TotalSimYears) {
ofstream output;
string OutputFileName;
OutputFileName.append(*Outdir);
OutputFileName.append("/");
OutputFileName.append("_CAInc");
OutputFileName.append(extension);
output.open(OutputFileName.c_str (), ios::out);
if(output){
output << "" << '\t';
for(int j = 15; j < ModelStopAge; j++) {
output << j << '\t';
}
output << endl;
for(int i = 100; i < TotalSimYears; i++) {
output << "SimYear" << i << '\t';
for(int j = 15; j < ModelStopAge; j++) {
output << 100000*static_cast<double>(TotalDetectedCancer[j][i])/TotalCancerDenom[j][i] << '\t';
}
output << endl;
}
}
else
cerr << "Warning: Unable to open " << OutputFileName << endl;
output.close();
output.clear();
OutputFileName.clear();
OutputFileName.append(*Outdir);
OutputFileName.append("/");
OutputFileName.append("_CAInc_byyear");
OutputFileName.append(extension);
output.open(OutputFileName.c_str (), ios::out);
if(output){
for(int j = 100; j < TotalSimYears; j++) {
output << "SimYear" << j << '\t';
output << 100000*static_cast<double>(TotalDetectedCancer_byyear[j])/CancerDenom_byyear[j] << '\t';
output << endl;
}
}
else
cerr << "Warning: Unable to open " << OutputFileName << endl;
output.close();
output.clear();
OutputFileName.clear();
OutputFileName.append(*Outdir);
OutputFileName.append("/");
OutputFileName.append("_HPVInc");
OutputFileName.append(extension);
output.open(OutputFileName.c_str (), ios::out);
if(output){
output << "" << '\t';
for(int j = ModelStartAge; j < ModelStopAge; j++) {
output << j << '\t';
}
output << endl;
for(int i = 100; i < TotalSimYears; i++) {
output << "SimYear" << i << '\t';
for(int j = 15; j < ModelStopAge; j++) {
output << static_cast<double>(HPVcount[j][i])/HPVdenom[j][i] << '\t';
}
output << endl;
}
}
else
cerr << "Warning: Unable to open " << OutputFileName << endl;
output.close();
output.clear();
OutputFileName.clear();
OutputFileName.append(*Outdir);
}
void Output::writeMort(std::string *Outdir, int ModelStopAge, int TotalSimYears) {
ofstream output;
string OutputFileName;
OutputFileName.append(*Outdir);
OutputFileName.append("/");
OutputFileName.append("_Mort");
OutputFileName.append(extension);
output.open(OutputFileName.c_str (), ios::out);
if(output){
output << "" << '\t';
for(int j = 15; j < ModelStopAge; j++) {
output << j << '\t';
}
output << endl;
for(int i = 100; i < TotalSimYears; i++) {
output << "SimYear" << i << '\t';
for(int j = 15; j < ModelStopAge; j++) {
output << 100000 * static_cast<double>(CAdead[j][i]) / total_alive[j][i] << '\t';
}
output << endl;
}
}
else
cerr << "Warning: Unable to open " << OutputFileName << endl;
output.close();
output.clear();
}
void Output::calcDwellTime(Woman &Data) {
if(Data.CA16 > 0){
DwellTime_HPV_CIN_16_num += Data.CIN16;
DwellTime_CIN_CA_16_num += Data.CA16;
Dormancy_HPV_CIN_16_num += Data.CIN_dormant_16;
Latency_HPV_CIN_16_num += Data.CIN_latent_16;
age16 = Data.CurrentAge - (Data.HPVinfectionTimer[Woman::High16] + Data.DormancyTimer[Woman::High16] +
Data.ca1Timer + Data.ca2Timer + Data.ca3Timer);
causalHPV16age += age16;
causalHPV16ageMatrix[age16][Data.year16]++;
if(Data.CIN_latent_16 > 0){
DwellTime_CA_16_latent_denom++;
}
DwellTime_CA_16_denom++;
Latency_HPV_CIN_allhr_num += Data.CIN_latent_16;
Dormancy_HPV_CIN_allhr_num += Data.CIN_dormant_16;
DwellTime_HPV_CIN_allhr_num += Data.CIN16;
DwellTime_CIN_CA_allhr_num += Data.CA16;
causalHPVallhrage += age16;
causalHPVallhrageMatrix[age16][Data.year16]++;
DwellTime_CA_allhr_denom++;
if(Data.CIN_latent_16 > 0){
DwellTime_CA_allhr_latent_denom++;
}
}
if(Data.CA18 > 0){
DwellTime_HPV_CIN_18_num += Data.CIN18;
DwellTime_CIN_CA_18_num += Data.CA18;
Dormancy_HPV_CIN_18_num += Data.CIN_dormant_18;
Latency_HPV_CIN_18_num += Data.CIN_latent_18;
age18 = Data.CurrentAge - (Data.HPVinfectionTimer[Woman::High18] + Data.DormancyTimer[Woman::High18] +
Data.ca1Timer + Data.ca2Timer + Data.ca3Timer);
causalHPV18age += age18;
causalHPV18ageMatrix[age18][Data.year18]++;
DwellTime_CA_18_denom++;
if(Data.CIN_latent_18 > 0){
DwellTime_CA_18_latent_denom++;
}
Latency_HPV_CIN_allhr_num += Data.CIN_latent_18;
Dormancy_HPV_CIN_allhr_num += Data.CIN_dormant_18;
DwellTime_HPV_CIN_allhr_num += Data.CIN18;
DwellTime_CIN_CA_allhr_num += Data.CA18;
causalHPVallhrage += age18;
causalHPVallhrageMatrix[age18][Data.year18]++;
DwellTime_CA_allhr_denom++;
if(Data.CIN_latent_18 > 0){
DwellTime_CA_allhr_latent_denom++;
}
}
if(Data.CA31 > 0){
DwellTime_HPV_CIN_hi5_num += Data.CIN31;
DwellTime_CIN_CA_hi5_num += Data.CA31;
Dormancy_HPV_CIN_hi5_num += Data.CIN_dormant_31;
Latency_HPV_CIN_hi5_num += Data.CIN_latent_31;
age31 = Data.CurrentAge - (Data.HPVinfectionTimer[Woman::High31] + Data.DormancyTimer[Woman::High31] +
Data.ca1Timer + Data.ca2Timer + Data.ca3Timer);
causalHPVhi5age += age31;
causalHPVhi5ageMatrix[age31][Data.year31]++;
DwellTime_CA_hi5_denom++;
if(Data.CIN_latent_31 > 0){
DwellTime_CA_hi5_latent_denom++;
}
Latency_HPV_CIN_allhr_num += Data.CIN_latent_31;
Dormancy_HPV_CIN_allhr_num += Data.CIN_dormant_31;
DwellTime_HPV_CIN_allhr_num += Data.CIN31;
DwellTime_CIN_CA_allhr_num += Data.CA31;
causalHPVallhrage += age31;
causalHPVallhrageMatrix[age31][Data.year31]++;
DwellTime_CA_allhr_denom++;
if(Data.CIN_latent_31 > 0){
DwellTime_CA_allhr_latent_denom++;
}
}
if(Data.CA33 > 0){
DwellTime_HPV_CIN_hi5_num += Data.CIN33;
DwellTime_CIN_CA_hi5_num += Data.CA33;
Dormancy_HPV_CIN_hi5_num += Data.CIN_dormant_33;
Latency_HPV_CIN_hi5_num += Data.CIN_latent_33;
age33 = Data.CurrentAge - (Data.HPVinfectionTimer[Woman::High33] + Data.DormancyTimer[Woman::High33] +
Data.ca1Timer + Data.ca2Timer + Data.ca3Timer);
causalHPVhi5age += age33;
causalHPVhi5ageMatrix[age33][Data.year33]++;
DwellTime_CA_hi5_denom++;
if(Data.CIN_latent_33 > 0){
DwellTime_CA_hi5_latent_denom++;
}
Latency_HPV_CIN_allhr_num += Data.CIN_latent_33;
Dormancy_HPV_CIN_allhr_num += Data.CIN_dormant_33;
DwellTime_HPV_CIN_allhr_num += Data.CIN33;
DwellTime_CIN_CA_allhr_num += Data.CA33;
causalHPVallhrage += age33;
causalHPVallhrageMatrix[age33][Data.year33]++;
DwellTime_CA_allhr_denom++;
if(Data.CIN_latent_33 > 0){
DwellTime_CA_allhr_latent_denom++;
}
}
if(Data.CA45 > 0){
DwellTime_HPV_CIN_hi5_num += Data.CIN45;
DwellTime_CIN_CA_hi5_num += Data.CA45;
Latency_HPV_CIN_hi5_num += Data.CIN_latent_45;
Dormancy_HPV_CIN_hi5_num += Data.CIN_dormant_45;
age45 = Data.CurrentAge - (Data.HPVinfectionTimer[Woman::High45] + Data.DormancyTimer[Woman::High45] +
Data.ca1Timer + Data.ca2Timer + Data.ca3Timer);
causalHPVhi5age += age45;
causalHPVhi5ageMatrix[age45][Data.year45]++;
DwellTime_CA_hi5_denom++;
if(Data.CIN_latent_45 > 0){
DwellTime_CA_hi5_latent_denom++;
}
Dormancy_HPV_CIN_allhr_num += Data.CIN_dormant_45;
Latency_HPV_CIN_allhr_num += Data.CIN_latent_45;
DwellTime_HPV_CIN_allhr_num += Data.CIN45;
DwellTime_CIN_CA_allhr_num += Data.CA45;
causalHPVallhrage += age45;
causalHPVallhrageMatrix[age45][Data.year45]++;
DwellTime_CA_allhr_denom++;
if(Data.CIN_latent_45 > 0){
DwellTime_CA_allhr_latent_denom++;
}
}
if(Data.CA52 > 0){
DwellTime_HPV_CIN_hi5_num += Data.CIN52;
DwellTime_CIN_CA_hi5_num += Data.CA52;
Latency_HPV_CIN_hi5_num += Data.CIN_latent_52;
Dormancy_HPV_CIN_hi5_num += Data.CIN_dormant_52;
age52 = Data.CurrentAge - (Data.HPVinfectionTimer[Woman::High52] + Data.DormancyTimer[Woman::High52] +
Data.ca1Timer + Data.ca2Timer + Data.ca3Timer);
causalHPVhi5age += age52;
causalHPVhi5ageMatrix[age52][Data.year52]++;
DwellTime_CA_hi5_denom++;
if(Data.CIN_latent_52 > 0){
DwellTime_CA_hi5_latent_denom++;
}
Latency_HPV_CIN_allhr_num += Data.CIN_latent_52;
Dormancy_HPV_CIN_allhr_num += Data.CIN_dormant_52;
DwellTime_HPV_CIN_allhr_num += Data.CIN52;
DwellTime_CIN_CA_allhr_num += Data.CA52;
causalHPVallhrage += age52;
causalHPVallhrageMatrix[age52][Data.year52]++;
DwellTime_CA_allhr_denom++;
if(Data.CIN_latent_52 > 0){
DwellTime_CA_allhr_latent_denom++;
}
}
if(Data.CA58 > 0){
DwellTime_HPV_CIN_hi5_num += Data.CIN58;
DwellTime_CIN_CA_hi5_num += Data.CA58;
Latency_HPV_CIN_hi5_num += Data.CIN_latent_58;
Dormancy_HPV_CIN_hi5_num += Data.CIN_dormant_58;
age58 = Data.CurrentAge - (Data.HPVinfectionTimer[Woman::High58] + Data.DormancyTimer[Woman::High58] +
Data.ca1Timer + Data.ca2Timer + Data.ca3Timer);
causalHPVhi5age += age58;
causalHPVhi5ageMatrix[age58][Data.year58]++;
DwellTime_CA_hi5_denom++;
if(Data.CIN_latent_58 > 0){
DwellTime_CA_hi5_latent_denom++;
}
DwellTime_HPV_CIN_allhr_num += Data.CIN58;
Latency_HPV_CIN_allhr_num += Data.CIN_latent_58;
DwellTime_CIN_CA_allhr_num += Data.CA58;
Dormancy_HPV_CIN_allhr_num += Data.CIN_dormant_58;
causalHPVallhrage += age58;
causalHPVallhrageMatrix[age58][Data.year58]++;
DwellTime_CA_allhr_denom++;
if(Data.CIN_latent_58 > 0){
DwellTime_CA_allhr_latent_denom++;
}
}
if(Data.CAoHR > 0){
DwellTime_HPV_CIN_allhr_num += Data.CINoHR;
Latency_HPV_CIN_allhr_num += Data.CIN_latent_oHR;
DwellTime_CIN_CA_allhr_num += Data.CAoHR;
Dormancy_HPV_CIN_allhr_num += Data.CIN_dormant_oHR;
ageoHR = Data.CurrentAge - (Data.HPVinfectionTimer[Woman::otherHR] + Data.DormancyTimer[Woman::otherHR] +
Data.ca1Timer + Data.ca2Timer + Data.ca3Timer);
causalHPVallhrage += ageoHR;
causalHPVallhrageMatrix[ageoHR][Data.yearoHR]++;
DwellTime_CA_allhr_denom++;
if(Data.CIN_latent_oHR > 0){
DwellTime_CA_allhr_latent_denom++;
}
}
}
void Output::writeDwellTime(std::string *Outdir, int TotalSimYears) {
ofstream output;
string OutputFileName;
OutputFileName.append(*Outdir);
OutputFileName.append("/");
OutputFileName.append("_Dwelltime");
OutputFileName.append(extension);