EndMonthUpdater.cpp

#include "include.h"

/** \brief Constructor takes in the patient object and determines if updates can occur */
EndMonthUpdater::EndMonthUpdater(Patient *patient) : StateUpdater(patient) {

}

/** \brief Destructor is empty, no cleanup required */
EndMonthUpdater::~EndMonthUpdater(void) {

}

/** \brief performInitialUpdates perform all of the state and statistics updates upon patient creation */
void EndMonthUpdater::performInitialUpdates() {
	/** Call the parent function to perform general updates and initialization */
	StateUpdater::performInitialUpdates();
} /* end performInitialUpdates */

/** \brief performMonthlyUpdates perform all of the state and statistics updates for a simulated month */
void EndMonthUpdater::performMonthlyUpdates() {
	/** Uses a half month for applicable costs and survival stats in the month of death */
	double percentOfMonth = 1.0;
	if (!patient->isAlive()) {
		percentOfMonth = 0.5;
	}

	SimContext::PEDS_COST_AGE pedsCostAgeCat = patient->getPedsState()->ageCategoryPedsCost;
	int costAgeCat = patient->getGeneralState()->ageCategoryCost;
	SimContext::GENDER_TYPE gender = patient->getGeneralState()->gender;
	/** Increment the monthly patient costs and statistics for routine care */
	if(pedsCostAgeCat == SimContext::PEDS_COST_AGE_ADULT){
		double multiplier = simContext->getLTFUInputs()->propGeneralMedicineCost[patient->getMonitoringState()->careState];
		incrementCostsGeneralMedicine(simContext->getCostInputs()->generalMedicineCost[gender][costAgeCat], percentOfMonth, multiplier);
	}

	if (patient->getDiseaseState()->infectedHIVState == SimContext::HIV_INF_NEG) {
		if(pedsCostAgeCat==SimContext::PEDS_COST_AGE_ADULT){
			if (simContext->getCostInputs()->routineCareCostHIVNegativeStopAge == SimContext::NOT_APPL ||
					patient->getGeneralState()->ageMonths < simContext->getCostInputs()->routineCareCostHIVNegativeStopAge)
				incrementCostsMisc(simContext->getCostInputs()->routineCareCostHIVNegative[gender][costAgeCat], percentOfMonth);
		}
		else{
			incrementCostsMisc(simContext->getPedsCostInputs()->routineCareCostHIVNegative[gender][pedsCostAgeCat], percentOfMonth);
		}
	}
	else if (!patient->getMonitoringState()->isDetectedHIVPositive) {
		//add costs from two different areas
		SimContext::CD4_STRATA cd4Strata = patient->getDiseaseState()->currTrueCD4Strata;
		incrementCostsMisc(simContext->getHIVTestInputs()->monthCostHIVUndetected[cd4Strata], percentOfMonth);
		if (simContext->getCostInputs()->routineCareCostHIVPositiveUndetectedStopAge == SimContext::NOT_APPL ||
				patient->getGeneralState()->ageMonths < simContext->getCostInputs()->routineCareCostHIVPositiveUndetectedStopAge)
			incrementCostsMisc(simContext->getCostInputs()->routineCareCostHIVPositiveUndetected[gender][costAgeCat], percentOfMonth);

	}
	else {
		SimContext::CD4_STRATA cd4Strata = patient->getDiseaseState()->currTrueCD4Strata;
		SimContext::GENDER_TYPE gender = patient->getGeneralState()->gender;
		SimContext::ART_STATES artState = (patient->getARTState()->isOnART) ? SimContext::ART_ON_STATE : SimContext::ART_OFF_STATE;	
		if(pedsCostAgeCat==SimContext::PEDS_COST_AGE_ADULT){
			incrementCostsRoutineCare(simContext->getCostInputs()->routineCareCostHIVPositive[artState][cd4Strata][gender][costAgeCat], percentOfMonth);
		}
		else{
			incrementCostsRoutineCare(simContext->getPedsCostInputs()->routineCareCostHIVPositive[artState][cd4Strata][gender][pedsCostAgeCat], percentOfMonth);
		}
	}

	/**Increment costs for those on PrEP */
    if(simContext->getHIVTestInputs()->enableHIVTesting && simContext->getHIVTestInputs()->enablePrEP && patient->getMonitoringState()->everPrEP){
		if(patient->getMonitoringState()->hasPrEP){
            SimContext::HIV_BEHAV risk = patient->getMonitoringState()->isHighRiskForHIV?SimContext::HIV_BEHAV_HI:SimContext::HIV_BEHAV_LO;
			// For now, we are incrementing the full cost in the month of death - may revisit later
			incrementCostsPrEP(simContext->getHIVTestInputs()->costPrEPMonthly[risk], 1.0);
		}	
		// For those who have ever had PrEP and died this month, accumulate their final PrEP costs by PrEP state
		if(!patient->isAlive())
			finalizePrEPCostsByState();
    }

	/** Increment costs for ART treatments */
	if (patient->getARTState()->isOnART) {
		int artLineNum = patient->getARTState()->currRegimenNum;
		double cost = 0.0;
		if (patient->getGeneralState()->isAdolescent){
			int ayaAgeCat = getAgeCategoryAdolescent();
			cost = simContext->getAdolescentARTInputs(artLineNum)->costMonthly[ayaAgeCat];
		}
		else if (patient->getPedsState()->ageCategoryPediatrics == SimContext::PEDS_AGE_ADULT) {
			cost = simContext->getARTInputs(artLineNum)->costMonthly;
		}
		else{
			cost = simContext->getPedsARTInputs(artLineNum)->costMonthly[patient->getPedsState()->ageCategoryPedsARTCost];
		}

		//always incur full cost on month of regimen start
		if (patient->getARTState()->monthOfCurrRegimenStart != patient->getGeneralState()->monthNum){
			/** - Adjust cost for non-responders by the proportion of monthly costs they incur */
			double responseFactor = patient->getARTState()->responseFactorCurrRegimen[SimContext::HET_OUTCOME_COST];
			double upperValue = cost;
			double lowerValue = cost * patient->getARTState()->propMthCostNonResponders;
			cost = lowerValue+responseFactor*(upperValue-lowerValue);
		}
		incrementCostsARTMonthly(artLineNum, cost);
	}


	/** Increment costs for OI prophylaxis treatments */
	if (patient->getProphState()->currTotalNumProphsOn > 0) {
		for (int i = 0; i < SimContext::OI_NUM; i++) {
			if (patient->getProphState()->isOnProph[i]) {
				int prophNum = patient->getProphState()->currProphNum[i];
				SimContext::PROPH_TYPE prophType = patient->getProphState()->currProphType[i];
				double cost;
				if(patient->getPedsState()->ageCategoryPediatrics>=SimContext::PEDS_AGE_LATE){
					cost=simContext->getProphInputs(prophType,i,prophNum)->costMonthly;
				}
				else{
					cost=simContext->getPedsProphInputs(prophType,i,prophNum)->costMonthly;
				}
				incrementCostsProph((SimContext::OI_TYPE) i, prophNum, cost);
			}
		}
	}

	/** Increment costs for TB proph and treatments */
	if (patient->getTBState()->isOnProph) {
		int prophNum = patient->getTBState()->currProphNum;
		double cost = simContext->getTBInputs()->tbProphInputs[prophNum].costMonthly;
		incrementCostsTBProph(prophNum, cost);
	}
	//Due to the timing of treatment start within the simulation month, the first TB treatment stage is calculated differently depending on whether it is at the end of the month (LTFU and costs: threshold month excluded) or the beginning of the month (toxicity: threshold month included)
	if (patient->getTBState()->isOnTreatment) {
		int treatNum = patient->getTBState()->currTreatmentNum;
		int stage = 1;
		if((patient->getGeneralState()->monthNum - patient->getTBState()->monthOfTreatmentStart + patient->getTBState()->previousTreatmentDuration) < simContext->getTBInputs()->TBTreatments[treatNum].stage1Duration)
			stage = 0;
		double cost = simContext->getTBInputs()->TBTreatments[treatNum].costMonthly[stage];
		incrementCostsTBTreatment(cost, treatNum);
	}
	if (patient->getTBState()->isOnEmpiricTreatment) {
		int treatNum = patient->getTBState()->currEmpiricTreatmentNum;
		int stage = 1;
		if((patient->getGeneralState()->monthNum - patient->getTBState()->monthOfEmpiricTreatmentStart + patient->getTBState()->previousEmpiricTreatmentDuration) < simContext->getTBInputs()->TBTreatments[treatNum].stage1Duration)
			stage = 0;
		double cost = simContext->getTBInputs()->TBTreatments[treatNum].costMonthly[stage];
		incrementCostsTBTreatment(cost, treatNum);
	}

	/** Increment costs of mortality in the month of death */
	if (!patient->isAlive()) {
		SimContext::DTH_CAUSES causeOfDeath = patient->getDiseaseState()->causeOfDeath;
		SimContext::ART_STATES artState = (patient->getARTState()->isOnART) ? SimContext::ART_ON_STATE : SimContext::ART_OFF_STATE;

		if (causeOfDeath < SimContext::OI_NUM) {
			if (patient->getMonitoringState()->clinicVisitType != SimContext::CLINIC_INITIAL) {
				if(pedsCostAgeCat==SimContext::PEDS_COST_AGE_ADULT){
					incrementCostsDeath(simContext->getCostInputs()->deathCostTreated[costAgeCat][artState][causeOfDeath], 1.0);
				}
				else{
					incrementCostsDeath(simContext->getPedsCostInputs()->deathCostTreated[pedsCostAgeCat][artState][causeOfDeath], 1.0);
				}
			}
			else {
				if(pedsCostAgeCat==SimContext::PEDS_COST_AGE_ADULT){
					incrementCostsDeath(simContext->getCostInputs()->deathCostUntreated[costAgeCat][artState][causeOfDeath], 1.0);
				}
				else{
					incrementCostsDeath(simContext->getPedsCostInputs()->deathCostUntreated[pedsCostAgeCat][artState][causeOfDeath], 1.0);
				}
			}
		}
		else if(causeOfDeath == SimContext::DTH_ACTIVE_TB){
			if(pedsCostAgeCat == SimContext::PEDS_COST_AGE_ADULT){
				incrementCostsDeath(simContext->getTBInputs()->costTBDeath, 1.0);
			}
			else{
				incrementCostsDeath(simContext->getTBInputs()->costTBDeathPeds[pedsCostAgeCat], 1.0);
			}
		}
		else if (causeOfDeath == SimContext::DTH_HIV) {
			if (patient->getMonitoringState()->isDetectedHIVPositive) {
				if (patient->getMonitoringState()->clinicVisitType != SimContext::CLINIC_INITIAL) {
					if(pedsCostAgeCat==SimContext::PEDS_COST_AGE_ADULT){
						incrementCostsDeath(simContext->getCostInputs()->deathCostTreated[costAgeCat][artState][SimContext::DTH_HIV], 1.0);
					}
					else{
						incrementCostsDeath(simContext->getPedsCostInputs()->deathCostTreated[pedsCostAgeCat][artState][SimContext::DTH_HIV], 1.0);
					}
				}
				else {
					if(pedsCostAgeCat==SimContext::PEDS_COST_AGE_ADULT){
						incrementCostsDeath(simContext->getCostInputs()->deathCostUntreated[costAgeCat][artState][SimContext::DTH_HIV], 1.0);
					}
					else{
						incrementCostsDeath(simContext->getPedsCostInputs()->deathCostUntreated[pedsCostAgeCat][artState][SimContext::DTH_HIV], 1.0);
					}
				}
			}
			else {
				double cost = simContext->getHIVTestInputs()->HIVDeathCostHIVUndetected;
				incrementCostsMisc(cost, 1.0);
			}
		}
		else if (causeOfDeath == SimContext::DTH_BKGD_MORT) {
			if (patient->getDiseaseState()->infectedHIVState == SimContext::HIV_INF_NEG) {
				double cost = simContext->getHIVTestInputs()->deathCostHIVNegative;
				incrementCostsMisc(cost, 1.0);
			}
			// HIV+ detected
			else if (patient->getMonitoringState()->isDetectedHIVPositive) {
				if (patient->getMonitoringState()->clinicVisitType != SimContext::CLINIC_INITIAL) {
					if(pedsCostAgeCat==SimContext::PEDS_COST_AGE_ADULT){
						incrementCostsDeath(simContext->getCostInputs()->deathCostTreated[costAgeCat][artState][SimContext::DTH_BKGD_MORT], 1.0);
					}
					else{
						incrementCostsDeath(simContext->getPedsCostInputs()->deathCostTreated[pedsCostAgeCat][artState][SimContext::DTH_BKGD_MORT], 1.0);
					}
				}
				else {
					if(pedsCostAgeCat==SimContext::PEDS_COST_AGE_ADULT){
						incrementCostsDeath(simContext->getCostInputs()->deathCostUntreated[costAgeCat][artState][SimContext::DTH_BKGD_MORT], 1.0);
					}
					else{
						incrementCostsDeath(simContext->getPedsCostInputs()->deathCostUntreated[pedsCostAgeCat][artState][SimContext::DTH_BKGD_MORT], 1.0);
					}
				}
			}
			// HIV+ undetected
			else {
				double cost = simContext->getHIVTestInputs()->backgroundMortDeathCostHIVUndetected;
				incrementCostsMisc(cost, 1.0);
			}
		}
		else if ((causeOfDeath >= SimContext::DTH_CHRM_1) && (causeOfDeath < SimContext::DTH_CHRM_1 + SimContext::CHRM_NUM)) {
			double cost = simContext->getCHRMsInputs()->costDeathCHRMs[causeOfDeath - SimContext::DTH_CHRM_1];
			incrementCostsMisc(cost, 1.0);
		}
		/**  - ART toxicity death is incurred in the MortalityUpdater
			 - Other causes of death incur no additional costs */
	}
	/** Assess routine care QOL or QOL in the month of death */
	if (patient->isAlive()) {
		/** If alive, use QOL modifier with either acute OI, undetected HIV, or routine care levels */
		if (patient->getDiseaseState()->hasCurrTrueOI) {
			SimContext::OI_TYPE oiType = patient->getDiseaseState()->typeCurrTrueOI;
			accumulateQOLModifier(simContext->getQOLInputs()->acuteOIQOL[oiType]);
		}
		else if ((!patient->getMonitoringState()->isDetectedHIVPositive)&& !patient->getDiseaseState()->infectedHIVState==SimContext::HIV_INF_NEG) {
			SimContext::CD4_STRATA cd4Strata = patient->getDiseaseState()->currTrueCD4Strata;
			accumulateQOLModifier(simContext->getHIVTestInputs()->monthQOLHIVUndetected[cd4Strata]);
		}
		else if(!patient->getDiseaseState()->infectedHIVState==SimContext::HIV_INF_NEG){
			SimContext::CD4_STRATA cd4Strata = patient->getDiseaseState()->currTrueCD4Strata;
			double routineCareQOL = simContext->getQOLInputs()->routineCareQOL[cd4Strata][SimContext::HIST_EXT_N];
			// if they are within the OI history effect duration, use their OI history to determine the QOL modifier
			for (int i = 0; i < SimContext::OI_NUM; i++) {
				if ((patient->getGeneralState()->monthNum - patient->getDiseaseState()->lastMonthSevereOI[i]) <= simContext->getQOLInputs()->routineCareQOLSevereOIHistDuration[cd4Strata]){
					routineCareQOL = simContext->getQOLInputs()->routineCareQOL[cd4Strata][patient->getDiseaseState()->typeTrueOIHistory];
					break;
				}
			}
			accumulateQOLModifier(routineCareQOL);
		}
		if((patient->getTBState()->currTrueTBDiseaseState == SimContext::TB_STATE_ACTIVE_PULM) || (patient->getTBState()->currTrueTBDiseaseState == SimContext::TB_STATE_ACTIVE_EXTRAPULM)){
			accumulateQOLModifier(simContext->getTBInputs()->QOLModActiveTB);
		}
		/** Accumulate PrEP QoL modifier if applicable */
		if(simContext->getHIVTestInputs()->enableHIVTesting && simContext->getHIVTestInputs()->enablePrEP && patient->getMonitoringState()->hasPrEP){
            SimContext::HIV_BEHAV risk = patient->getMonitoringState()->isHighRiskForHIV?SimContext::HIV_BEHAV_HI:SimContext::HIV_BEHAV_LO;
            accumulateQOLModifier(simContext->getHIVTestInputs()->PrEPQOL[risk]);
		}
	}
	else {
		/** If month of death, use QOL modifier for the cause of death */
		SimContext::DTH_CAUSES causeOfDeath = patient->getDiseaseState()->causeOfDeath;
		if ((causeOfDeath < SimContext::OI_NUM)) {
			accumulateQOLModifier(simContext->getQOLInputs()->deathBasicQOL[causeOfDeath]);
		}
		else if (causeOfDeath == SimContext::DTH_HIV) {
			if (!patient->getMonitoringState()->isDetectedHIVPositive) {
				accumulateQOLModifier(simContext->getHIVTestInputs()->HIVDeathQOLHIVUndetected);
			}
			else {
				accumulateQOLModifier(simContext->getQOLInputs()->deathBasicQOL[SimContext::DTH_HIV]);
			}
		}
		else if (causeOfDeath == SimContext::DTH_BKGD_MORT) {
			if (patient->getDiseaseState()->infectedHIVState == SimContext::HIV_INF_NEG) {
				accumulateQOLModifier(simContext->getHIVTestInputs()->deathQOLHIVNegative);
			}
			else if (!patient->getMonitoringState()->isDetectedHIVPositive) {
				accumulateQOLModifier(simContext->getHIVTestInputs()->backgroundMortDeathQOLHIVUndetected);
			}
			else {
				accumulateQOLModifier(simContext->getQOLInputs()->deathBasicQOL[SimContext::DTH_BKGD_MORT]);
			}
		}
		else if(causeOfDeath == SimContext::DTH_ACTIVE_TB){
			accumulateQOLModifier(simContext->getTBInputs()->QOLModDeathActiveTB);
		}
		else if ((causeOfDeath >= SimContext::DTH_CHRM_1) && (causeOfDeath < SimContext::DTH_CHRM_1 + SimContext::CHRM_NUM)) {
			accumulateQOLModifier(simContext->getCHRMsInputs()->QOLModDeathCHRMs[causeOfDeath - SimContext::DTH_CHRM_1]);
		}
		/** Other causes of death incur no additional QOL modifiers */
	}
	/** now all the QOL modifiers have been applied, finalize the patient's QOL value */
	finalizeQOLValue();

	/** update statistics for the coststats file */
	updateCostStats(percentOfMonth);

	/** update Pediatric HIV exposure statistics regardless of whether the patient died this month */
	if(patient->getPedsState()->ageCategoryPediatrics < SimContext::PEDS_AGE_LATE && patient->getDiseaseState()->infectedPediatricsHIVState == SimContext::PEDS_HIV_NEG){
		updatePedsHIVExposureStats(patient->getPedsState()->maternalStatus);
	}
	/** Update additional state, statistics and tracing for regular month or month of death */
	if (patient->isAlive()) {
		/** Increment the patient, overall, and longitudinal survival stats */
		updatePatientSurvival(percentOfMonth);
		updateOverallSurvival(percentOfMonth);
		updateLongitSurvival();

		/** update the patients OI history with any new OIs and OI history logging stats */
		if (patient->getDiseaseState()->infectedHIVState != SimContext::HIV_INF_NEG) {
			setOIHistory();
			updateOIHistoryLogging();
			/** Update the ART suppression stats */
			updateARTEfficacyStats();
		}

		/** If tracing is enabled, print out either monthly status */
		if (patient->getGeneralState()->tracingEnabled) {
			if (patient->getDiseaseState()->infectedHIVState != SimContext::HIV_INF_NEG) {
				if (patient->getPedsState()->ageCategoryPediatrics < SimContext::PEDS_AGE_LATE) {
					tracer->printTrace(1, "  %d upd: true CD4 perc %1.3f %s, true HVL %s;\n", patient->getGeneralState()->monthNum,
						patient->getDiseaseState()->currTrueCD4Percentage, SimContext::CD4_STRATA_STRS[patient->getDiseaseState()->currTrueCD4Strata],
						SimContext::HVL_STRATA_STRS[patient->getDiseaseState()->currTrueHVLStrata]);
				}
				else {
					tracer->printTrace(1, "  %d upd: true CD4 %1.0f %s, true HVL %s;\n", patient->getGeneralState()->monthNum,
						patient->getDiseaseState()->currTrueCD4, SimContext::CD4_STRATA_STRS[patient->getDiseaseState()->currTrueCD4Strata],
						SimContext::HVL_STRATA_STRS[patient->getDiseaseState()->currTrueHVLStrata]);
				}
			}

			tracer->printTrace(1, "  %d mth: ", patient->getGeneralState()->monthNum);
			if (simContext->getTBInputs()->enableTB)
				tracer->printTrace(1, "TB Symptoms: %s, ", patient->getTBState()->currTrueTBTracker[SimContext::TB_TRACKER_SYMPTOMS]?"Yes":"No");

			tracer->printTrace(1, "LM %1.2lf QA %1.2lf, $ %1.0lf;\n",
				patient->getGeneralState()->LMsDiscounted, patient->getGeneralState()->qualityAdjustLMsDiscounted,
				patient->getGeneralState()->costsDiscounted);

		}

		/** Increment the simulation month number and patient age */
		incrementMonth();
		/** Increment the discount factor */
		incrementDiscountFactor(simContext->getRunSpecsInputs()->discountFactor);
		for(int i = 0; i < simContext->NUM_DISCOUNT_RATES; i++){
			incrementMultDiscountFactor(simContext->getRunSpecsInputs()->multDiscountRatesCost[i], simContext->getRunSpecsInputs()->multDiscountRatesBenefit[i], i);
		}
	} /** end if patient is alive */
	else {
		/** Increment the patient and overall survival stats */
		updatePatientSurvival(percentOfMonth);
		updateOverallSurvival(percentOfMonth);

		/** Update population statistics and add the patient summary if death occurred */
		updatePopulationStats();
		addPatientSummary();

		/** If tracing is enabled, print out death tracing */
		if (patient->getGeneralState()->tracingEnabled) {
			tracer->printTrace(1, "**%d DEATH %s;\n", patient->getGeneralState()->monthNum,
				SimContext::DTH_CAUSES_STRS[patient->getDiseaseState()->causeOfDeath]);
			tracer->printTrace(1, "  LMs %1.2lf QA %1.2lf $ %1.0lf ;\n",
				patient->getGeneralState()->LMsDiscounted,
				patient->getGeneralState()->qualityAdjustLMsDiscounted,
				patient->getGeneralState()->costsDiscounted);
			tracer->printTrace(1, "  END PATIENT\n\n");
		}
	}

} /* end performMonthlyUpdates */